ChangeLog

* 2024-10-12(Tal Galili) Fixes issue #126 (linewidth in heatmaply not respected) |cf49949| 
|  R/ggdend.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2024-10-05(Tal Galili) Update citation URL to use DOI |950afec| 
|  DESCRIPTION       | 2 +-
|  README.md         | 2 +-
|  docs/authors.html | 2 +-
|  inst/CITATION     | 2 +-
|  4 files changed, 4 insertions(+), 4 deletions(-)

* 2024-10-05(Tal Galili) Fix redirect url |a4c6206| 
|  README.md         | 2 +-
|  docs/authors.html | 2 +-
|  inst/CITATION     | 2 +-
|  3 files changed, 3 insertions(+), 3 deletions(-)

* 2024-10-05(Tal Galili) Fix NEWS.rmd and update pkgdown |b85fc40| 
|  DESCRIPTION                                       |    2 +-
|  NEWS.md                                           |  618 ++---
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|  docs/CONDUCT.html                                 |   20 +-
|  docs/articles/Cluster_Analysis.html               | 1213 +++++----
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|  docs/reference/pvrect2.html                       |   48 +-
|  docs/reference/raise.dendrogram-1.png             |  Bin 35684 -> 36085 bytes
|  docs/reference/raise.dendrogram.html              |   36 +-
|  docs/reference/rank_branches-1.png                |  Bin 28420 -> 28713 bytes
|  docs/reference/rank_branches.html                 |   38 +-
|  docs/reference/rank_order.dendrogram.html         |   30 +-
|  docs/reference/rank_values_with_clusters.html     |   32 +-
|  docs/reference/rect.dendrogram-1.png              |  Bin 17732 -> 18765 bytes
|  docs/reference/rect.dendrogram-2.png              |  Bin 47531 -> 47991 bytes
|  docs/reference/rect.dendrogram-3.png              |  Bin 22507 -> 25051 bytes
|  docs/reference/rect.dendrogram-4.png              |  Bin 21187 -> 23622 bytes
|  docs/reference/rect.dendrogram-5.png              |  Bin 19688 -> 20767 bytes
|  docs/reference/rect.dendrogram.html               |   74 +-
|  docs/reference/reexports.html                     |   20 +-
|  docs/reference/reindex_dend.html                  |   28 +-
|  docs/reference/remove_branches_edgePar.html       |   38 +-
|  docs/reference/remove_leaves_nodePar.html         |   38 +-
|  docs/reference/remove_nodes_nodePar.html          |   38 +-
|  docs/reference/rllply.html                        |   40 +-
|  docs/reference/rotate-1.png                       |  Bin 26012 -> 26132 bytes
|  docs/reference/rotate-2.png                       |  Bin 37568 -> 39362 bytes
|  docs/reference/rotate-3.png                       |  Bin 32003 -> 32524 bytes
|  docs/reference/rotate-4.png                       |  Bin 33951 -> 33510 bytes
|  docs/reference/rotate-5.png                       |  Bin 25971 -> 26150 bytes
|  docs/reference/rotate.html                        |  113 +-
|  docs/reference/rotate_DendSer.html                |   36 +-
|  docs/reference/sample.dendrogram.html             |   52 +-
|  docs/reference/seriate_dendrogram.html            |   40 +-
|  docs/reference/set.html                           |  134 +-
|  docs/reference/set_labels-1.png                   |  Bin 29370 -> 29193 bytes
|  docs/reference/set_labels-2.png                   |  Bin 48924 -> 49755 bytes
|  docs/reference/set_labels-3.png                   |  Bin 25357 -> 25504 bytes
|  docs/reference/set_labels.html                    |   38 +-
|  docs/reference/shuffle-1.png                      |  Bin 241178 -> 241522 bytes
|  docs/reference/shuffle-2.png                      |  Bin 107161 -> 109320 bytes
|  docs/reference/shuffle.html                       |   42 +-
|  docs/reference/sort_2_clusters_vectors.html       |   40 +-
|  docs/reference/sort_dist_mat.html                 |   36 +-
|  docs/reference/sort_levels_values.html            |   38 +-
|  docs/reference/tanglegram.html                    |  130 +-
|  docs/reference/theme_dendro.html                  |   20 +-
|  docs/reference/unbranch-1.png                     |  Bin 28570 -> 28422 bytes
|  docs/reference/unbranch.html                      |   50 +-
|  docs/reference/unclass_dend.html                  |   30 +-
|  docs/reference/untangle.html                      |   63 +-
|  docs/reference/untangle_DendSer.html              |   38 +-
|  docs/reference/untangle_random_search.html        |   42 +-
|  docs/reference/untangle_step_rotate_1side.html    |   46 +-
|  docs/reference/untangle_step_rotate_2side.html    |   46 +-
|  .../reference/untangle_step_rotate_both_side.html |  232 ++
|  docs/reference/which_leaf.html                    |   38 +-
|  docs/reference/which_node-1.png                   |  Bin 13637 -> 14338 bytes
|  docs/reference/which_node.html                    |   38 +-
|  docs/sitemap.xml                                  |  153 ++
|  360 files changed, 8102 insertions(+), 5765 deletions(-)

* 2024-10-05(Tal Galili) Fix various .rd issues |1de78d0| 
|  R/DendSer.R                            |  2 +-
|  R/attr_access.R                        |  4 ++--
|  R/data.R                               |  4 ++--
|  R/prune.R                              |  2 +-
|  R/rotate.R                             | 35 +++++++++++++++-----------------
|  R/unbranch.R                           |  2 +-
|  R/untangle.R                           |  8 ++++++--
|  man/assign_values_to_leaves_edgePar.Rd |  2 +-
|  man/khan.Rd                            |  4 ++--
|  man/ladderize.Rd                       |  3 +--
|  man/prune.Rd                           |  2 +-
|  man/rllply.Rd                          |  2 +-
|  man/rotate.Rd                          | 31 ++++++++++++++--------------
|  man/unbranch.Rd                        |  2 +-
|  man/untangle_DendSer.Rd                |  2 +-
|  man/untangle_step_rotate_both_side.Rd  |  8 ++++++--
|  16 files changed, 58 insertions(+), 55 deletions(-)

* 2024-09-28(Tal Galili) URL fixes |d8beb1a| 
|  DESCRIPTION |    6 +-
|  NEWS        | 1477 ---------------------------------------------------------
|  NEWS.md     |    2 +-
|  README.md   |    2 +-
|  4 files changed, 5 insertions(+), 1482 deletions(-)

* 2024-09-24(Tal Galili) Updating yaml for code coverage. |586b59c| 
|  .github/workflows/test-coverage.yaml | 27 +++++++++++++++++++--------
|  1 file changed, 19 insertions(+), 8 deletions(-)

* 2024-09-24(Tal Galili) Update DESCRIPTION and NEWS |0f15497| 
|  DESCRIPTION | 2 +-
|  NEWS        | 9 +++++----
|  NEWS.md     | 9 +++++----
|  R/zzz.R     | 2 +-
|  4 files changed, 12 insertions(+), 10 deletions(-)

* 2024-09-24(alecbuetow) Fixed rect.dendogram 2 rectangle bug (#124) |370e535| 
|  R/rect.dendrogram.R | 6 +++---
|  1 file changed, 3 insertions(+), 3 deletions(-)

* 2024-09-23(alecbuetow) Added 2 Tests for Untangle.R (#123) |36b035b| 
|  tests/testthat/test-untangle.R | 44 ++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 44 insertions(+)

* 2024-08-31(Tal Galili) Update docs and NEWS to 1.18.0 |f5c5d0b| 
|  DESCRIPTION     |  2 +-
|  NAMESPACE       |  8 +++++---
|  NEWS            | 11 +++--------
|  NEWS.md         | 11 +++++++++--
|  R/untangle.R    | 12 +++++++-----
|  man/untangle.Rd | 12 +++++++-----
|  6 files changed, 32 insertions(+), 24 deletions(-)

* 2024-08-31(Tal Galili) Stop tracking linter for the time being |d906461| 
|  .github/workflows/lint.yaml | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2024-08-31(Tal Galili) Remove windoes r: 4.1 check (since it seems to fail on installing Hmisc for some reason) |6eb3b3a| 
|  .github/workflows/R-CMD-check.yaml | 1 -
|  1 file changed, 1 deletion(-)

* 2024-08-31(Tal Galili) Trying to fix the Hmisc error |7eaa20d| 
|  .github/workflows/R-CMD-check.yaml | 13 ++-----------
|  1 file changed, 2 insertions(+), 11 deletions(-)

* 2024-08-31(Tal Galili) Update untangle_step_rotate_both_side to not need dplyr |67355f7| 
|  tests/testthat/test-untangle.R | 17 +++++++++++------
|  1 file changed, 11 insertions(+), 6 deletions(-)

* 2024-08-31(Tal Galili) Fix warnings in tests and roxygen2 |c65d34c| 
|  .gitignore                       |  4 ++-
|  NAMESPACE                        |  9 +++---
|  R/dendextend-package.R           |  2 +-
|  R/entanglement.R                 |  1 +
|  R/ggdend.R                       | 61 +++++++++++++++++++++-----------------
|  tests/{test-all.R => testthat.R} |  2 +-
|  tests/testthat/test-ggdend.R     |  8 ++---
|  7 files changed, 47 insertions(+), 40 deletions(-)

* 2024-08-31(Tal Galili) Fix untange test failure |3c2d436| 
|  tests/testthat/test-untangle.R | 7 ++++---
|  1 file changed, 4 insertions(+), 3 deletions(-)

* 2024-08-31(Tal Galili) Fix tests to be able to run again |ef919e1| 
|  tests/testthat/test-attr_access.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2024-08-31(alecbuetow) Added stepBothSides algorithm to untangle methods (#122) |d4d6530| 
|  DESCRIPTION                           |   5 +-
|  NAMESPACE                             |   1 +
|  NEWS                                  |   6 ++
|  R/untangle.R                          | 133 +++++++++++++++++++++++++++++++-
|  man/dendextend-package.Rd             |  41 ++++++++++
|  man/untangle.Rd                       |   3 +-
|  man/untangle_step_rotate_both_side.Rd | 108 ++++++++++++++++++++++++++
|  tests/testthat/test-untangle.R        |  26 ++++++-
|  8 files changed, 317 insertions(+), 6 deletions(-)

* 2023-12-16(Tal Galili) Another attempt to deal with Hmisc installation |278999b| 
|  .github/workflows/R-CMD-check.yaml | 12 ++++++++----
|  1 file changed, 8 insertions(+), 4 deletions(-)

* 2023-12-16(Tal Galili) Try another R-CMD-check.yaml file - try 2 |402ce1d| 
|  .github/workflows/R-CMD-check.yaml | 25 ++++++++++++-------------
|  1 file changed, 12 insertions(+), 13 deletions(-)

* 2023-12-16(Tal Galili) Try another R-CMD-check.yaml file |5435367| 
|  .github/workflows/R-CMD-check.yaml | 18 +++---------------
|  1 file changed, 3 insertions(+), 15 deletions(-)

* 2023-12-16(Tal Galili) Add tests to attr_access |82c908b| 
|  tests/testthat/test-attr_access.R | 82 +++++++++++++++++++++++++++++++++++++
|  1 file changed, 82 insertions(+)

* 2023-12-16(Tal Galili) Remove broken test |fcd3eae| 
|  tests/testthat/test-ggdend.R | 9 ---------
|  1 file changed, 9 deletions(-)

* 2023-12-16(Tal Galili) Add tests to ggdend |a82de2b| 
|  tests/testthat/test-ggdend.R | 92 ++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 92 insertions(+)

* 2023-12-16(Tal Galili) Add and update tests for get_nodes_xy function |96bc5cd| 
|  DESCRIPTION                        |  4 ++--
|  NEWS                               |  6 ++++++
|  tests/testthat/test-get_nodes_xy.R | 41 ++++++++++++++++++++++++++++++++++++
|  3 files changed, 49 insertions(+), 2 deletions(-)

* 2023-03-31(Tal Galili) Fix type in missing seriation package message |c1f8608| 
|  R/seriate_dendrogram.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2023-03-25(Tal Galili) Fix misc 500 error in a url |dcf42ee| 
|  vignettes/dendextend.Rmd | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2023-03-25(Tal Galili) Remove "https://www.r-statistics.com" from being directly linked to |c76aa00| 
|  vignettes/dendextend.Rmd | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2023-03-25(Tal Galili) Fix misc url issues |8991549| 
|  DESCRIPTION              |  4 ++--
|  NEWS                     |  6 ++++++
|  NEWS.md                  |  6 ++++++
|  README.md                |  1 -
|  docs/404.html            |  4 ++--
|  docs/CONDUCT.html        |  4 ++--
|  docs/authors.html        |  4 ++--
|  docs/index.html          |  6 +++---
|  docs/news/index.html     | 23 ++++++++++++++++++-----
|  vignettes/dendextend.Rmd |  2 +-
|  10 files changed, 42 insertions(+), 18 deletions(-)

* 2023-03-24(Tal Galili) Update github workflows to use v2 |7a9c4e5| 
|  .github/workflows/R-CMD-check.yaml    | 31 +++++++++++++++++++++++++++----
|  .github/workflows/check-release.yaml  | 25 +++++++------------------
|  .github/workflows/check-standard.yaml | 29 ++++++++++-------------------
|  .github/workflows/lint.yaml           | 13 ++++++++-----
|  .github/workflows/pkgdown.yaml        | 33 ++++++++++++++++++++++-----------
|  .github/workflows/pr-commands.yaml    |  4 ++--
|  .github/workflows/test-coverage.yaml  | 32 ++++++++++++++++++++++++++------
|  R/zzz.R                               |  4 ++++
|  8 files changed, 106 insertions(+), 65 deletions(-)

* 2023-03-24(Tal Galili) Fix "Cannot process chunk/lines:" in the NEWS file |e568c21| 
|  NEWS    | 17 +++--------------
|  NEWS.md | 15 +++++++++++++--
|  2 files changed, 16 insertions(+), 16 deletions(-)

* 2023-03-24(Tal Galili) Fixed: "Package CITATION file contains call(s) to old-style citEntry().  Please use bibentry() instead." |e5c594f| 
|  NEWS          |  2 ++
|  inst/CITATION | 17 +++++++----------
|  2 files changed, 9 insertions(+), 10 deletions(-)

* 2023-03-24(Tal Galili) Fix ggplot.ggdend S3 generic/method consistency |5865a99| 
|  DESCRIPTION   |  6 +++---
|  NEWS          | 18 +++++++++++++++---
|  R/ggdend.R    |  9 ++++++---
|  man/ggdend.Rd | 10 ++++++++--
|  man/set.Rd    | 16 ++++++++--------
|  5 files changed, 40 insertions(+), 19 deletions(-)

* 2022-11-01(Tal Galili) document elipsis |a52e7d7| 
|  R/get_subdendrograms.R | 1 +
|  man/collapse_labels.Rd | 2 ++
|  2 files changed, 3 insertions(+)

* 2022-11-01(Tal Galili) Add tests to collapse_labels |d6899eb| 
|  tests/testthat/test-get_subdendrograms.R | 27 ++++++++++++++++++++++++++-
|  1 file changed, 26 insertions(+), 1 deletion(-)

* 2022-11-01(Tal Galili) Added the collapse_labels function |eb8fa9b| 
|  DESCRIPTION            |  4 +--
|  NAMESPACE              |  1 +
|  NEWS                   |  8 +++++
|  R/get_subdendrograms.R | 79 ++++++++++++++++++++++++++++++++++++++++++++++++
|  man/collapse_labels.Rd | 45 +++++++++++++++++++++++++++
|  5 files changed, 135 insertions(+), 2 deletions(-)

* 2022-10-08(Tal Galili) update github actions |0a53957| 
|  .github/workflows/R-CMD-check.yaml | 49 ++++++++++++++++++++++++++++++++++++
|  .github/workflows/pr-commands.yaml | 28 ++++++++++++---------
|  README.md                          |  3 +++
|  3 files changed, 68 insertions(+), 12 deletions(-)

* 2022-08-06(Tal Galili) Add github actions |87b55e1| 
|  .github/workflows/check-release.yaml  | 40 ++++++++++++++++++
|  .github/workflows/check-standard.yaml | 58 +++++++++++++++++++++++++
|  .github/workflows/lint.yaml           | 29 +++++++++++++
|  .github/workflows/pr-commands.yaml    | 75 +++++++++++++++++++++++++++++++++
|  .github/workflows/test-coverage.yaml  | 30 +++++++++++++
|  5 files changed, 232 insertions(+)

* 2022-08-06(Tal Galili) Added usethis::use_github_action("pkgdown") |74b9d01| 
|  .github/.gitignore             |  1 +
|  .github/workflows/pkgdown.yaml | 35 +++++++++++++++++++++++++++++++++++
|  2 files changed, 36 insertions(+)

* 2022-07-16(Tal Galili) Some updating on the pkgdown |f02d7b3| 
|  docs/pkgdown.yml                         |   2 +-
|  docs/reference/FM_index_permutation.html |  10 ++++-----
|  docs/reference/Rplot001.png              | Bin 7062 -> 4480 bytes
|  docs/reference/Rplot002.png              | Bin 9877 -> 4588 bytes
|  docs/reference/Rplot003.png              | Bin 11879 -> 9529 bytes
|  docs/reference/Rplot004.png              | Bin 14430 -> 10574 bytes
|  docs/reference/Rplot005.png              | Bin 22110 -> 7394 bytes
|  docs/reference/Rplot006.png              | Bin 9450 -> 49630 bytes
|  docs/reference/Rplot007.png              | Bin 34304 -> 5468 bytes
|  docs/reference/Rplot008.png              | Bin 37110 -> 49630 bytes
|  docs/reference/khan.html                 |  34 ++++++++++++++---------------
|  11 files changed, 22 insertions(+), 24 deletions(-)

* 2022-07-04(Tal Galili) Fix: |70b6e03| 
|  DESCRIPTION              |  2 +-
|  NEWS                     |  4 ++--
|  NEWS.md                  |  4 ++--
|  R/data.R                 | 34 +++++++++++++++++-----------------
|  R/dendlist.R             |  2 +-
|  man/khan.Rd              | 34 +++++++++++++++++-----------------
|  vignettes/dendextend.Rmd |  2 +-
|  7 files changed, 41 insertions(+), 41 deletions(-)

* 2022-07-03(Tal Galili) Shorten the skew function a bit more |500925b| 
|  R/bk_method.R               | 10 ++++------
|  man/FM_index_permutation.Rd | 10 ++++------
|  2 files changed, 8 insertions(+), 12 deletions(-)

* 2022-07-03(Tal Galili) Update pkgdown files a bit |ecd2f82| 
|  docs/404.html                                     |  119 +-
|  docs/CONDUCT.html                                 |  115 +-
|  docs/articles/index.html                          |  127 +-
|  docs/authors.html                                 |  358 ++-
|  docs/index.html                                   |  185 +-
|  docs/news/index.html                              | 2362 ++++---------------
|  docs/pkgdown.css                                  |   83 +-
|  docs/pkgdown.js                                   |    4 +-
|  docs/pkgdown.yml                                  |    6 +-
|  docs/reference/Bk.html                            |  279 +--
|  docs/reference/Bk_permutations.html               |  271 +--
|  docs/reference/Bk_plot.html                       |  485 ++--
|  docs/reference/DendSer.dendrogram.html            |  199 +-
|  docs/reference/FM_index.html                      |  303 +--
|  docs/reference/FM_index_R.html                    |  289 +--
|  docs/reference/FM_index_permutation.html          |  309 +--
|  docs/reference/Rplot001.png                       |  Bin 4480 -> 7062 bytes
|  docs/reference/Rplot002.png                       |  Bin 4588 -> 9877 bytes
|  docs/reference/Rplot003.png                       |  Bin 9529 -> 11879 bytes
|  docs/reference/Rplot004.png                       |  Bin 10574 -> 14430 bytes
|  docs/reference/Rplot005.png                       |  Bin 7394 -> 22110 bytes
|  docs/reference/Rplot006.png                       |  Bin 49630 -> 9450 bytes
|  docs/reference/Rplot007.png                       |  Bin 5468 -> 34304 bytes
|  docs/reference/Rplot008.png                       |  Bin 49630 -> 37110 bytes
|  docs/reference/all.equal.dendrogram.html          |  327 +--
|  docs/reference/all_couple_rotations_at_k.html     |  227 +-
|  docs/reference/all_unique.html                    |  194 +-
|  docs/reference/as.dendlist.html                   |  192 +-
|  docs/reference/as.phylo.dendrogram.html           |  235 +-
|  docs/reference/as_hclust_fixed.html               |  223 +-
|  docs/reference/assign_dendextend_options.html     |  121 +-
|  .../assign_values_to_branches_edgePar.html        |  284 +--
|  .../assign_values_to_leaves_edgePar.html          |  249 +-
|  .../assign_values_to_leaves_nodePar.html          |  271 +--
|  .../reference/assign_values_to_nodes_nodePar.html |  265 +--
|  docs/reference/bakers_gamma_for_2_k_matrix.html   |  183 +-
|  docs/reference/branches_attr_by_clusters.html     |  365 ++-
|  docs/reference/branches_attr_by_labels.html       |  289 +--
|  docs/reference/branches_attr_by_lists.html        |  265 +--
|  docs/reference/circlize_dendrogram.html           |  295 +--
|  docs/reference/click_rotate.html                  |  266 +--
|  docs/reference/collapse_branch.html               |  255 +-
|  docs/reference/color_branches.html                |  578 ++---
|  docs/reference/color_labels.html                  |  278 +--
|  docs/reference/color_unique_labels.html           |  181 +-
|  docs/reference/colored_bars.html                  |  518 ++--
|  docs/reference/colored_dots.html                  |  550 ++---
|  docs/reference/common_subtrees_clusters.html      |  226 +-
|  docs/reference/cor.dendlist.html                  |  253 +-
|  docs/reference/cor_FM_index.html                  |  242 +-
|  docs/reference/cor_bakers_gamma.html              |  325 +--
|  docs/reference/cor_common_nodes.html              |  214 +-
|  docs/reference/cor_cophenetic.html                |  343 ++-
|  docs/reference/count_terminal_nodes.html          |  222 +-
|  docs/reference/cut_lower_fun.html                 |  254 +-
|  docs/reference/cutree-methods.html                |  487 ++--
|  docs/reference/cutree_1h.dendrogram.html          |  279 +--
|  docs/reference/cutree_1k.dendrogram.html          |  317 +--
|  docs/reference/dend_diff.html                     |  247 +-
|  docs/reference/dendextend-package.html            |  126 +-
|  docs/reference/dendextend_options.html            |  185 +-
|  docs/reference/dendlist.html                      |  255 +-
|  docs/reference/depth.html                         |  191 +-
|  docs/reference/dist.dendlist.html                 |  244 +-
|  docs/reference/dist_long.html                     |  211 +-
|  docs/reference/distinct_edges.html                |  207 +-
|  docs/reference/duplicate_leaf.html                |  256 +-
|  docs/reference/entanglement.html                  |  328 +--
|  docs/reference/fac2num.html                       |  192 +-
|  docs/reference/find_dend.html                     |  285 +--
|  docs/reference/find_dendrogram.html               |  226 +-
|  docs/reference/find_k.html                        |  266 +--
|  docs/reference/fix_members_attr.dendrogram.html   |  255 +-
|  docs/reference/flatten.dendrogram.html            |  195 +-
|  docs/reference/flip_leaves.html                   |  212 +-
|  docs/reference/get_branches_heights.html          |  207 +-
|  docs/reference/get_childrens_heights.html         |  170 +-
|  docs/reference/get_leaves_attr.html               |  268 +--
|  docs/reference/get_leaves_branches_attr.html      |  224 +-
|  docs/reference/get_leaves_branches_col.html       |  208 +-
|  docs/reference/get_leaves_edgePar.html            |  362 ++-
|  docs/reference/get_leaves_nodePar.html            |  325 +--
|  docs/reference/get_nodes_attr.html                |  385 ++-
|  docs/reference/get_nodes_xy.html                  |  274 +--
|  docs/reference/get_root_branches_attr.html        |  213 +-
|  docs/reference/get_subdendrograms.html            |  371 ++-
|  docs/reference/ggdend.html                        |  450 ++--
|  docs/reference/hang.dendrogram.html               |  232 +-
|  docs/reference/has_component_in_attribute.html    |  246 +-
|  docs/reference/heights_per_k.dendrogram.html      |  206 +-
|  docs/reference/highlight_branches.html            |  349 ++-
|  docs/reference/highlight_distinct_edges.html      |  308 +--
|  docs/reference/identify.dendrogram.html           |  291 +--
|  docs/reference/index.html                         |  678 ++----
|  docs/reference/intersect_trees.html               |  226 +-
|  docs/reference/is.natural.number.html             |  197 +-
|  docs/reference/is_null_list.html                  |  200 +-
|  docs/reference/is_some_class.html                 |  182 +-
|  docs/reference/khan.html                          |  198 +-
|  docs/reference/labels-assign.html                 |  295 +--
|  docs/reference/labels_cex.html                    |  210 +-
|  docs/reference/labels_colors.html                 |  268 +--
|  docs/reference/ladderize.html                     |  256 +-
|  docs/reference/leaf_Colors.html                   |  213 +-
|  docs/reference/lowest_common_branch.html          |  188 +-
|  docs/reference/match_order_by_labels.html         |  227 +-
|  .../match_order_dendrogram_by_old_order.html      |  257 +-
|  docs/reference/na_locf.html                       |  230 +-
|  docs/reference/nleaves.html                       |  224 +-
|  docs/reference/nnodes.html                        |  198 +-
|  docs/reference/noded_with_condition.html          |  281 +--
|  docs/reference/order.dendrogram-assign.html       |  253 +-
|  docs/reference/order.hclust.html                  |  182 +-
|  docs/reference/partition_leaves.html              |  244 +-
|  docs/reference/plot_horiz.dendrogram.html         |  380 ++-
|  docs/reference/prune.html                         |  275 +--
|  .../reference/prune_common_subtrees.dendlist.html |  166 +-
|  docs/reference/prune_leaf.html                    |  190 +-
|  docs/reference/pvclust_edges.html                 |  171 +-
|  docs/reference/pvclust_show_signif.html           |  285 +--
|  docs/reference/pvclust_show_signif_gradient.html  |  277 +--
|  docs/reference/pvrect2.html                       |  286 +--
|  docs/reference/raise.dendrogram.html              |  183 +-
|  docs/reference/rank_branches.html                 |  210 +-
|  docs/reference/rank_order.dendrogram.html         |  198 +-
|  docs/reference/rank_values_with_clusters.html     |  199 +-
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|  docs/reference/tanglegram.html                    |  968 ++++----
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* 2022-07-03(Tal Galili) Update log files |172e35a| 
|  ChangeLog | 117 +++++++++++++++++++++++++++++++++++++++++++++++++++++-------
|  NEWS.md   |  18 ++++++++++
|  R/zzz.R   |   1 +
|  README.md |   7 ++--
|  4 files changed, 129 insertions(+), 14 deletions(-)

* 2022-07-03(Tal Galili) comment out library(zoo) - to let pkgdown run properly. |6b87e9e| 
|  R/pvclust.R    | 21 +++++++++++----------
|  man/na_locf.Rd | 25 +++++++++++++------------
|  2 files changed, 24 insertions(+), 22 deletions(-)

* 2022-07-03(Tal Galili) Remove dependancy on `dendextendRcpp` in some tests and documentation files (.Rd). |19228aa| 
|  NEWS                             |  3 ++
|  R/branches_attr_by.R             |  1 -
|  R/color_branches.R               | 11 -----
|  R/cut_lower_fun.R                | 13 +-----
|  R/cutree.dendrogram.R            | 16 +------
|  R/zzz.R                          | 85 +-------------------------------------
|  man/branches_attr_by_clusters.Rd |  1 -
|  man/cut_lower_fun.Rd             | 11 -----
|  man/heights_per_k.dendrogram.Rd  | 14 -------
|  tests/testthat/test-rotate.R     | 15 -------
|  vignettes/FAQ.Rmd                |  1 -
|  11 files changed, 7 insertions(+), 164 deletions(-)

* 2022-07-03(Tal Galili) as.phylo - Remove example dependancy on ggdendro |e28fb02| 
|  NEWS                       |  2 +-
|  R/ape.R                    | 24 ++++++++++--------------
|  man/as.phylo.dendrogram.Rd | 24 ++++++++++--------------
|  3 files changed, 21 insertions(+), 29 deletions(-)

* 2022-07-03(Tal Galili) Fix an issue with running `pkgdown::build_site()` (see: https://github.com/r-lib/pkgdown/issues/2155). Props to @dmurdoch. |f4cacbd| 
|  NEWS      | 2 +-
|  README.md | 2 +-
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* 2022-07-03(Tal Galili) Remove (undocumented!) dependancy on the psych library. |4397909| 
|  NEWS                        |  2 +-
|  R/bk_method.R               | 15 ++++++++++++---
|  man/FM_index_permutation.Rd | 13 +++++++++++--
|  3 files changed, 24 insertions(+), 6 deletions(-)

* 2022-07-03(Tal Galili) Fix doc for the new node and leaves bg parameter. |03a9ffc| 
|  DESCRIPTION              | 10 ++++++----
|  NEWS                     |  8 ++++++--
|  R/set.dendrogram.R       | 24 ++++++++++++++++++++++++
|  man/set.Rd               | 37 +++++++++++++++++++++++++++++++------
|  vignettes/dendextend.Rmd | 21 +++++++++++++--------
|  5 files changed, 80 insertions(+), 20 deletions(-)

* 2022-07-03(pschupp) added support for "bg" attribute for nodes and leaves (#109) |38a3eac| 
|  R/set.dendrogram.R       | 4 ++++
|  vignettes/dendextend.Rmd | 4 +++-
|  2 files changed, 7 insertions(+), 1 deletion(-)

* 2022-02-19(Tal Galili) Fix minor error in the docs of color_branches |fcdb0d5| 
|  DESCRIPTION           |  4 ++--
|  NEWS                  | 11 +++++++++++
|  R/color_branches.R    |  4 ++--
|  man/color_branches.Rd |  4 ++--
|  4 files changed, 17 insertions(+), 6 deletions(-)

* 2021-10-27(Tal Galili) Update broken url in the docs. |9d6ae05| 
|  R/color_branches.R | 5 +++--
|  R/data.R           | 2 +-
|  man/all_unique.Rd  | 3 ++-
|  man/khan.Rd        | 2 +-
|  4 files changed, 7 insertions(+), 5 deletions(-)

*   2021-10-27(Tal Galili) Merge branch 'master' of github.com:talgalili/dendextend |402090d
|\  
| *   2021-06-20(Tal Galili) Merge pull request #107 from juba/master |ce0bf8c
| |\  
| | * 2021-06-18(Julien) Replace FALSE with "none" in ggplot2::guides() |9f28a77
| |/  | |   
| |    R/ggdend.R | 8 ++++----
| |    1 file changed, 4 insertions(+), 4 deletions(-)

* / 2021-10-27(Tal Galili) update NEWS |3daf4af
|/  |   
|    DESCRIPTION | 2 +-
|    NEWS        | 5 ++++-
|    2 files changed, 5 insertions(+), 2 deletions(-)

* 2021-05-23(Tal Galili) update startup message to include stackoverflow. |4b8711c| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 6 ++++++
|  R/zzz.R     | 2 +-
|  3 files changed, 9 insertions(+), 3 deletions(-)

* 2021-05-08(Tal Galili) dendextend.Rmd - fixed misc url redirect |f6a949a| 
|  DESCRIPTION              | 2 +-
|  NEWS                     | 5 +++++
|  R/data.R                 | 2 +-
|  vignettes/dendextend.Rmd | 2 +-
|  4 files changed, 8 insertions(+), 3 deletions(-)

* 2021-05-08(Tal Galili) update pkgdown website |f6174ce| 
|  ChangeLog                                         | 1545 ++++++++++++-------
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* 2021-05-08(Tal Galili) fix broken url |dfea91c| 
|  R/data.R    | 4 ++--
|  man/khan.Rd | 4 ++--
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2021-05-08(Tal Galili) colored_dots - add missing roxygen2 documentation for the new dot_size argument |3eb1614| 
|  DESCRIPTION         | 4 ++--
|  NEWS                | 5 ++++-
|  R/colored_dots.R    | 1 +
|  man/colored_dots.Rd | 2 ++
|  4 files changed, 9 insertions(+), 3 deletions(-)

*   2021-05-08(Tal Galili) Merge pull request #100 from chasemc/master |f625516
|\  
| * 2020-04-07(Chase Clark) Add argument colored_dots(dot_size) |3dc3ba9| | 
| |  man/colored_dots.Rd | 1 +
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| * 2020-04-07(Chase Clark) Add argument colored_dots(dot_size) |b52e9ee| | 
| |  R/colored_dots.R | 5 +++--
| |  1 file changed, 3 insertions(+), 2 deletions(-)

* | 2021-04-11(Tal Galili) get_subdendrograms - fix it to sort the output sub-dendrograms to be in the original order of the clusters in the dengrogram (instead of the order of the original data, which is less useful for exploration) |e4e3032| | 
| |  DESCRIPTION                              |  4 +--
| |  NEWS                                     |  7 ++++
| |  R/get_subdendrograms.R                   | 42 ++++++++++++++++++++----
| |  man/get_subdendrograms.Rd                | 39 +++++++++++++++++++---
| |  tests/testthat/test-get_subdendrograms.R | 48 +++++++++++++---------------
| |  5 files changed, 102 insertions(+), 38 deletions(-)

* |   2021-04-11(Tal Galili) Merge pull request #105 from chasemc/master |a89f28e
|\ \  
| * | 2021-04-11(Chase Clark) Create test-get_subdendrograms.R |7f17c10| | | 
| | |  tests/testthat/test-get_subdendrograms.R | 80 ++++++++++++++++++++++++++
| | |  1 file changed, 80 insertions(+)

| * | 2021-04-11(Chase Clark) Update get_subdendrograms.R |f937009
|/ /  | |   
| |    R/get_subdendrograms.R | 2 +-
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* | 2020-09-12(Tal Galili) Fix http to be https - so to keep the homepage secure. |0a08071| | 
| |  README.md       | 16 ++++++++--------
| |  docs/index.html | 12 ++++++------
| |  2 files changed, 14 insertions(+), 14 deletions(-)

* | 2020-08-25(Tal Galili) Date bump |7df8887| | 
| |  ChangeLog                             | 488 ++++++++++++++++++++++++++++++
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| |  12 files changed, 512 insertions(+), 36 deletions(-)

* | 2020-08-24(Tal Galili) Fix: "Found the following (possibly) invalid URLs:" (2) |6ba5e50| | 
| |  R/color_branches.R | 2 +-
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| |  6 files changed, 6 insertions(+), 6 deletions(-)

* | 2020-08-24(Tal Galili) Fix: "Found the following (possibly) invalid URLs:" |92689e6| | 
| |  ChangeLog                                        |   16 +
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| |  NEWS.md                                          |    4 +-
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* | 2020-08-15(Tal Galili) update pkgdown |a3431fc| | 
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| |  docs/news/index.html | 1077 ++++++++++------------------------------------
| |  4 files changed, 273 insertions(+), 861 deletions(-)

* | 2020-08-15(Tal Galili) Fix warning "checkRd: (5) dendextend-package.Rd:0-15: Must have a \description" |cabc151| | 
| |  ChangeLog                 | 248 +++++++++++++++++++++++++++++++++++++++++-
| |  DESCRIPTION               |   2 +-
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| |  6 files changed, 278 insertions(+), 9 deletions(-)

* | 2020-08-15(Tal Galili) Update tests to suppress warnings around RNGversion("3.5.0") |1c869df| | 
| |  tests/test-all.R                       | 2 +-
| |  tests/testthat/test-bk_method.R        | 5 +++--
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| |  tests/testthat/test-untangle.R         | 7 +++++--
| |  8 files changed, 18 insertions(+), 16 deletions(-)

* | 2020-08-15(Tal Galili) Fix some tests to not flag errors/warnings |68916c7| | 
| |  tests/test-all.R                      | 24 ++----------------------
| |  tests/testthat/test-ggdend.R          |  2 ++
| |  tests/testthat/test-pvclust_extract.R |  2 +-
| |  3 files changed, 5 insertions(+), 23 deletions(-)

* | 2020-08-15(Tal Galili) Remove warnings from .Rd files. |f4e243c| | 
| |  R/get_subdendrograms.R    | 2 +-
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* | 2020-08-14(Tal Galili) Update .Rd for find_dendrogram (and some other functions) |5745a79| | 
| |  DESCRIPTION               |  2 +-
| |  R/get_subdendrograms.R    | 14 ++++++++++++++
| |  man/dendextend-package.Rd |  3 ---
| |  man/find_dendrogram.Rd    | 31 +++++++++++++++++++++----------
| |  man/khan.Rd               |  6 ++++--
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| |  7 files changed, 45 insertions(+), 21 deletions(-)

* | 2020-08-14(Tal Galili) Fix #102 - find_dendrogram deals with more edge cases, the documentation does what it says it does, and there are now tests. |3f3d5ab| | 
| |  DESCRIPTION                           |  2 +-
| |  NEWS                                  |  3 ++-
| |  R/get_subdendrograms.R                | 33 +++++++++++++++++--------------
| |  tests/testthat/test-find_dendrogram.R | 32 ++++++++++++++++++++++++++++++
| |  4 files changed, 53 insertions(+), 17 deletions(-)

* | 2020-06-01(Tal Galili) remove d3heatmap from DESCRIPTION (since the package became orphaned) |99dbf6d| | 
| |  DESCRIPTION                    |  1 -
| |  vignettes/Cluster_Analysis.Rmd | 10 +++-------
| |  vignettes/dendextend.Rmd       |  2 +-
| |  3 files changed, 4 insertions(+), 9 deletions(-)

* | 2020-06-01(Tal Galili) ggdend - add type='triang': - bump package version - update NEWS - added Hauyn as a contributor - updated function doc (added an example) |3f938f8| | 
| |  DESCRIPTION   | 8 +++++---
| |  NEWS          | 5 ++++-
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| |  man/ggdend.Rd | 6 ++++++
| |  4 files changed, 21 insertions(+), 4 deletions(-)

* |   2020-05-31(Tal Galili) Merge branch 'master' of github.com:talgalili/dendextend |cd77a0e
|\ \  
| * \   2020-05-31(Tal Galili) Merge pull request #99 from houyunhuang/master |7043bde
| |\ \  
| | |/  
| |/|   
| | * 2020-04-15(houyun) check the type param |2e5ebc1| | | 
| | |  R/ggdend.R | 2 +-
| | |  1 file changed, 1 insertion(+), 1 deletion(-)

| | * 2020-04-07(houyun) fixed 'type = "triangle"' error |6cb664f
| |/  | |   
| |    R/ggdend.R | 11 +++++++----
| |    1 file changed, 7 insertions(+), 4 deletions(-)

* / 2020-05-15(Tal Galili) For future spell checking |65b9b67
|/  |   
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|    2 files changed, 236 insertions(+)

* 2020-03-27(Tal Galili) update version |49ad39c| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 7 +++++++
|  2 files changed, 9 insertions(+), 2 deletions(-)

* 2020-03-27(Tal Galili) update pkgdown website |23255e8| 
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|  152 files changed, 4350 insertions(+), 4601 deletions(-)

* 2020-02-28(Tal Galili) Update dates |df4d11c| 
|  ChangeLog            | 40 ++++++++++++++++++++++++++--------------
|  NEWS.md              |  2 +-
|  docs/news/index.html |  6 +++---
|  3 files changed, 30 insertions(+), 18 deletions(-)

* 2020-02-28(Tal Galili) Fix some tests using include_EV (since this arugment was removed - I removed these tests) |0534e90| 
|  DESCRIPTION                     |  2 +-
|  NEWS                            |  2 +-
|  tests/testthat/test-bk_method.R | 13 ++++---------
|  3 files changed, 6 insertions(+), 11 deletions(-)

* 2020-02-28(Tal Galili) Update the website |6258cb1| 
|  ChangeLog                                   | 185 ++++++++++++++++++++++++++
|  docs/articles/Cluster_Analysis.html         |   2 +-
|  docs/articles/FAQ.html                      |   2 +-
|  docs/articles/Quick_Introduction.html       |   2 +-
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|  13 files changed, 204 insertions(+), 62 deletions(-)

* 2020-02-28(Tal Galili) Remove profdpm dependacy |a0b8160| 
|  DESCRIPTION                     |   1 -
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|  R/bk_method.R                   | 183 ++++----------------------------------
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|  tests/testthat/test-bk_method.R |  64 -------------
|  vignettes/dendextend.Rmd        |   4 -
|  14 files changed, 33 insertions(+), 372 deletions(-)

* 2020-02-27(Tal Galili) update site |afabe37| 
|  ChangeLog                                         | 203 +++++++++++++++++-
|  NEWS.md                                           |  15 ++
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|  docs/reference/set.html                           |   2 +-
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|  docs/reference/sort_2_clusters_vectors.html       |   2 +-
|  docs/reference/sort_dist_mat.html                 |   2 +-
|  docs/reference/sort_levels_values.html            |   2 +-
|  docs/reference/tanglegram.html                    |   2 +-
|  docs/reference/theme_dendro.html                  |   2 +-
|  docs/reference/unbranch.html                      |   2 +-
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|  docs/reference/which_leaf.html                    |   2 +-
|  docs/reference/which_node.html                    |   2 +-
|  150 files changed, 506 insertions(+), 276 deletions(-)

* 2020-02-27(Tal Galili) Add stringsAsFactors = TRUE to all data.frame calls (in preperation for R 4.0.0) |b603a7a| 
|  NEWS          | 1 +
|  R/dist_long.R | 2 +-
|  R/find_dend.R | 2 +-
|  R/ggdend.R    | 3 ++-
|  R/ggdendro.R  | 4 ++--
|  R/pvclust.R   | 2 +-
|  6 files changed, 8 insertions(+), 6 deletions(-)

* 2020-02-27(Tal Galili) remove old rnw vignette (that was changed to Rmd years ago) |e3a7fe9| 
|  vignettes/disabled/dendextend-tutorial.rnw | 2024 --------------------------
|  1 file changed, 2024 deletions(-)

* 2020-02-27(Tal Galili) Fix "Failed with error: 'there is no package called 'profdpm''" |0b67101| 
|  DESCRIPTION                     |   4 +-
|  NEWS                            |   7 +++
|  tests/testthat/test-bk_method.R | 109 ++++++++++++++++++++------------------
|  vignettes/dendextend.Rmd        |   6 ++-
|  4 files changed, 69 insertions(+), 57 deletions(-)

* 2020-02-07(Tal Galili) Fixed doc warning for bakers_gamma_for_2_k_matrix |971bccf| 
|  DESCRIPTION                        | 6 +++---
|  NEWS                               | 7 +++++++
|  R/cor_bakers_gamma.R               | 2 +-
|  man/bakers_gamma_for_2_k_matrix.Rd | 7 ++++++-
|  4 files changed, 17 insertions(+), 5 deletions(-)

* 2019-11-27(Tal Galili) Going back to 1.13.2 |7d3b420| 
|  DESCRIPTION                                             |  2 +-
|  NEWS                                                    |  4 ++--
|  NEWS.md                                                 |  4 ++--
|  docs/404.html                                           |  2 +-
|  docs/CONDUCT.html                                       |  2 +-
|  docs/articles/Cluster_Analysis.html                     |  4 ++--
|  docs/articles/FAQ.html                                  |  4 ++--
|  docs/articles/Quick_Introduction.html                   |  4 ++--
|  docs/articles/dendextend.html                           |  8 ++++----
|  docs/articles/index.html                                |  2 +-
|  docs/authors.html                                       |  2 +-
|  docs/index.html                                         |  2 +-
|  docs/news/index.html                                    | 10 +++++-----
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|  vignettes/dendextend.Rmd                                |  2 +-
|  152 files changed, 164 insertions(+), 164 deletions(-)

* 2019-11-27(Tal Galili) Bump to 1.14.0 |2fd54e3| 
|  ChangeLog            | 391 +++++++++++++++++++++++++++++++++++++++++++++++++
|  DESCRIPTION          |   4 +-
|  NEWS                 |   9 +-
|  NEWS.md              |   3 +-
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|  docs/authors.html    |   2 +-
|  docs/index.html      |   6 +-
|  docs/news/index.html |   9 +-
|  9 files changed, 409 insertions(+), 19 deletions(-)

* 2019-11-25(Tal Galili) minor doc fixes to comply with CRAN. |5178c38| 
|  DESCRIPTION               | 4 ++--
|  NEWS                      | 6 ++++++
|  R/dendextend-package.R    | 2 +-
|  README.md                 | 4 ++--
|  man/dendextend-package.Rd | 4 +++-
|  5 files changed, 14 insertions(+), 6 deletions(-)

* 2019-11-23(Tal Galili) README - remove motivation section (why did I put it there this way?!?!) |97371fe| 
|  README.md       | 6 +-----
|  docs/index.html | 7 +------
|  2 files changed, 2 insertions(+), 11 deletions(-)

* 2019-11-23(Tal Galili) README - more tweaks |3509cf6| 
|  README.md       | 50 ++++++++++++++++++++------------------------------
|  docs/index.html | 47 +++++++++++++++++++----------------------------
|  2 files changed, 39 insertions(+), 58 deletions(-)

* 2019-11-23(Tal Galili) Update the README |89fae94| 
|  README.md       | 27 ++++++++++++++-------------
|  docs/index.html | 24 +++++++++++-------------
|  2 files changed, 25 insertions(+), 26 deletions(-)

* 2019-11-23(Tal Galili) Fix Rd error, and update pkgdown site. |cafada6| 
|  ChangeLog                                         | 179 +++++-
|  NEWS.md                                           |   3 +
|  R/bk_method.R                                     |  14 +-
|  R/tanglegram.R                                    |   2 +-
|  docs/404.html                                     | 156 +++++
|  docs/CONDUCT.html                                 |  20 +-
|  docs/articles/Cluster_Analysis.html               | 203 +++----
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|  docs/news/index.html                              | 207 ++++---
|  docs/pkgdown.css                                  |  46 +-
|  docs/pkgdown.js                                   |  14 +-
|  docs/pkgdown.yml                                  |   4 +-
|  docs/reference/Bk.html                            |  76 +--
|  docs/reference/Bk_permutations.html               |  68 ++-
|  docs/reference/Bk_plot.html                       | 131 +++--
|  docs/reference/DendSer.dendrogram.html            |  42 +-
|  docs/reference/FM_index.html                      | 101 ++--
|  docs/reference/FM_index_R.html                    |  75 ++-
|  docs/reference/FM_index_permutation.html          |  85 +--
|  docs/reference/FM_index_profdpm.html              |  77 ++-
|  docs/reference/all.equal.dendrogram.html          | 103 ++--
|  docs/reference/all_couple_rotations_at_k.html     |  53 +-
|  docs/reference/all_unique.html                    |  25 +-
|  docs/reference/as.dendlist.html                   |  41 +-
|  docs/reference/as.phylo.dendrogram.html           |  71 ++-
|  docs/reference/as_hclust_fixed.html               |  38 +-
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|  docs/reference/bakers_gamma_for_2_k_matrix.html   |  23 +-
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|  docs/reference/branches_attr_by_labels.html       |  84 ++-
|  docs/reference/branches_attr_by_lists.html        |  65 ++-
|  docs/reference/circlize_dendrogram.html           |  87 +--
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|  docs/reference/color_branches.html                | 278 +++++----
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|  docs/reference/colored_dots.html                  | 141 +++--
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|  docs/reference/common_subtrees_clusters.html      |  36 +-
|  docs/reference/cor.dendlist.html                  |  69 ++-
|  docs/reference/cor_FM_index.html                  |  39 +-
|  docs/reference/cor_bakers_gamma.html              | 100 ++--
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|  docs/reference/cor_common_nodes.html              |  41 +-
|  docs/reference/cor_cophenetic.html                | 125 ++--
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|  docs/reference/count_terminal_nodes.html          |  42 +-
|  docs/reference/cut_lower_fun.html                 |  51 +-
|  docs/reference/cutree-methods.html                | 173 +++---
|  docs/reference/cutree_1h.dendrogram.html          |  80 +--
|  docs/reference/cutree_1k.dendrogram.html          | 100 ++--
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|  docs/reference/dendextend-package.html            |  22 +-
|  docs/reference/dendextend_options.html            |  31 +-
|  docs/reference/dendlist.html                      |  65 ++-
|  docs/reference/depth-1.png                        | Bin 27875 -> 119772 bytes
|  docs/reference/depth.html                         |  27 +-
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|  docs/reference/dist.dendlist.html                 |  79 ++-
|  docs/reference/dist_long.html                     |  35 +-
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|  docs/reference/distinct_edges.html                |  30 +-
|  docs/reference/duplicate_leaf.html                |  53 +-
|  docs/reference/entanglement.html                  | 100 ++--
|  docs/reference/fac2num.html                       |  27 +-
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|  docs/reference/find_k.html                        |  74 ++-
|  docs/reference/fix_members_attr.dendrogram.html   |  36 +-
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|  docs/reference/get_branches_heights.html          |  37 +-
|  docs/reference/get_childrens_heights.html         |  30 +-
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|  docs/reference/get_nodes_attr.html                |  73 ++-
|  docs/reference/get_nodes_xy.html                  |  71 ++-
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|  docs/reference/ggdend.html                        | 105 ++--
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|  docs/reference/highlight_branches.html            | 134 +++--
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|  docs/reference/highlight_distinct_edges.html      |  85 ++-
|  docs/reference/identify.dendrogram.html           |  93 +--
|  docs/reference/index.html                         | 180 +++---
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|  docs/reference/khan.html                          |  63 +-
|  docs/reference/labels-assign.html                 |  68 ++-
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|  docs/reference/lowest_common_branch.html          |  27 +-
|  docs/reference/match_order_by_labels.html         |  65 ++-
|  .../match_order_dendrogram_by_old_order.html      |  70 ++-
|  docs/reference/na_locf.html                       |  51 +-
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|  docs/reference/nnodes.html                        |  28 +-
|  docs/reference/noded_with_condition.html          |  78 ++-
|  docs/reference/order.dendrogram-assign.html       |  45 +-
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|  docs/reference/partition_leaves.html              |  51 +-
|  docs/reference/plot_horiz.dendrogram.html         | 104 ++--
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|  docs/reference/pvclust_show_signif.html           |  89 +--
|  docs/reference/pvclust_show_signif_gradient.html  |  89 +--
|  docs/reference/pvrect2.html                       |  72 ++-
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|  docs/reference/rank_branches.html                 |  51 +-
|  docs/reference/rank_order.dendrogram.html         |  36 +-
|  docs/reference/rank_values_with_clusters.html     |  26 +-
|  docs/reference/rect.dendrogram-1.png              | Bin 11503 -> 40429 bytes
|  docs/reference/rect.dendrogram-2.png              | Bin 17636 -> 77148 bytes
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|  docs/reference/rect.dendrogram-5.png              | Bin 9476 -> 40417 bytes
|  docs/reference/rect.dendrogram.html               | 123 ++--
|  docs/reference/reexports.html                     |  22 +-
|  docs/reference/reindex_dend.html                  |  38 +-
|  docs/reference/remove_branches_edgePar.html       |  38 +-
|  docs/reference/remove_leaves_nodePar.html         |  39 +-
|  docs/reference/remove_nodes_nodePar.html          |  38 +-
|  docs/reference/rllply.html                        |  68 ++-
|  docs/reference/rotate-1.png                       | Bin 11354 -> 51153 bytes
|  docs/reference/rotate-2.png                       | Bin 19995 -> 72500 bytes
|  docs/reference/rotate-3.png                       | Bin 19001 -> 63729 bytes
|  docs/reference/rotate-4.png                       | Bin 13884 -> 59646 bytes
|  docs/reference/rotate-5.png                       | Bin 15639 -> 61278 bytes
|  docs/reference/rotate.html                        | 120 ++--
|  docs/reference/rotate_DendSer.html                |  43 +-
|  docs/reference/sample.dendrogram.html             |  72 ++-
|  docs/reference/seriate_dendrogram.html            |  48 +-
|  docs/reference/set.html                           | 327 +++++++----
|  docs/reference/set_labels-1.png                   | Bin 12496 -> 58601 bytes
|  docs/reference/set_labels-2.png                   | Bin 17788 -> 95820 bytes
|  docs/reference/set_labels-3.png                   | Bin 11488 -> 50751 bytes
|  docs/reference/set_labels.html                    |  93 +--
|  docs/reference/shuffle-1.png                      | Bin 52788 -> 327193 bytes
|  docs/reference/shuffle-2.png                      | Bin 34116 -> 172385 bytes
|  docs/reference/shuffle.html                       |  43 +-
|  docs/reference/sort_2_clusters_vectors.html       |  57 +-
|  docs/reference/sort_dist_mat.html                 |  22 +-
|  docs/reference/sort_levels_values.html            |  71 ++-
|  docs/reference/tanglegram.html                    | 283 ++++++---
|  docs/reference/theme_dendro.html                  |  20 +-
|  docs/reference/unbranch-1.png                     | Bin 15676 -> 65817 bytes
|  docs/reference/unbranch.html                      |  40 +-
|  docs/reference/unclass_dend.html                  |  44 +-
|  docs/reference/untangle.html                      |  92 ++-
|  docs/reference/untangle_DendSer.html              |  57 +-
|  docs/reference/untangle_random_search.html        |  75 ++-
|  docs/reference/untangle_step_rotate_1side.html    |  75 ++-
|  docs/reference/untangle_step_rotate_2side.html    |  88 +--
|  docs/reference/which_leaf.html                    |  47 +-
|  docs/reference/which_node-1.png                   | Bin 9211 -> 34456 bytes
|  docs/reference/which_node.html                    |  40 +-
|  man/FM_index_R.Rd                                 |  14 +-
|  man/tanglegram.Rd                                 |   8 +-
|  354 files changed, 6603 insertions(+), 4211 deletions(-)

* 2019-11-23(Tal Galili) Update docs to the recent roxygen2 (7.0.1) output |0ee3c7d| 
|  R/distinct_edges.R                         |   7 +-
|  man/Bk.Rd                                  |  35 ++--
|  man/Bk_permutations.Rd                     |  39 ++--
|  man/Bk_plot.Rd                             |  82 +++++---
|  man/DendSer.dendrogram.Rd                  |   4 +-
|  man/FM_index.Rd                            |  70 ++++---
|  man/FM_index_R.Rd                          |  36 ++--
|  man/FM_index_permutation.Rd                |  40 ++--
|  man/FM_index_profdpm.Rd                    |  44 ++--
|  man/all.equal.dendrogram.Rd                |  44 ++--
|  man/all_couple_rotations_at_k.Rd           |  25 ++-
|  man/all_unique.Rd                          |   9 +-
|  man/as.dendlist.Rd                         |  13 +-
|  man/as.phylo.dendrogram.Rd                 |  24 ++-
|  man/as_hclust_fixed.Rd                     |  10 +-
|  man/assign_values_to_branches_edgePar.Rd   |  46 +++--
|  man/assign_values_to_leaves_edgePar.Rd     |  25 ++-
|  man/assign_values_to_leaves_nodePar.Rd     |  25 ++-
|  man/assign_values_to_nodes_nodePar.Rd      |  37 ++--
|  man/bakers_gamma_for_2_k_matrix.Rd         |   3 +-
|  man/branches_attr_by_clusters.Rd           |  42 ++--
|  man/branches_attr_by_labels.Rd             |  63 +++---
|  man/branches_attr_by_lists.Rd              |  40 ++--
|  man/circlize_dendrogram.Rd                 |  48 +++--
|  man/click_rotate.Rd                        |  20 +-
|  man/collapse_branch.Rd                     |  35 +++-
|  man/color_branches.Rd                      | 177 +++++++++-------
|  man/color_labels.Rd                        |  32 +--
|  man/color_unique_labels.Rd                 |   4 +-
|  man/colored_bars.Rd                        |  91 ++++----
|  man/colored_dots.Rd                        |  89 +++++---
|  man/common_subtrees_clusters.Rd            |   8 +-
|  man/cor.dendlist.Rd                        |  36 +++-
|  man/cor_FM_index.Rd                        |  11 +-
|  man/cor_bakers_gamma.Rd                    |  66 +++---
|  man/cor_common_nodes.Rd                    |  15 +-
|  man/cor_cophenetic.Rd                      |  69 ++++---
|  man/count_terminal_nodes.Rd                |  16 +-
|  man/cut_lower_fun.Rd                       |  20 +-
|  man/cutree-methods.Rd                      | 138 +++++++------
|  man/cutree_1h.dendrogram.Rd                |  39 ++--
|  man/cutree_1k.dendrogram.Rd                |  59 +++---
|  man/dend_diff.Rd                           |  17 +-
|  man/dendextend_options.Rd                  |   1 -
|  man/dendlist.Rd                            |  33 ++-
|  man/depth.Rd                               |   1 -
|  man/dist.dendlist.Rd                       |  47 +++--
|  man/dist_long.Rd                           |  13 +-
|  man/distinct_edges.Rd                      |   6 +-
|  man/duplicate_leaf.Rd                      |  18 +-
|  man/entanglement.Rd                        |  66 +++---
|  man/fac2num.Rd                             |   1 -
|  man/find_dend.Rd                           |  16 +-
|  man/find_dendrogram.Rd                     |  10 +-
|  man/find_k.Rd                              |  32 +--
|  man/fix_members_attr.dendrogram.Rd         |  12 +-
|  man/flatten.dendrogram.Rd                  |   6 +-
|  man/flip_leaves.Rd                         |  12 +-
|  man/get_branches_heights.Rd                |  13 +-
|  man/get_childrens_heights.Rd               |   6 +-
|  man/get_leaves_attr.Rd                     |  20 +-
|  man/get_leaves_branches_attr.Rd            |  16 +-
|  man/get_leaves_branches_col.Rd             |  22 +-
|  man/get_leaves_edgePar.Rd                  |   7 +-
|  man/get_leaves_nodePar.Rd                  |   5 +-
|  man/get_nodes_attr.Rd                      |  50 +++--
|  man/get_nodes_xy.Rd                        |  42 ++--
|  man/get_root_branches_attr.Rd              |   7 +-
|  man/get_subdendrograms.Rd                  |  16 +-
|  man/ggdend.Rd                              |  57 ++---
|  man/hang.dendrogram.Rd                     |  18 +-
|  man/has_component_in_attribute.Rd          |  30 ++-
|  man/heights_per_k.dendrogram.Rd            |  30 +--
|  man/highlight_branches.Rd                  |  88 +++++---
|  man/highlight_distinct_edges.Rd            |  49 +++--
|  man/identify.dendrogram.Rd                 |  41 ++--
|  man/intersect_trees.Rd                     |  23 ++-
|  man/is.natural.number.Rd                   |   7 +-
|  man/is_null_list.Rd                        |   2 +-
|  man/khan.Rd                                |  39 ++--
|  man/labels-assign.Rd                       |  24 +--
|  man/labels_cex.Rd                          |   5 +-
|  man/labels_colors.Rd                       |  12 +-
|  man/ladderize.Rd                           |  19 +-
|  man/leaf_Colors.Rd                         |   7 +-
|  man/lowest_common_branch.Rd                |   1 -
|  man/match_order_by_labels.Rd               |  17 +-
|  man/match_order_dendrogram_by_old_order.Rd |  31 +--
|  man/na_locf.Rd                             |  15 +-
|  man/nleaves.Rd                             |  16 +-
|  man/nnodes.Rd                              |   4 +-
|  man/noded_with_condition.Rd                |  37 ++--
|  man/order.dendrogram-assign.Rd             |   9 +-
|  man/order.hclust.Rd                        |  15 +-
|  man/partition_leaves.Rd                    |  18 +-
|  man/plot_horiz.dendrogram.Rd               |  66 +++---
|  man/prune.Rd                               |  14 +-
|  man/prune_common_subtrees.dendlist.Rd      |   3 +-
|  man/prune_leaf.Rd                          |   8 +-
|  man/pvclust_edges.Rd                       |   5 +-
|  man/pvclust_show_signif.Rd                 |  53 +++--
|  man/pvclust_show_signif_gradient.Rd        |  59 +++---
|  man/pvrect2.Rd                             |  32 +--
|  man/raise.dendrogram.Rd                    |   6 +-
|  man/rank_branches.Rd                       |  17 +-
|  man/rank_order.dendrogram.Rd               |   8 +-
|  man/rank_values_with_clusters.Rd           |  20 +-
|  man/rect.dendrogram.Rd                     |  99 +++++----
|  man/reindex_dend.Rd                        |  16 +-
|  man/remove_branches_edgePar.Rd             |   8 +-
|  man/remove_leaves_nodePar.Rd               |   9 +-
|  man/remove_nodes_nodePar.Rd                |   8 +-
|  man/rllply.Rd                              |  30 ++-
|  man/rotate.Rd                              |  80 ++++----
|  man/rotate_DendSer.Rd                      |   7 +-
|  man/sample.dendrogram.Rd                   |  31 ++-
|  man/seriate_dendrogram.Rd                  |   2 -
|  man/set.Rd                                 | 297 ++++++++++++++++-----------
|  man/set_labels.Rd                          |  61 +++---
|  man/shuffle.Rd                             |  15 +-
|  man/sort_2_clusters_vectors.Rd             |  30 +--
|  man/sort_levels_values.Rd                  |  29 +--
|  man/theme_dendro.Rd                        |   2 +-
|  man/unbranch.Rd                            |  14 +-
|  man/unclass_dend.Rd                        |  20 +-
|  man/untangle.Rd                            |  62 ++++--
|  man/untangle_DendSer.Rd                    |  25 ++-
|  man/untangle_random_search.Rd              |  45 ++--
|  man/untangle_step_rotate_1side.Rd          |  47 +++--
|  man/untangle_step_rotate_2side.Rd          |  58 +++---
|  man/which_leaf.Rd                          |  14 +-
|  man/which_node.Rd                          |  30 +--
|  132 files changed, 2459 insertions(+), 1716 deletions(-)

* 2019-11-23(Tal Galili) Update tangelgram docs due to a recent code change |b3e49ee| 
|  DESCRIPTION       |   5 +-
|  NEWS              |   3 +
|  R/tanglegram.R    |   3 +-
|  man/tanglegram.Rd | 251 +++++++++++++++++++++++++++++++++++-----------------
|  4 files changed, 178 insertions(+), 84 deletions(-)

*   2019-11-23(Tal Galili) Merge pull request #96 from DBradley27/patch-1 |344d6d3
|\  
| * 2019-11-07(David Bradley) Update tanglegram.R |38915c4| | 
| |  R/tanglegram.R | 2 +-
| |  1 file changed, 1 insertion(+), 1 deletion(-)

| * 2019-11-06(David Bradley) Update tanglegram.R |e1a29e8| | 
| |  R/tanglegram.R | 7 +++++--
| |  1 file changed, 5 insertions(+), 2 deletions(-)

* | 2019-11-23(Tal Galili) Send output to console |ba7ffa6| | 
| |  vignettes/Quick_Introduction.Rmd | 4 +++-
| |  vignettes/dendextend.Rmd         | 2 ++
| |  2 files changed, 5 insertions(+), 1 deletion(-)

* | 2019-11-23(Tal Galili) Move from d3heatmap to heatmaply |f321dc1| | 
| |  NEWS                     |  1 +
| |  NEWS.md                  |  1 +
| |  vignettes/dendextend.Rmd | 16 ++++++++++------
| |  3 files changed, 12 insertions(+), 6 deletions(-)

* | 2019-11-23(Tal Galili) Fixed testthat failure due to RNG changes in R (test for pvclust) |6156fea
|/  |   
|    ChangeLog                             | 743 +++++++++++++++++++++++++++++-
|    DESCRIPTION                           |   2 +-
|    NEWS                                  |   3 +-
|    NEWS.md                               |   6 +-
|    R/zzz.R                               |   2 +-
|    tests/testthat/test-pvclust_extract.R |   4 +-
|    6 files changed, 752 insertions(+), 8 deletions(-)

* 2019-09-27(Tal Galili) Update issue templates 2 |06753dc| 
|  .github/ISSUE_TEMPLATE/bug_report.md      |  7 +++++--
|  .github/ISSUE_TEMPLATE/feature_request.md | 20 ++++++++++++++++++++
|  2 files changed, 25 insertions(+), 2 deletions(-)

* 2019-09-27(Tal Galili) Update issue templates |b07f633| 
|  .github/ISSUE_TEMPLATE/bug_report.md | 26 ++++++++++++++++++++++++++
|  1 file changed, 26 insertions(+)

*   2019-09-24(Tal Galili) Merge pull request #95 from Alanocallaghan/styler |46a2b12
|\  
| * 2019-09-23(Alan O'Callaghan) Style package using styler::style_pkg |64b5e5c| | 
| |  R/DendSer.R                              |   79 +-
| |  R/Hmisc.R                                |    4 +-
| |  R/all.equal.R                            |  266 ++---
| |  R/ape.R                                  |   72 +-
| |  R/as.dendrogram.randomForest.R           |   43 +-
| |  R/attr_access.R                          | 1402 ++++++++++++------------
| |  R/bk_method.R                            | 1161 ++++++++++----------
| |  R/branches_attr_by.R                     |  500 +++++----
| |  R/circlize.R                             |  171 +--
| |  R/color_branches.R                       |  776 ++++++-------
| |  R/colored_bars.R                         |  545 +++++-----
| |  R/colored_dots.R                         |   81 +-
| |  R/common_subtrees.R                      |  242 ++---
| |  R/cor.dendlist.R                         |  173 +--
| |  R/cor_bakers_gamma.R                     |  229 ++--
| |  R/cor_cophenetic.R                       |  185 ++--
| |  R/cut_lower_fun.R                        |   57 +-
| |  R/cutree.dendrogram.R                    | 1124 +++++++++----------
| |  R/data.R                                 |   64 +-
| |  R/dendextend-package.R                   |    5 +-
| |  R/dendextend.R                           |   43 +-
| |  R/dendextend_options.R                   |   93 +-
| |  R/dendlist.R                             |  319 +++---
| |  R/depth.R                                |   63 +-
| |  R/dist_long.R                            |   37 +-
| |  R/distinct_edges.R                       |  414 +++----
| |  R/entanglement.R                         |  455 ++++----
| |  R/find_dend.R                            |  113 +-
| |  R/find_k.R                               |  780 +++++++------
| |  R/get_nodes_xy.R                         |  354 +++---
| |  R/get_subdendrograms.R                   |   36 +-
| |  R/ggdend.R                               |  872 +++++++--------
| |  R/ggdendro.R                             |  369 ++++---
| |  R/has_edgePar.R                          |   67 +-
| |  R/highlight_branches.R                   |  222 ++--
| |  R/is.functions.R                         |   37 +-
| |  R/labels.R                               |  459 ++++----
| |  R/labels_colors.R                        |  209 ++--
| |  R/magrittr.R                             |    3 +-
| |  R/nleaves.R                              |  237 ++--
| |  R/noded_with_condition.R                 |  195 ++--
| |  R/prune.R                                |  413 ++++---
| |  R/pvclust.R                              |  790 +++++++-------
| |  R/rainbow_fun.R                          |   14 +-
| |  R/rect.dendrogram.R                      |  506 +++++----
| |  R/rotate.R                               |  420 +++----
| |  R/sample.dendrogram.R                    |  344 +++---
| |  R/seriate_dendrogram.R                   |   35 +-
| |  R/set.dendrogram.R                       |  508 +++++----
| |  R/stats_imports.R                        |  536 +++++----
| |  R/tanglegram.R                           | 1510 ++++++++++++++------------
| |  R/unbranch.R                             |  371 ++++---
| |  R/untangle.R                             | 1379 ++++++++++++-----------
| |  R/zzz.R                                  |  270 ++---
| |  tests/test-all.R                         |   24 +-
| |  tests/testthat/test-attr_access.R        |  372 ++++---
| |  tests/testthat/test-bk_method.R          |  502 ++++-----
| |  tests/testthat/test-branches_attr_by.R   |  190 ++--
| |  tests/testthat/test-common_subtrees.R    |   87 +-
| |  tests/testthat/test-cor_bakers_gamma.R   |   74 +-
| |  tests/testthat/test-cor_cophenetic.R     |   78 +-
| |  tests/testthat/test-cut_lower_fun.R      |  119 +-
| |  tests/testthat/test-cutree.dendrogram.R  |  852 ++++++++-------
| |  tests/testthat/test-dendlist.R           |  171 +--
| |  tests/testthat/test-distinct_edges.R     |   62 +-
| |  tests/testthat/test-entanglement.R       |  226 ++--
| |  tests/testthat/test-general.R            |   13 +-
| |  tests/testthat/test-ggdend.R             |  195 ++--
| |  tests/testthat/test-highlight_branches.R |   56 +-
| |  tests/testthat/test-labels-assign.R      |  287 +++--
| |  tests/testthat/test-labels_colors.R      |  198 ++--
| |  tests/testthat/test-nleaves.R            |   85 +-
| |  tests/testthat/test-pvclust_extract.R    |   27 +-
| |  tests/testthat/test-rect.dendrogram.R    |   20 +-
| |  tests/testthat/test-rotate.R             |  109 +-
| |  tests/testthat/test-set.dendrogram.R     |  305 +++---
| |  tests/testthat/test-trim.R               |  368 +++----
| |  tests/testthat/test-unbranch.R           |   65 +-
| |  tests/testthat/test-untangle.R           |  237 ++--
| |  vignettes/dendextend.Rmd                 |    4 +-
| |  80 files changed, 12703 insertions(+), 11675 deletions(-)

| * 2019-09-23(Alan O'Callaghan) test for na.rm warning |1d1f3b6| | 
| |  tests/testthat/test-ggdend.R | 5 ++++-
| |  1 file changed, 4 insertions(+), 1 deletion(-)

| * 2019-09-18(Alan O'Callaghan) na.rm option for ggplot.ggdend |2375da2
|/  |   
|    DESCRIPTION        |  1 +
|    R/distinct_edges.R | 14 ++++++++++----
|    R/ggdend.R         |  8 +++++---
|    man/ggdend.Rd      |  5 ++++-
|    4 files changed, 20 insertions(+), 8 deletions(-)

* 2019-09-17(Tal Galili) update pkgdown site |901d812| 
|  docs/articles/Cluster_Analysis.html           |   6 +-
|  docs/articles/FAQ.html                        |   4 +-
|  docs/articles/Quick_Introduction.html         |   2 +-
|  docs/articles/dendextend.html                 | 105 +++++++++---------------
|  docs/reference/branches_attr_by_clusters.html |   4 +-
|  docs/reference/color_branches.html            |   8 +-
|  docs/reference/color_labels.html              |   2 +-
|  docs/reference/colored_bars.html              |   4 +-
|  docs/reference/dist.dendlist-2.png            | Bin 0 -> 8147 bytes
|  docs/reference/dist.dendlist.html             |  16 ++--
|  10 files changed, 64 insertions(+), 87 deletions(-)

* 2019-09-17(Tal Galili) improve dist.dendlist documentation |8f4019f| 
|  DESCRIPTION          |  2 +-
|  NEWS                 |  5 ++++-
|  R/distinct_edges.R   | 17 ++++++++++++++---
|  man/dist.dendlist.Rd | 16 +++++++++++-----
|  4 files changed, 30 insertions(+), 10 deletions(-)

* 2019-09-17(Tal Galili) build pkgdown before release |ff6303c| 
|  R/zzz.R | 1 +
|  1 file changed, 1 insertion(+)

* 2019-07-17(Tal Galili) ignore stuff for CRAN |8343ae8| 
|  .Rbuildignore | 20 ++++++++++++++++++++
|  1 file changed, 20 insertions(+)

* 2019-07-17(Tal Galili) rename vignette file to work with pkgdown and recreated the site |230a6c8| 
|  docs/CONDUCT.html                                 |    6 +-
|  docs/articles/Cluster_Analysis.html               |    6 +-
|  docs/articles/FAQ.html                            |    6 +-
|  docs/articles/Quick_Introduction.html             |    6 +-
|  docs/articles/dendextend.html                     | 1448 +++
|  .../dendextend_files/d3-3.5.3/CONTRIBUTING.md     |   25 +
|  docs/articles/dendextend_files/d3-3.5.3/LICENSE   |   26 +
|  docs/articles/dendextend_files/d3-3.5.3/README.md |    9 +
|  docs/articles/dendextend_files/d3-3.5.3/d3.js     | 9466 +++++++++++++++++++
|  docs/articles/dendextend_files/d3-3.5.3/d3.min.js |    5 +
|  .../dendextend_files/d3-tip-0.6.6/LICENSE         |    8 +
|  .../dendextend_files/d3-tip-0.6.6/README.md       |   43 +
|  .../dendextend_files/d3-tip-0.6.6/index.js        |  299 +
|  .../dendextend_files/d3-tip-0.6.6/package.json    |   28 +
|  .../d3heatmap-binding-0.6.1.2/d3heatmap.js        |  115 +
|  .../d3heatmapcore-0.0.0/heatmapcore.css           |  100 +
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|  vignettes/{introduction.Rmd => dendextend.Rmd}    |    0
|  225 files changed, 13496 insertions(+), 440 deletions(-)

* 2019-07-17(Tal Galili) Started using pkgdown :) |435447b| 
|  ChangeLog                                         |   20 +
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|  NEWS                                              |    5 +
|  NEWS.md                                           |    5 +
|  docs/CONDUCT.html                                 |  156 +
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|  docs/articles/introduction_files/d3-3.5.3/LICENSE |   26 +
|  .../introduction_files/d3-3.5.3/README.md         |    9 +
|  docs/articles/introduction_files/d3-3.5.3/d3.js   | 9466 +++++++++++++++++++
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|  .../introduction_files/d3-tip-0.6.6/LICENSE       |    8 +
|  .../introduction_files/d3-tip-0.6.6/README.md     |   43 +
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|  docs/news/index.html                              | 2542 +++++
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* 2019-05-11(Tal Galili) Remove plyr from suggests |92c5e64| 
|  DESCRIPTION  | 1 -
|  R/untangle.R | 3 ---
|  2 files changed, 4 deletions(-)

* 2019-05-11(Tal Galili) Remove old URL and some dendextendRcpp ref |812c671| 
|  README.md | 4 ----
|  1 file changed, 4 deletions(-)

* 2019-05-11(Tal Galili) Use newer devtools functions for testing. |1db72ed| 
|  R/zzz.R | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2019-05-11(Tal Galili) update docs |55d47a4| 
|  ChangeLog              | 62 ++++++++++++++++++++++++++++++++++++++++++++++++
|  NAMESPACE              |  1 -
|  NEWS.md                | 19 +++++++++++----
|  R/dendextend-package.R |  1 -
|  4 files changed, 76 insertions(+), 7 deletions(-)

* 2019-05-11(Tal Galili) Remove d3dendrogram |eb432c8| 
|  DESCRIPTION             |   3 +-
|  NEWS                    |   6 +-
|  R/d3dendrogram.R        | 290 ----------------------------------------------
|  R/zzz.R                 |   2 -
|  man/d3dendro_options.Rd |  41 -------
|  man/d3dendrogram.Rd     |  48 --------
|  6 files changed, 5 insertions(+), 385 deletions(-)

* 2019-05-11(Tal Galili) Remove dendextendRcpp from introduction.Rmd |deb7181| 
|  NEWS                             |   1 +
|  inst/doc/dendextend-tutorial.pdf | Bin 564592 -> 0 bytes
|  vignettes/introduction.Rmd       |  20 --------------------
|  3 files changed, 1 insertion(+), 20 deletions(-)

* 2019-05-11(Tal Galili) Add missing function from fpc |dec5e9e| 
|  DESCRIPTION |   2 +-
|  NEWS        |   5 +-
|  R/find_k.R  | 298 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  3 files changed, 303 insertions(+), 2 deletions(-)

* 2019-05-10(Tal Galili) RoxygenNote: 6.1.1 |309397f| 
|  DESCRIPTION                              |  4 +--
|  NEWS                                     |  5 +++
|  man/Bk.Rd                                |  4 +--
|  man/Bk_plot.Rd                           |  9 +++---
|  man/FM_index.Rd                          |  3 +-
|  man/all.equal.dendrogram.Rd              |  5 +--
|  man/assign_values_to_branches_edgePar.Rd |  4 +--
|  man/assign_values_to_nodes_nodePar.Rd    |  4 +--
|  man/bakers_gamma_for_2_k_matrix.Rd       |  3 +-
|  man/branches_attr_by_labels.Rd           |  4 +--
|  man/branches_attr_by_lists.Rd            |  4 +--
|  man/circlize_dendrogram.Rd               |  5 +--
|  man/cor_bakers_gamma.Rd                  |  8 ++---
|  man/cut_lower_fun.Rd                     |  3 +-
|  man/cutree-methods.Rd                    |  1 -
|  man/find_dend.Rd                         |  6 ++--
|  man/get_root_branches_attr.Rd            |  3 +-
|  man/plot_horiz.dendrogram.Rd             | 11 ++++---
|  man/pvclust_show_signif.Rd               |  3 +-
|  man/pvclust_show_signif_gradient.Rd      |  5 +--
|  man/rect.dendrogram.Rd                   |  6 ++--
|  man/set.Rd                               | 16 +++++-----
|  man/sort_2_clusters_vectors.Rd           |  3 +-
|  man/tanglegram.Rd                        | 49 ++++++++++++++++--------------
|  man/unbranch.Rd                          |  8 ++---
|  man/untangle.Rd                          |  8 ++---
|  man/untangle_step_rotate_1side.Rd        |  4 +--
|  man/untangle_step_rotate_2side.Rd        |  4 +--
|  28 files changed, 106 insertions(+), 86 deletions(-)

* 2019-05-10(Tal Galili) Bumped to 1.11.0 |9a156c8| 
|  DESCRIPTION | 2 +-
|  NEWS        | 8 +++-----
|  2 files changed, 4 insertions(+), 6 deletions(-)

* 2019-05-10(Tal Galili) Update NEWS files. |70486f3| 
|  ChangeLog | 1081 +++++++++++++++++++++++++++++------------------------------
|  NEWS.md   |   44 ++-
|  2 files changed, 573 insertions(+), 552 deletions(-)

* 2019-05-10(Tal Galili) find_k - now imports pamk into dendextend so to remove the depndancy on fpc |07581dd| 
|  DESCRIPTION |  9 +++++----
|  NAMESPACE   |  1 -
|  NEWS        |  5 +++++
|  R/find_k.R  | 49 ++++++++++++++++++++++++++++++++++++++++++++-----
|  4 files changed, 54 insertions(+), 10 deletions(-)

* 2019-03-18(Tal Galili) use labels, and fix sementic versioning to reflect recent fix. |68e008f| 
|  DESCRIPTION                    | 2 +-
|  NEWS                           | 9 ++-------
|  tests/testthat/test-unbranch.R | 3 +--
|  3 files changed, 4 insertions(+), 10 deletions(-)

*   2019-03-18(Tal Galili) Merge pull request #87 from samperochkin/unbranch-keep-original-ordering |f52ef1d
|\  
| * 2019-03-17(Samuel Perreault) Typo** |0ff2c5c| | 
| |  NEWS | 4 ++--
| |  1 file changed, 2 insertions(+), 2 deletions(-)

| *   2019-03-17(Samuel Perreault) Merge pull request #1 from samperochkin/patch-1 |70a87c6
| |\  
| | * 2019-03-17(Samuel Perreault) Add Samuel Perreault (myself) contributor. |b1384d7
| |/  
|/|   | |   
| |    DESCRIPTION | 7 ++++---
| |    1 file changed, 4 insertions(+), 3 deletions(-)

| *   2019-03-17(Samuel Perreault) Merge pull request #2 from samperochkin/patch-2 |ab09572
| |\  
| | * 2019-03-17(Samuel Perreault) bug fix unbranch -- order of leaves now unchanged |3b012f8
| |/  
|/|   | |   
| |    NEWS | 12 ++++++++++++
| |    1 file changed, 12 insertions(+)

* | 2019-03-15(Tal Galili) Added RNGversion("3.5.0") to tests so as to comply with the new R RNG change that is coming up in R 3.6.0. |f331c51| | 
| |  DESCRIPTION                            |  4 ++--
| |  NEWS                                   | 10 ++++------
| |  tests/testthat/test-bk_method.R        |  1 +
| |  tests/testthat/test-cor_bakers_gamma.R |  1 +
| |  tests/testthat/test-cor_cophenetic.R   |  1 +
| |  tests/testthat/test-pvclust_extract.R  |  1 +
| |  tests/testthat/test-set.dendrogram.R   |  1 +
| |  tests/testthat/test-untangle.R         |  2 +-
| |  8 files changed, 12 insertions(+), 9 deletions(-)

* | 2019-03-15(Tal Galili) reogranize roxygen2 code order |d853fa9| | 
| |  R/pvclust.R          | 12 ++++++------
| |  man/pvclust_edges.Rd |  3 ++-
| |  2 files changed, 8 insertions(+), 7 deletions(-)

* |   2019-03-15(Tal Galili) Merge pull request #91 from SplitInf/master |b72d5b0
|\ \  
| * | 2019-03-14(C2H4) updated test-pvclust_extract.R (refer to Issues #83) |805af67| | | 
| | |  tests/testthat/test-pvclust_extract.R | 2 +-
| | |  1 file changed, 1 insertion(+), 1 deletion(-)

| * | 2019-03-14(C2H4) updated test-pvclust_extract.R (refer to Issues #83) |668c862| | | 
| | |  tests/testthat/test-pvclust_extract.R | 1 +
| | |  1 file changed, 1 insertion(+)

| * | 2019-03-13(C2H4) updated pvclust_edges.Rd (refer to Issues #83) |4778a43| | | 
| | |  man/pvclust_edges.Rd | 9 ++++++++-
| | |  1 file changed, 8 insertions(+), 1 deletion(-)

| * | 2019-03-13(C2H4) updated pvclust.R (refer to Issues #83) |d6af29e| | | 
| | |  R/pvclust.R | 10 +++++++++-
| | |  1 file changed, 9 insertions(+), 1 deletion(-)

| * | 2019-03-13(C2H4) updated pvclust.R (refer to Issues #83) |5f366fb| | | 
| | |  R/pvclust.R | 2 +-
| | |  1 file changed, 1 insertion(+), 1 deletion(-)

| * | 2019-03-13(C2H4) updated test case (refer to Issues #83) |ef372af| | | 
| | |  tests/testthat/test-pvclust_extract.R | 8 ++++----
| | |  1 file changed, 4 insertions(+), 4 deletions(-)

| * | 2019-03-13(C2H4) updated DESCRIPTION (refer to Issues #83) |9ce51dc| | | 
| | |  DESCRIPTION | 4 ++--
| | |  1 file changed, 2 insertions(+), 2 deletions(-)

| * | 2019-03-13(C2H4) updated DESCRIPTION, NEWS and test case (refer to Issues #83) |71f766f| | | 
| | |  DESCRIPTION                           |   3 +-
| | |  NAMESPACE                             |   1 +
| | |  NEWS                                  |  10 +-
| | |  R/pvclust.R                           |   4 +-
| | |  man/pvclust_edges.Rd                  |  24 ++
| | |  man/tanglegram.Rd                     | 570 ++++++++++++++--------------
| | |  tests/testthat/test-pvclust_extract.R |   2 +-
| | |  7 files changed, 324 insertions(+), 290 deletions(-)

| * | 2019-03-12(C2H4) added testcases and refactored codebase |c90b1f2| | | 
| | |  R/pvclust.R                           | 19 +++++++++++++++++++
| | |  R/pvclust_extract.R                   | 11 -----------
| | |  tests/testthat/test-pvclust_extract.R | 12 ++++++++++++
| | |  3 files changed, 31 insertions(+), 11 deletions(-)

| * | 2019-03-12(C2H4) added function that extract au/bp info (refer to Issues #83) |9672790
|/ /  | |   
| |    R/pvclust_extract.R | 11 +++++++++++
| |    1 file changed, 11 insertions(+)

* | 2019-02-08(Tal Galili) cutree.default now works with any object that has an as.dendrogram method by default. (including agnes and diana). Fix #90 |f28e912| | 
| |  DESCRIPTION           |  4 ++--
| |  NAMESPACE             |  2 ++
| |  NEWS                  |  7 +++++++
| |  R/cutree.dendrogram.R | 19 ++++++++++++++++++-
| |  man/cutree-methods.Rd |  9 +++++++++
| |  5 files changed, 38 insertions(+), 3 deletions(-)

| * 2019-03-16(samperochkin) remove unlist from unbranch -- will file a seperate issue |9bbfcf3| | 
| |  R/unbranch.R | 2 +-
| |  1 file changed, 1 insertion(+), 1 deletion(-)

| * 2019-03-16(samperochkin) added a test checking whether the order of leaves is preserved (for function unbranch) |825e735| | 
| |  tests/testthat/test-unbranch.R | 3 +++
| |  1 file changed, 3 insertions(+)

| * 2019-03-16(samperochkin) solved midpoint problem with unlist. When all root nodes are leafs, get_root_branches_attr(new_dend, 'midpoint') returns a list... |fe39676| | 
| |  R/unbranch.R | 9 ++-------
| |  1 file changed, 2 insertions(+), 7 deletions(-)

| * 2018-10-27(samperochkin) problems plotting the dend after an application of unbranch -- midpoint sometimes is NA |51beb55| | 
| |  R/unbranch.R | 8 +++++++-
| |  1 file changed, 7 insertions(+), 1 deletion(-)

| * 2018-10-27(samperochkin) silly mistake... |90cf152| | 
| |  R/unbranch.R | 4 ++--
| |  1 file changed, 2 insertions(+), 2 deletions(-)

| * 2018-10-26(samperochkin) correct mistake |0988f42| | 
| |  R/unbranch.R | 2 +-
| |  1 file changed, 1 insertion(+), 1 deletion(-)

| * 2018-10-26(samperochkin) removed (now) useless stuff |7068a5c| | 
| |  R/unbranch.R | 3 +--
| |  1 file changed, 1 insertion(+), 2 deletions(-)

| * 2018-10-26(samperochkin) if branch_becoming_root is K, then the new roots are positionned at K, K+1, ... K+length(dend[[branch_becoming_root]])-1 |f750beb
|/  |   
|    R/unbranch.R | 13 +++++++------
|    1 file changed, 7 insertions(+), 6 deletions(-)

* 2018-10-19(Tal Galili) Objects equal but not identical |f60bb18| 
|  tests/testthat/test-highlight_branches.R | 3 ++-
|  1 file changed, 2 insertions(+), 1 deletion(-)

* 2018-10-19(Tal Galili) Add minimal test for highlight_branches |17ad842| 
|  tests/testthat/test-highlight_branches.R | 29 +++++++++++++++++++++++++++++
|  1 file changed, 29 insertions(+)

* 2018-10-19(Tal Galili) fix highlight_branches_lwd and highlight_branches_col |e593ef1| 
|  R/highlight_branches.R | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2018-10-19(Tal Galili) Removed some old deprecated code relating to dendextendRcpp. |e3856fd| 
|  DESCRIPTION                             |  2 +-
|  NAMESPACE                               |  4 ----
|  NEWS                                    |  3 ++-
|  R/ape.R                                 | 18 +++++++-------
|  R/attr_access.R                         | 23 +-----------------
|  R/cut_lower_fun.R                       | 12 ----------
|  R/cutree.dendrogram.R                   |  9 -------
|  R/dendextend_options.R                  |  8 +++----
|  R/stats_imports.R                       | 29 ----------------------
|  man/as.phylo.dendrogram.Rd              |  5 ++++
|  man/dendextend_labels.dendrogram.Rd     | 29 ----------------------
|  man/get_branches_heights.Rd             | 12 ----------
|  tests/testthat/test-attr_access.R       |  4 ++--
|  tests/testthat/test-cut_lower_fun.R     | 40 +------------------------------
|  tests/testthat/test-cutree.dendrogram.R |  6 ++---
|  15 files changed, 29 insertions(+), 175 deletions(-)

* 2018-10-19(Tal Galili) Fix the new test result: "S3 method lookup found 'as.phylo.dendrogram' on search path" |c7d28c7| 
|  DESCRIPTION |  2 +-
|  NAMESPACE   |  6 +++++-
|  NEWS        |  4 +++-
|  R/ape.R     | 13 ++++++++++---
|  4 files changed, 19 insertions(+), 6 deletions(-)

* 2018-10-06(Tal Galili) update NEWS and DESCRIPTION due to the recent code merges. |9299df3| 
|  DESCRIPTION | 7 ++++++-
|  NEWS        | 9 ++++++++-
|  2 files changed, 14 insertions(+), 2 deletions(-)

*   2018-10-06(Tal Galili) Merge pull request #80 from jdetribol/patch-1 |43ded96
|\  
| * 2018-08-08(jdetribol) Update distinct_edges.R |ad3bb48| | 
| |  R/distinct_edges.R | 4 ++--
| |  1 file changed, 2 insertions(+), 2 deletions(-)

* | 2018-10-05(Lucas Gray) Modification of non-binary pruning and adding many tests for non-binary dendrograms |555bbe6| | 
| |  R/prune.R                  |  64 ++++++++++---------
| |  tests/testthat/test-trim.R | 136 ++++++++++++++++++++++++++++++++++++++++-
| |  2 files changed, 168 insertions(+), 32 deletions(-)

* | 2018-04-23(Lucas Graybuck) Changed prune_leaf() to prune non-binary trees |61f4e68
|/  |   
|    R/prune.R | 29 ++++++++++++++++++++---------
|    1 file changed, 20 insertions(+), 9 deletions(-)

* 2018-07-21(Tal Galili) Improve the doc |46ca013| 
|  DESCRIPTION        | 4 ++--
|  NEWS               | 7 +++++++
|  R/set.dendrogram.R | 6 +++---
|  man/set.Rd         | 6 +++---
|  4 files changed, 15 insertions(+), 8 deletions(-)

* 2018-05-02(Tal Galili) release candidate 0.18.0 |c0885f6| 
|  ChangeLog   | 81 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  DESCRIPTION |  2 +-
|  NEWS        | 12 ++-------
|  NEWS.md     | 12 ++++++++-
|  4 files changed, 95 insertions(+), 12 deletions(-)

* 2018-04-28(Tal Galili) update docs |4cb6652| 
|  NAMESPACE           |   1 +
|  man/colored_dots.Rd | 192 ++++++++++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 193 insertions(+)

* 2018-04-28(Tal Galili) temp rename 2 |2be950c| 
|  R/{colored_dots111.R => colored_dots.R} | 0
|  1 file changed, 0 insertions(+), 0 deletions(-)

* 2018-04-28(Tal Galili) temp rename |d8b1ce7| 
|  R/colored_dots.R                        | 441 ------------------------------
|  R/{colored_Dots.R => colored_dots111.R} |   0
|  2 files changed, 441 deletions(-)

* 2018-04-28(Tal Galili) stlyr the colored_dots file/functions |3f9da97| 
|  NEWS             |   9 +
|  R/colored_Dots.R | 493 ++++++++++++++++++++++++++---------------------------
|  R/colored_dots.R | 493 ++++++++++++++++++++++++++---------------------------
|  3 files changed, 485 insertions(+), 510 deletions(-)

* 2018-04-28(Tal Galili) rename color_dots file to be lower case |c1351e3| 
|  R/colored_dots.R | 458 +++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 458 insertions(+)

* 2018-04-28(Tal Galili) Added Chase Clark as a contributor |949cebf| 
|  DESCRIPTION | 10 +++++++---
|  1 file changed, 7 insertions(+), 3 deletions(-)

* 2018-03-03(Chase Clark) Added Roxygen, added examples similar to "colored_bars" |9cb4b46| 
|  R/colored_Dots.R | 504 ++++++++++++++++++++++++++++++++++++++++-------------
|  1 file changed, 385 insertions(+), 119 deletions(-)

* 2018-01-15(Chase Clark) Add two comments |cbd2e2d| 
|  R/colored_Dots.R | 8 +++++---
|  1 file changed, 5 insertions(+), 3 deletions(-)

* 2018-01-01(Chase Clark) Create colored_Dots.R |501fa8b| 
|  R/colored_Dots.R | 190 +++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 190 insertions(+)

* 2018-03-16(Tal Galili) Update version and added Manuela Hummel as author of: branches_attr_by_lists - Change col/lwd/lty of branches from the root down to clusters defined by list of labels of respective members |26f20b6| 
|  DESCRIPTION | 8 +++++---
|  NEWS        | 9 +++++++++
|  2 files changed, 14 insertions(+), 3 deletions(-)

* 2018-03-14(Hummel) added test unit for branches_attr_by_labels |6cf0d62| 
|  tests/testthat/test-branches_attr_by.R | 32 ++++++++++++++++++++++++++++++++
|  1 file changed, 32 insertions(+)

* 2018-02-28(Hummel) added documentation for branches_attr_by_lists |1950401| 
|  man/branches_attr_by_lists.Rd | 59 +++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 59 insertions(+)

* 2018-02-28(Hummel) added documentation for branches_attr_by_lists |e02f1ef| 
|  man/set.Rd | 21 +++++++++++++++++----
|  1 file changed, 17 insertions(+), 4 deletions(-)

* 2018-02-28(Hummel) added function branches_attr_by_lists |11a232f| 
|  NAMESPACE            |  1 +
|  R/branches_attr_by.R | 75 ++++++++++++++++++++++++++++++++++++++++++++++++++
|  R/set.dendrogram.R   | 24 ++++++++++++++--
|  3 files changed, 97 insertions(+), 3 deletions(-)

* 2018-02-10(Tal Galili) remove labeltodendro. |49dde87| 
|  DESCRIPTION | 2 +-
|  NEWS        | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2018-02-10(Tal Galili) Fix: Rd line widths ... NOTE |54b9889| 
|  R/get_subdendrograms.R    | 6 ++++--
|  man/find_dendrogram.Rd    | 3 ++-
|  man/get_subdendrograms.Rd | 3 ++-
|  3 files changed, 8 insertions(+), 4 deletions(-)

* 2018-02-10(Tal Galili) update NEWS.md |c13a2c6| 
|  ChangeLog | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++++
|  NEWS.md   | 16 ++++++++++++++++
|  2 files changed, 69 insertions(+)

* 2018-02-10(Tal Galili) Remove NMF from suggested |846f881| 
|  DESCRIPTION                |  3 +--
|  NEWS                       |  7 +++++--
|  vignettes/introduction.Rmd | 34 ++++++++++++++++++++--------------
|  3 files changed, 26 insertions(+), 18 deletions(-)

* 2018-01-19(Tal Galili) add docs and fix #61 |1d12d13| 
|  NAMESPACE                 |  2 ++
|  man/find_dendrogram.Rd    | 39 ++++++++++++++++++++++++++++++
|  man/get_subdendrograms.Rd | 59 +++++++++++++++++++++++++++++++++++++++++++++
|  man/seriate_dendrogram.Rd |  4 +--
|  4 files changed, 102 insertions(+), 2 deletions(-)

* 2018-01-19(Tal Galili) Updated NEWS and added storaged as a contributor |dccff9b| 
|  DESCRIPTION | 10 ++++++----
|  NEWS        | 13 +++++++++++++
|  2 files changed, 19 insertions(+), 4 deletions(-)

* 2018-01-19(Tal Galili) update get_dendrograms example to demonstrate how to plot it in a heatmap.2 |f9c576e| 
|  R/get_subdendrograms.R | 24 ++++++++++++++++++++++--
|  1 file changed, 22 insertions(+), 2 deletions(-)

* 2018-01-19(Tal Galili) styler the functions |e02364d| 
|  R/get_subdendrograms.R | 52 ++++++++++++++++++++++++------------------------
|  1 file changed, 26 insertions(+), 26 deletions(-)

* 2018-01-19(Tal Galili) move to using _ instead of . |cb1f7bb| 
|  R/get_subdendrograms.R | 34 +++++++++++++++-------------------
|  1 file changed, 15 insertions(+), 19 deletions(-)

* 2018-01-11(storaged) Functions that help to extract subdendrogram structures based on given number of expected stuctures |14130e4| 
|  R/get_subdendrograms.R | 77 ++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 77 insertions(+)

*   2017-12-19(Tal Galili) Merge pull request #58 from Alanocallaghan/master |7d11920
|\  
| * 2017-12-19(Alan O'Callaghan) Bugfix seriate_dendrogram |e77e2be
|/  |   
|    R/seriate_dendrogram.R | 32 ++++++++++++++++----------------
|    1 file changed, 16 insertions(+), 16 deletions(-)

* 2017-12-10(Tal Galili) Adding some #' par(mfrow = c(1,2)) |f5ad443| 
|  R/color_branches.R    | 7 ++++++-
|  man/color_branches.Rd | 7 ++++++-
|  2 files changed, 12 insertions(+), 2 deletions(-)

* 2017-11-13(Tal Galili) Bump version to 0.16.0 |879d98c| 
|  ChangeLog   | 275 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  DESCRIPTION |   2 +-
|  NEWS        |   2 +-
|  NEWS.md     | 198 ++++++++++++++++++++++++------------------
|  4 files changed, 390 insertions(+), 87 deletions(-)

* 2017-11-13(Tal Galili) fix long url: |3e9f0d6| 
|  R/color_branches.R    | 2 +-
|  man/color_branches.Rd | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2017-11-13(Tal Galili) Fix: (invalid URL) |e0386e1| 
|  vignettes/introduction.Rmd | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2017-11-13(Tal Galili) how to cite |eeb1c1e| 
|  README.md | 23 +++++++++++++++++++++++
|  1 file changed, 23 insertions(+)

* 2017-10-26(Tal Galili) typo |c806acf| 
|  inst/CITATION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2017-09-27(Tal Galili) Another example for color_branches |99bfa39| 
|  R/color_branches.R    | 34 ++++++++++++++++++++++++++++++++++
|  man/color_branches.Rd | 21 +++++++++++++++++++++
|  2 files changed, 55 insertions(+)

* 2017-09-27(Tal Galili) circlize_dendrogram - can now handle dendrograms with non unique labels. A warning is issued, and a running number is padded to the labels. |44d1ca9| 
|  DESCRIPTION  | 2 +-
|  NEWS         | 3 ++-
|  R/circlize.R | 8 ++++++++
|  3 files changed, 11 insertions(+), 2 deletions(-)

* 2017-06-10(Tal Galili) update date |2a303ef| 
|  DESCRIPTION | 2 +-
|  NEWS        | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2017-06-10(Tal Galili) Added min_depth, max_depth - measures the min/max depth of a tree (from the root to the closest/furtherest leaf). |d88249c| 
|  NAMESPACE    |  2 ++
|  NEWS         |  1 +
|  R/depth.R    | 60 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/depth.Rd | 34 +++++++++++++++++++++++++++++++++
|  4 files changed, 97 insertions(+)

* 2017-05-31(Tal Galili) Updating pvrect2 example |33efee8| 
|  R/pvclust.R    | 4 ++--
|  man/pvrect2.Rd | 4 ++--
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2017-05-29(Tal Galili) Fix rect.dendrogram - it now deals much better with setting the lower part of the rectangle to be below the labels. |a756d9a| 
|  NEWS                |  2 ++
|  R/rect.dendrogram.R | 21 +++++++++++++++++++--
|  2 files changed, 21 insertions(+), 2 deletions(-)

* 2017-05-29(Tal Galili) pvrect2 function added - Draw Rectangles Around a Dendrogram's Clusters with High/Low P-values |56f9e92| 
|  DESCRIPTION    |   4 +-
|  NAMESPACE      |   1 +
|  NEWS           | 187 +++++++++++++++++++++++++++++--------------------------
|  R/pvclust.R    | 114 +++++++++++++++++++++++++++++++--
|  man/pvrect2.Rd |  61 ++++++++++++++++++
|  5 files changed, 271 insertions(+), 96 deletions(-)

* 2017-05-28(Tal Galili) Update bioinformatics link |82a3df7| 
|  DESCRIPTION   | 6 +++---
|  inst/CITATION | 4 ++--
|  2 files changed, 5 insertions(+), 5 deletions(-)

* 2017-05-19(Tal Galili) Fix #38 by using alternative default for prune (i.e.: reindex_dend=TRUE). Also added examples in the doc to demonstrate its use. |8b948b6| 
|  R/prune.R           | 28 ++++++++++++++++++++--------
|  man/prune.Rd        | 19 +++++++++++++++----
|  man/reindex_dend.Rd |  2 +-
|  3 files changed, 36 insertions(+), 13 deletions(-)

* 2017-05-19(Tal Galili) * refactor reindex_dend to use order.dendrogram * Simpler consolidation of the prune documentation. * added reindex_dend parameter to allow the leaves of a pruned dendrogram to be of the vector of 1:nleaves |f5f09f7| 
|  NAMESPACE                                  |  2 +-
|  NEWS                                       |  2 +-
|  R/prune.R                                  | 72 +++++++++++-----------------
|  man/prune.Rd                               | 10 +++-
|  man/{reindex_dendro.Rd => reindex_dend.Rd} | 16 ++++---
|  5 files changed, 48 insertions(+), 54 deletions(-)

* 2017-05-19(Tal Galili) Added John Ma as contributor |10d732d| 
|  DESCRIPTION | 7 ++++---
|  NEWS        | 6 +++++-
|  2 files changed, 9 insertions(+), 4 deletions(-)

* 2017-05-19(Tal Galili) Added reindex_dendro doc |9cc6ca6| 
|  NAMESPACE             |  1 +
|  man/reindex_dendro.Rd | 43 +++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 44 insertions(+)

*   2017-05-19(Tal Galili) Merge pull request #39 from JohnMCMa/master |b02dcca
|\  
| * 2017-03-30(John Ma) Adding function reindex_dendro to resolve problems with as.hclust |1e25e5b| | 
| |  R/prune.R | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++++++--
| |  1 file changed, 54 insertions(+), 2 deletions(-)

* | 2017-05-17(Tal Galili) Fix print.ggdend |c3c0a00| | 
| |  R/ggdend.R | 2 +-
| |  1 file changed, 1 insertion(+), 1 deletion(-)

* | 2017-05-17(Tal Galili) refresh .Rd files. |8b0df89| | 
| |  man/Bk.Rd                                  |  1 -
| |  man/Bk_permutations.Rd                     |  1 -
| |  man/Bk_plot.Rd                             |  1 -
| |  man/DendSer.dendrogram.Rd                  |  1 -
| |  man/FM_index.Rd                            |  1 -
| |  man/FM_index_R.Rd                          |  1 -
| |  man/FM_index_permutation.Rd                |  1 -
| |  man/FM_index_profdpm.Rd                    |  1 -
| |  man/all.equal.dendrogram.Rd                |  3 +--
| |  man/all_couple_rotations_at_k.Rd           |  1 -
| |  man/all_unique.Rd                          |  1 -
| |  man/as.dendlist.Rd                         |  1 -
| |  man/as.phylo.dendrogram.Rd                 |  1 -
| |  man/as_hclust_fixed.Rd                     |  1 -
| |  man/assign_dendextend_options.Rd           |  1 -
| |  man/assign_values_to_branches_edgePar.Rd   |  1 -
| |  man/assign_values_to_leaves_edgePar.Rd     |  1 -
| |  man/assign_values_to_leaves_nodePar.Rd     |  1 -
| |  man/assign_values_to_nodes_nodePar.Rd      |  1 -
| |  man/bakers_gamma_for_2_k_matrix.Rd         |  1 -
| |  man/branches_attr_by_clusters.Rd           |  1 -
| |  man/branches_attr_by_labels.Rd             |  1 -
| |  man/circlize_dendrogram.Rd                 |  7 +++----
| |  man/click_rotate.Rd                        |  7 +++----
| |  man/collapse_branch.Rd                     |  1 -
| |  man/color_branches.Rd                      |  9 ++++-----
| |  man/color_labels.Rd                        |  1 -
| |  man/color_unique_labels.Rd                 |  1 -
| |  man/colored_bars.Rd                        |  9 ++++-----
| |  man/common_subtrees_clusters.Rd            |  1 -
| |  man/cor.dendlist.Rd                        |  1 -
| |  man/cor_FM_index.Rd                        |  1 -
| |  man/cor_common_nodes.Rd                    |  1 -
| |  man/cor_cophenetic.Rd                      |  1 -
| |  man/count_terminal_nodes.Rd                |  1 -
| |  man/cut_lower_fun.Rd                       |  7 +++----
| |  man/cutree_1h.dendrogram.Rd                |  7 +++----
| |  man/cutree_1k.dendrogram.Rd                |  7 +++----
| |  man/dend_diff.Rd                           |  3 +--
| |  man/dendextend-package.Rd                  |  3 +--
| |  man/dendextend_labels.dendrogram.Rd        |  1 -
| |  man/dendextend_options.Rd                  |  1 -
| |  man/dendlist.Rd                            |  1 -
| |  man/dist.dendlist.Rd                       |  1 -
| |  man/dist_long.Rd                           |  1 -
| |  man/distinct_edges.Rd                      |  1 -
| |  man/duplicate_leaf.Rd                      |  1 -
| |  man/entanglement.Rd                        |  5 ++---
| |  man/fac2num.Rd                             |  1 -
| |  man/find_dend.Rd                           |  1 -
| |  man/find_k.Rd                              |  1 -
| |  man/fix_members_attr.dendrogram.Rd         |  1 -
| |  man/flatten.dendrogram.Rd                  |  1 -
| |  man/flip_leaves.Rd                         |  1 -
| |  man/get_branches_heights.Rd                |  3 +--
| |  man/get_childrens_heights.Rd               |  1 -
| |  man/get_leaves_attr.Rd                     |  1 -
| |  man/get_leaves_branches_attr.Rd            |  1 -
| |  man/get_leaves_branches_col.Rd             |  1 -
| |  man/get_leaves_edgePar.Rd                  |  1 -
| |  man/get_leaves_nodePar.Rd                  |  1 -
| |  man/get_nodes_attr.Rd                      |  1 -
| |  man/get_nodes_xy.Rd                        |  1 -
| |  man/get_root_branches_attr.Rd              |  1 -
| |  man/hang.dendrogram.Rd                     |  1 -
| |  man/has_component_in_attribute.Rd          |  1 -
| |  man/heights_per_k.dendrogram.Rd            |  3 +--
| |  man/highlight_branches.Rd                  |  3 +--
| |  man/highlight_distinct_edges.Rd            |  3 +--
| |  man/identify.dendrogram.Rd                 |  1 -
| |  man/intersect_trees.Rd                     |  1 -
| |  man/is.natural.number.Rd                   |  7 +++----
| |  man/is_null_list.Rd                        |  1 -
| |  man/is_some_class.Rd                       |  9 ++++-----
| |  man/khan.Rd                                |  1 -
| |  man/labels-assign.Rd                       | 11 +++++------
| |  man/labels_cex.Rd                          |  1 -
| |  man/labels_colors.Rd                       |  3 +--
| |  man/ladderize.Rd                           |  3 +--
| |  man/leaf_Colors.Rd                         |  7 +++----
| |  man/lowest_common_branch.Rd                |  1 -
| |  man/match_order_by_labels.Rd               |  1 -
| |  man/match_order_dendrogram_by_old_order.Rd |  1 -
| |  man/na_locf.Rd                             |  1 -
| |  man/nleaves.Rd                             |  3 +--
| |  man/nnodes.Rd                              |  1 -
| |  man/noded_with_condition.Rd                |  1 -
| |  man/order.dendrogram-assign.Rd             |  1 -
| |  man/order.hclust.Rd                        |  1 -
| |  man/partition_leaves.Rd                    |  1 -
| |  man/plot_horiz.dendrogram.Rd               |  1 -
| |  man/prune.Rd                               |  1 -
| |  man/prune_common_subtrees.dendlist.Rd      |  1 -
| |  man/prune_leaf.Rd                          |  1 -
| |  man/pvclust_show_signif.Rd                 |  1 -
| |  man/pvclust_show_signif_gradient.Rd        |  1 -
| |  man/raise.dendrogram.Rd                    |  1 -
| |  man/rank_branches.Rd                       |  1 -
| |  man/rank_order.dendrogram.Rd               |  1 -
| |  man/rank_values_with_clusters.Rd           |  1 -
| |  man/rect.dendrogram.Rd                     |  1 -
| |  man/reexports.Rd                           |  4 ++--
| |  man/remove_branches_edgePar.Rd             |  1 -
| |  man/remove_leaves_nodePar.Rd               |  1 -
| |  man/remove_nodes_nodePar.Rd                |  1 -
| |  man/rllply.Rd                              |  1 -
| |  man/rotate.Rd                              |  5 ++---
| |  man/rotate_DendSer.Rd                      |  1 -
| |  man/sample.dendrogram.Rd                   |  1 -
| |  man/seriate_dendrogram.Rd                  |  1 -
| |  man/set.Rd                                 |  5 ++---
| |  man/set_labels.Rd                          |  9 ++++-----
| |  man/shuffle.Rd                             |  3 +--
| |  man/sort_2_clusters_vectors.Rd             |  1 -
| |  man/sort_dist_mat.Rd                       |  1 -
| |  man/sort_levels_values.Rd                  |  1 -
| |  man/tanglegram.Rd                          | 13 ++++++-------
| |  man/theme_dendro.Rd                        |  7 +++----
| |  man/unbranch.Rd                            |  1 -
| |  man/unclass_dend.Rd                        |  1 -
| |  man/untangle.Rd                            | 11 +++++------
| |  man/untangle_DendSer.Rd                    |  1 -
| |  man/untangle_random_search.Rd              |  1 -
| |  man/untangle_step_rotate_1side.Rd          |  1 -
| |  man/untangle_step_rotate_2side.Rd          |  1 -
| |  man/which_leaf.Rd                          |  1 -
| |  man/which_node.Rd                          |  1 -
| |  127 files changed, 75 insertions(+), 201 deletions(-)

* | 2017-05-17(Tal Galili) Add print.ggdend - a wrapper for ggplot2::ggplot of a ggdend object. |95ae952| | 
| |  DESCRIPTION             |  2 +-
| |  NAMESPACE               |  1 +
| |  NEWS                    |  3 +++
| |  R/ggdend.R              |  8 +++++++-
| |  man/cor_bakers_gamma.Rd |  6 ++++--
| |  man/cutree-methods.Rd   | 11 +++++------
| |  man/ggdend.Rd           | 18 ++++++++++--------
| |  7 files changed, 31 insertions(+), 18 deletions(-)

* | 2017-05-04(Tal Galili) Mention that dendextendRcpp is no longer supported. |f3e28e6
|/  |   
|    README.md | 8 ++++----
|    1 file changed, 4 insertions(+), 4 deletions(-)

* 2017-03-27(Tal Galili) remove dendextendRcpp further |af9921e| 
|  DESCRIPTION                |  4 ++--
|  NEWS                       |  3 ++-
|  vignettes/introduction.Rmd | 12 +++++++-----
|  3 files changed, 11 insertions(+), 8 deletions(-)

* 2017-03-27(Tal Galili) Rollback viridisLite to viridis (to check if this is what's breaking everything) |abe5348| 
|  DESCRIPTION | 2 +-
|  NAMESPACE   | 2 +-
|  R/zzz.R     | 2 +-
|  3 files changed, 3 insertions(+), 3 deletions(-)

* 2017-03-27(Tal Galili) Fix viridis to viridisLite in NAMESPACE |7ae8a29| 
|  NAMESPACE | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2017-03-27(Tal Galili) viridis to viridisLite |d183226| 
|  DESCRIPTION | 6 +++---
|  R/zzz.R     | 2 +-
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2017-03-27(Tal Galili) Remove dendextendRcpp :(  (from tests and suggests) |986bce1| 
|  DESCRIPTION      | 1 -
|  NEWS             | 5 +++++
|  tests/test-all.R | 4 ++--
|  3 files changed, 7 insertions(+), 3 deletions(-)

* 2017-03-24(Tal Galili) update NEWS |ba11350| 
|  ChangeLog | 131 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++--
|  NEWS.md   |  16 +++++++-
|  2 files changed, 142 insertions(+), 5 deletions(-)

* 2017-03-24(Tal Galili) 1.5.0 |d574b43| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 9 ++-------
|  2 files changed, 4 insertions(+), 9 deletions(-)

* 2017-03-24(Tal Galili) # this is behaving different for R 3.3.3 and 3.4 - I'm not sure why... (removing the test for now) |57042f7| 
|  tests/testthat/test-untangle.R | 23 ++++++++++++++++-------
|  1 file changed, 16 insertions(+), 7 deletions(-)

* 2017-03-19(Tal Galili) description not details! |6c7a8b0| 
|  R/find_dend.R    | 2 +-
|  man/find_dend.Rd | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2017-03-19(Tal Galili) Get cor_cophenetic to work with hclust again |3ee25a1| 
|  R/cor_cophenetic.R | 8 ++++----
|  1 file changed, 4 insertions(+), 4 deletions(-)

* 2017-03-19(Tal Galili) dend_expend and find_dend - functions for finding a "good" dendrogram for a dist |350de5d| 
|  NAMESPACE        |   2 +
|  NEWS             |   5 +++
|  R/find_dend.R    | 111 +++++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/find_dend.Rd |  58 ++++++++++++++++++++++++++++
|  4 files changed, 176 insertions(+)

* 2017-03-19(Tal Galili) cor_cophenetic - dend2 can now also be a dist object (allowing to check how close is some clustering to the original distance matrix). |76a479c| 
|  DESCRIPTION           |  4 ++--
|  NEWS                  |  4 ++++
|  R/cor_cophenetic.R    | 12 ++++++++++--
|  man/cor_cophenetic.Rd |  2 +-
|  4 files changed, 17 insertions(+), 5 deletions(-)

* 2017-02-15(Tal Galili) Fix "Undocumented arguments in documentation object 'find_k' ‘x’" |496294c| 
|  R/find_k.R    | 1 +
|  man/find_k.Rd | 2 ++
|  2 files changed, 3 insertions(+)

* 2017-02-15(Tal Galili) Fix "is_some_class" from being exported. |ef537ff| 
|  NAMESPACE        | 5 ++---
|  R/is.functions.R | 1 -
|  2 files changed, 2 insertions(+), 4 deletions(-)

* 2017-02-15(Tal Galili) document new ggplot S3 methods. |348d8ab| 
|  man/ggdend.Rd | 7 ++++---
|  1 file changed, 4 insertions(+), 3 deletions(-)

* 2017-02-15(Tal Galili) Simplified the roxygen2 code by using @rdname (and removing many instances of @allias and @usage) |71c8a0d| 
|  DESCRIPTION                     |  4 +-
|  NAMESPACE                       | 12 ++++-
|  NEWS                            | 10 ++++
|  R/cor_bakers_gamma.R            | 18 +++----
|  R/cor_cophenetic.R              | 16 ++-----
|  R/cutree.dendrogram.R           | 29 ++----------
|  R/dendlist.R                    |  9 +---
|  R/distinct_edges.R              | 34 +++-----------
|  R/entanglement.R                | 25 ++--------
|  R/find_k.R                      |  5 +-
|  R/ggdend.R                      | 29 +++---------
|  R/highlight_branches.R          | 13 ++----
|  R/is.functions.R                | 54 +++++++++------------
|  R/labels.R                      | 38 ++-------------
|  R/labels_colors.R               | 22 +++------
|  R/nleaves.R                     | 53 ++++++---------------
|  R/rotate.R                      | 68 +++++++--------------------
|  R/set.dendrogram.R              | 47 ++-----------------
|  R/tanglegram.R                  | 69 ++++-----------------------
|  R/unbranch.R                    | 20 ++------
|  R/untangle.R                    | 51 ++++++--------------
|  man/click_rotate.Rd             |  5 +-
|  man/cor_bakers_gamma.Rd         | 14 ++++--
|  man/cor_cophenetic.Rd           | 18 +++----
|  man/cutree-methods.Rd           | 37 +++++++--------
|  man/dend_diff.Rd                |  9 ++--
|  man/entanglement.Rd             | 12 ++---
|  man/find_k.Rd                   |  7 +++
|  man/ggdend.Rd                   | 20 ++++----
|  man/highlight_branches.Rd       | 18 +++----
|  man/highlight_distinct_edges.Rd | 13 ++----
|  man/is.dendlist.Rd              | 24 ----------
|  man/is.dendrogram.Rd            | 18 -------
|  man/is.dist.Rd                  | 24 ----------
|  man/is.hclust.Rd                | 18 -------
|  man/is.phylo.Rd                 | 18 -------
|  man/is_some_class.Rd            | 41 ++++++++++++++++
|  man/labels-assign.Rd            |  7 +--
|  man/labels_colors.Rd            |  4 +-
|  man/ladderize.Rd                |  4 +-
|  man/nleaves.Rd                  |  2 +
|  man/nnodes.Rd                   |  2 +
|  man/rotate.Rd                   | 13 ++++--
|  man/set.Rd                      | 38 ++++-----------
|  man/shuffle.Rd                  |  2 +
|  man/tanglegram.Rd               | 98 ++++++++++++++++++---------------------
|  man/unbranch.Rd                 |  8 +++-
|  man/untangle.Rd                 | 21 +++++----
|  48 files changed, 370 insertions(+), 751 deletions(-)

* 2017-02-14(Tal Galili) Fix dend_diff.dendrogram to return to original mfrow after finish plotting. ( fix issue #37 ) |a75223c| 
|  R/distinct_edges.R | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2017-01-22(Tal Galili) highlight_distinct_edges is now value 3 instead of 2 for tanglegram - so that the gap from lty are not too wide. |01d4a47| 
|  NEWS           | 2 +-
|  R/tanglegram.R | 4 ++--
|  2 files changed, 3 insertions(+), 3 deletions(-)

* 2017-01-21(Tal Galili) Namespace in Imports field not imported from: 'datasets' |89a52f4| 
|  NAMESPACE | 1 +
|  R/zzz.R   | 1 +
|  2 files changed, 2 insertions(+)

* 2017-01-21(Tal Galili) Fix  Undocumented arguments in documentation object 'has_component_in_attribute': 'the_attrib' |4e90cf3| 
|  R/has_edgePar.R                   | 2 ++
|  man/has_component_in_attribute.Rd | 3 +++
|  2 files changed, 5 insertions(+)

* 2017-01-21(Tal Galili) If dend is not a dendrogram, then has_edgePar will return FALSE. |25f4b4d| 
|  R/has_edgePar.R                   | 3 +++
|  man/has_component_in_attribute.Rd | 1 +
|  2 files changed, 4 insertions(+)

* 2017-01-21(Tal Galili) update dates |c612a6e| 
|  ChangeLog   | 254 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  DESCRIPTION |   2 +-
|  NEWS        |   6 +-
|  NEWS.md     |  19 +++++
|  4 files changed, 277 insertions(+), 4 deletions(-)

* 2017-01-21(Tal Galili) tanglegram function now highlights branches only if these parameters are NOT already set in the object. If the tree already has lty/lwd/col - these will not be updated by this parameter. These parameters can be removed from the tree by using `dend %>% set("clear_branches")`. |aef480e| 
|  NEWS                              |  2 +-
|  R/has_edgePar.R                   |  2 ++
|  R/tanglegram.R                    | 28 ++++++++++++++++++++++------
|  man/has_component_in_attribute.Rd |  2 ++
|  man/tanglegram.Rd                 | 18 +++++++++++++++---
|  5 files changed, 42 insertions(+), 10 deletions(-)

* 2017-01-21(Tal Galili) New functions has_edgePar, has_nodePar - Does a dendrogram has an edgePar/nodePar component? |28ec998| 
|  NAMESPACE                         |  3 +++
|  NEWS                              |  3 ++-
|  R/has_edgePar.R                   | 50 +++++++++++++++++++++++++++++++++++++
|  man/has_component_in_attribute.Rd | 43 +++++++++++++++++++++++++++++++
|  4 files changed, 98 insertions(+), 1 deletion(-)

* 2017-01-20(Tal Galili) https://cran.r-project.org/web/packages to https://CRAN.R-project.org/package= |531f990| 
|  R/bk_method.R                     | 2 +-
|  R/magrittr.R                      | 4 ++--
|  README.md                         | 2 +-
|  vignettes/Quick_Introduction.Rmd  | 2 +-
|  vignettes/dendextend-tutorial.bib | 2 +-
|  vignettes/introduction.Rmd        | 4 ++--
|  6 files changed, 8 insertions(+), 8 deletions(-)

* 2017-01-20(Tal Galili) Fix "\examples lines wider than 100 characters:" |dd84df4| 
|  R/highlight_branches.R    | 9 ++++++---
|  man/highlight_branches.Rd | 9 ++++++---
|  2 files changed, 12 insertions(+), 6 deletions(-)

* 2017-01-20(Tal Galili) http://cran.r-project to https://cran.r-project |460b3aa| 
|  R/bk_method.R                              |  4 ++--
|  R/colored_bars.R                           |  2 +-
|  R/distinct_edges.R                         |  2 +-
|  R/ggdendro.R                               |  2 +-
|  R/magrittr.R                               | 10 +++++-----
|  R/pvclust.R                                |  2 +-
|  man/colored_bars.Rd                        |  2 +-
|  vignettes/Quick_Introduction.Rmd           |  2 +-
|  vignettes/dendextend-tutorial.bib          | 18 +++++++++---------
|  vignettes/disabled/dendextend-tutorial.rnw |  2 +-
|  vignettes/introduction.Rmd                 | 14 +++++++-------
|  11 files changed, 30 insertions(+), 30 deletions(-)

* 2017-01-20(Tal Galili) "Possibly mis-spelled words in DESCRIPTION:" |b9cf5d3| 
|  DESCRIPTION | 8 ++++----
|  1 file changed, 4 insertions(+), 4 deletions(-)

* 2017-01-07(Tal Galili) Adding highlight_branches to the vignette. |e2cad21| 
|  vignettes/introduction.Rmd | 53 +++++++++++++++++++++++++++++++++++++++++++-
|  1 file changed, 52 insertions(+), 1 deletion(-)

* 2017-01-07(Tal Galili) Fix colored_bars example to work. props to Jerome Bartholome |4818699| 
|  vignettes/introduction.Rmd | 19 ++++++++++++++++++-
|  1 file changed, 18 insertions(+), 1 deletion(-)

* 2016-12-25(Tal Galili) highlight_branches - added a heatmap example. |ececc60| 
|  DESCRIPTION               |  1 +
|  R/highlight_branches.R    | 19 +++++++++++++++++++
|  man/highlight_branches.Rd | 19 +++++++++++++++++++
|  3 files changed, 39 insertions(+)

* 2016-12-24(Tal Galili) highlight_branches_col  - remove the yellow color (so that the leaves will be visible). |cae9254| 
|  R/highlight_branches.R    | 6 +++---
|  man/highlight_branches.Rd | 2 +-
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2016-12-24(Tal Galili) This fixes #33 - although it might be worth improving get_leaves_branches_col in the future. |8976a92| 
|  R/attr_access.R                |  4 ++++
|  R/tanglegram.R                 | 20 ++++++++++++++++++--
|  man/get_leaves_branches_col.Rd |  5 +++++
|  man/tanglegram.Rd              |  5 ++++-
|  4 files changed, 31 insertions(+), 3 deletions(-)

* 2016-12-24(Tal Galili) fix bug in branches_attr_by_clusters (should have values and not value) |93795d0| 
|  R/branches_attr_by.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2016-12-24(Tal Galili) using TRUE and FALSE instead of T and F. Also moved to using dendextend_get_branches_heights instead of get_branches_heights (so to be more robust). |57054dc| 
|  R/highlight_branches.R    | 14 +++++++-------
|  R/zzz.R                   |  1 +
|  man/highlight_branches.Rd |  6 +++---
|  3 files changed, 11 insertions(+), 10 deletions(-)

* 2016-12-24(Tal Galili) added viridis to the example. |eb4f21b| 
|  R/highlight_branches.R    | 1 +
|  man/highlight_branches.Rd | 1 +
|  2 files changed, 2 insertions(+)

* 2016-12-24(Tal Galili) Pass include_leaves in get_branches_heights (otherwise it will result in an error) |69461a4| 
|  R/attr_access.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2016-12-24(Tal Galili) Added example for set("highlight_branches_col") |b083f57| 
|  R/set.dendrogram.R | 6 ++++++
|  man/set.Rd         | 6 ++++++
|  2 files changed, 12 insertions(+)

* 2016-12-24(Tal Galili) Updated NEWS about the new "highlight_branches" capabilities. |9e2930c| 
|  DESCRIPTION | 2 +-
|  NEWS        | 5 ++++-
|  2 files changed, 5 insertions(+), 2 deletions(-)

* 2016-12-24(Tal Galili) tanglegram - added highlight_branches_col (FALSE) and highlight_branches_lwd (TRUE) parameters. |38346d5| 
|  R/tanglegram.R    | 22 +++++++++++++++++++---
|  man/tanglegram.Rd |  6 ++++++
|  2 files changed, 25 insertions(+), 3 deletions(-)

* 2016-12-24(Tal Galili) get_branches_heights - fix missing docs |cdfa4c7| 
|  R/attr_access.R             | 2 +-
|  man/get_branches_heights.Rd | 7 ++++---
|  2 files changed, 5 insertions(+), 4 deletions(-)

* 2016-12-24(Tal Galili) set - added highlight_branches_col and highlight_branches_lwd |21562f3| 
|  R/set.dendrogram.R | 8 ++++++++
|  man/set.Rd         | 4 ++++
|  2 files changed, 12 insertions(+)

* 2016-12-24(Tal Galili) New functions: highlight_branches, highlight_branches_col, highlight_branches_lwd - Highlight a dendrogram's branches heights via color and line-width. resolves #34 |a576a9e| 
|  NAMESPACE                 |   4 ++
|  R/highlight_branches.R    | 166 ++++++++++++++++++++++++++++++++++++++++++++
|  man/highlight_branches.Rd |  79 +++++++++++++++++++++
|  3 files changed, 249 insertions(+)

* 2016-12-24(Tal Galili) Adding viridis to imports |e095aa8| 
|  DESCRIPTION | 3 ++-
|  R/zzz.R     | 9 ++++++++-
|  2 files changed, 10 insertions(+), 2 deletions(-)

* 2016-12-24(Tal Galili) Add "include_leaves" to dendextend_get_branches_heights (required in highlight_branches) |4e07e26| 
|  R/attr_access.R             | 5 +++--
|  man/get_branches_heights.Rd | 2 ++
|  2 files changed, 5 insertions(+), 2 deletions(-)

* 2016-11-08(Tal Galili) Fix " \examples lines wider than 100 characters:" |e8cee13| 
|  R/set.dendrogram.R | 11 +++++++----
|  man/set.Rd         | 11 +++++++----
|  2 files changed, 14 insertions(+), 8 deletions(-)

* 2016-11-08(Tal Galili) fix "checking S3 generic/method consistency ... WARNING" |08b09f0| 
|  R/Hmisc.R | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2016-11-08(Tal Galili) Added as.dendrogram.varclus |87b1b5c| 
|  DESCRIPTION |  6 +++---
|  NAMESPACE   |  1 +
|  NEWS        |  5 ++++-
|  R/Hmisc.R   | 24 ++++++++++++++++++++++++
|  man/set.Rd  |  4 ++--
|  5 files changed, 34 insertions(+), 6 deletions(-)

* 2016-11-02(Tal Galili) set - added the parameter `order_value` to easily use values which are in the order of the original data. (related to issue #31 ) |8ea84b2| 
|  DESCRIPTION        |  4 ++--
|  NEWS               |  4 ++++
|  R/set.dendrogram.R | 19 +++++++++++++++++--
|  man/set.Rd         | 18 +++++++++++++++---
|  4 files changed, 38 insertions(+), 7 deletions(-)

* 2016-10-21(Tal Galili) Credit for recent pull request. |9db0f99| 
|  DESCRIPTION | 8 +++++---
|  NEWS        | 3 ++-
|  2 files changed, 7 insertions(+), 4 deletions(-)

* 2016-10-21(Tal Galili) How to cite. |ee6ceb9| 
|  R/zzz.R | 2 ++
|  1 file changed, 2 insertions(+)

* 2016-10-21(Tal Galili) Return the missing par reset from tanglegram. |1a21101| 
|  R/tanglegram.R | 10 ++++++++++
|  1 file changed, 10 insertions(+)

* 2016-10-21(Tal Galili) misc |8191070| 
|  TODO | 5 +++++
|  1 file changed, 5 insertions(+)

*   2016-10-21(Tal Galili) Merge pull request #30 from CathG/master |81796b6
|\  
| * 2016-10-19(Cath) Update tanglegram.R |69dd9b7| | 
| |  R/tanglegram.R | 8 ++++----
| |  1 file changed, 4 insertions(+), 4 deletions(-)

| * 2016-10-18(Cath) Add files via upload |407c394| | 
| |  man/tanglegram.Rd | 2 +-
| |  1 file changed, 1 insertion(+), 1 deletion(-)

| * 2016-10-18(Cath) Add files via upload |8896856| | 
| |  R/tanglegram.R | 2 +-
| |  1 file changed, 1 insertion(+), 1 deletion(-)

| * 2016-10-18(Cath) Update tanglegram.R |1432a24| | 
| |  R/tanglegram.R | 2 +-
| |  1 file changed, 1 insertion(+), 1 deletion(-)

| * 2016-10-18(Cath) Update tanglegram.R |a9639f2| | 
| |  R/tanglegram.R | 2 +-
| |  1 file changed, 1 insertion(+), 1 deletion(-)

| * 2016-10-18(Cath) Update tanglegram.R |6301067| | 
| |  R/tanglegram.R | 2 +-
| |  1 file changed, 1 insertion(+), 1 deletion(-)

| * 2016-10-18(Cath) Update tanglegram.R |2806ee9| | 
| |  R/tanglegram.R | 2 ++
| |  1 file changed, 2 insertions(+)

| * 2016-10-17(Cath) Add files via upload |8177483
| * 2016-10-17(Cath) Update tanglegram.R |41d96be| | 
| |  R/tanglegram.R | 2 +-
| |  1 file changed, 1 insertion(+), 1 deletion(-)

| * 2016-10-17(Cath) Update tanglegram.R |0107d70| | 
| |  R/tanglegram.R | 6 +++---
| |  1 file changed, 3 insertions(+), 3 deletions(-)

| * 2016-10-17(Cath) Delete tanglegram.Rd |5e932f5| | 
| |  tanglegram.Rd | 273 ------------------------------------------------------
| |  1 file changed, 273 deletions(-)

| * 2016-10-17(Cath) Add files via upload |080218e| | 
| |  man/tanglegram.Rd | 541 +++++++++++++++++++++++++-------------------------
| |  1 file changed, 273 insertions(+), 268 deletions(-)

| * 2016-10-17(Cath) Add files via upload |3bd61a7| | 
| |  tanglegram.Rd | 273 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
| |  1 file changed, 273 insertions(+)

| * 2016-10-17(Cath) Update tanglegram.R |f7fe826
|/  |   
|    R/tanglegram.R | 14 ++++++++------
|    1 file changed, 8 insertions(+), 6 deletions(-)

* 2016-10-12(Tal Galili) Add FAQ example: Plot a "mirror" (labels on the left) horizontal dendrogram |c1645ed| 
|  vignettes/FAQ.Rmd | 31 +++++++++++++++++++++++++++++++
|  1 file changed, 31 insertions(+)

* 2016-10-06(Tal Galili) find_k - now includes `k` in the output, which is a copy of `nc`. This is to make it easier to extract the value (i.e.: the suggested number of clusters). |ced7cc6| 
|  DESCRIPTION   | 4 ++--
|  NEWS          | 7 +++++++
|  R/find_k.R    | 2 ++
|  man/find_k.Rd | 1 +
|  4 files changed, 12 insertions(+), 2 deletions(-)

* 2016-08-27(Tal Galili) 1.3.0 |7a8fb04| 
|  ChangeLog | 31 +++++++++++++++++++++++++++++++
|  1 file changed, 31 insertions(+)

* 2016-08-27(Tal Galili) another http to https |cb9d1ab| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2016-08-27(Tal Galili) v1.3.0 |abb2d7f| 
|  NEWS.md | 13 +++++++++++++
|  1 file changed, 13 insertions(+)

* 2016-08-27(Tal Galili) http to https |fc6f403| 
|  DESCRIPTION       | 2 +-
|  man/set_labels.Rd | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2016-07-15(Tal Galili) Fix "labels_colors<-" - make it more robust for combinations of using it with assign_values_to_leaves_nodePar (as used in set("labels_colors", ...) for example) |1fa259e| 
|  DESCRIPTION                            |  2 +-
|  NEWS                                   |  5 ++++-
|  R/attr_access.R                        |  2 ++
|  R/labels_colors.R                      |  3 ++-
|  man/assign_values_to_leaves_nodePar.Rd |  2 ++
|  tests/testthat/test-labels_colors.R    | 19 +++++++++++++++++++
|  6 files changed, 30 insertions(+), 3 deletions(-)

* 2016-07-06(Tal Galili) Added set_labels and place_labels. These are convenience functions for updating the labels of a dendrogram. Props to Garrett Grolemund for the idea. |ccc43bc| 
|  DESCRIPTION       |  4 +--
|  NAMESPACE         |  2 ++
|  NEWS              | 10 +++++++
|  R/labels.R        | 85 +++++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/set_labels.Rd | 69 +++++++++++++++++++++++++++++++++++++++++++
|  5 files changed, 168 insertions(+), 2 deletions(-)

* 2016-06-22(Tal Galili) update log files. |962ea87| 
|  ChangeLog | 164 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  NEWS.md   |  28 +++++++++++
|  2 files changed, 192 insertions(+)

* 2016-06-21(Tal Galili) Improve vignette size for CRAN (moving to html_vignette) |ad2880c| 
|  .Rbuildignore                    |  1 +
|  NEWS                             |  1 +
|  vignettes/Cluster_Analysis.Rmd   | 17 +++++++++--------
|  vignettes/FAQ.Rmd                |  5 +++--
|  vignettes/Quick_Introduction.Rmd |  3 ++-
|  vignettes/introduction.Rmd       |  9 +++++----
|  6 files changed, 21 insertions(+), 15 deletions(-)

* 2016-06-21(Tal Galili) add requireNamespace("seriation") (since I can't use imports) |8c5ae04| 
|  R/seriate_dendrogram.R | 2 ++
|  1 file changed, 2 insertions(+)

* 2016-06-21(Tal Galili) Added seriate_dendrogram - rotates a dendrogram to fit the optimal ordering (via OLO or GW) of some distance matrix (very useful for heatmaps) |113c354| 
|  DESCRIPTION               |  4 ++-
|  NAMESPACE                 |  2 ++
|  NEWS                      |  3 +-
|  R/seriate_dendrogram.R    | 79 +++++++++++++++++++++++++++++++++++++++++++++
|  man/seriate_dendrogram.Rd | 48 +++++++++++++++++++++++++++
|  5 files changed, 134 insertions(+), 2 deletions(-)

* 2016-06-21(Tal Galili) reduce dpi to deal with vignette size |5245c28| 
|  vignettes/Cluster_Analysis.Rmd | 2 +-
|  vignettes/introduction.Rmd     | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2016-06-21(Tal Galili) trying a new untangle method (didn't work) |77e933c| 
|  R/untangle.R | 44 ++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 44 insertions(+)

* 2016-06-21(Tal Galili) copyright notice |c2b044b| 
|  R/find_k.R | 18 ++++++++++++++++++
|  1 file changed, 18 insertions(+)

* 2016-06-21(Tal Galili) added is.dist |d508a51| 
|  NEWS             |  1 +
|  R/is.functions.R | 18 ++++++++++++++++++
|  man/is.dist.Rd   | 24 ++++++++++++++++++++++++
|  3 files changed, 43 insertions(+)

* 2016-06-18(Tal Galili) reminder to myself on how to add SSH to github and connect it to RStudio |e59b44d| 
|  R/zzz.R | 29 +++++++++++++++++++++++++++++
|  1 file changed, 29 insertions(+)

* 2016-06-18(Tal Galili) bump date |3fd6e7f| 
|  DESCRIPTION | 2 +-
|  NAMESPACE   | 4 ++--
|  NEWS        | 2 +-
|  3 files changed, 4 insertions(+), 4 deletions(-)

* 2016-06-18(Tal Galili) find_k can now deal with smaller trees (n<10) by default. |3ff51db| 
|  R/find_k.R    | 2 +-
|  man/find_k.Rd | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2016-06-13(Tal Galili) ggplot2 is now imported (instead of just suggested). This is because the use of dendextend for transforming dendrograms into ggplot2 has become more important (thanks to the new plotly package). |3ab1886| 
|  DESCRIPTION | 2 +-
|  NEWS        | 6 ++++++
|  2 files changed, 7 insertions(+), 1 deletion(-)

* 2016-06-13(Tal Galili) Fix the tiny notch in angle of the branches (in ggplot.ggdend) |b085046| 
|  R/ggdend.R | 4 +++-
|  1 file changed, 3 insertions(+), 1 deletion(-)

* 2016-06-12(Tal Galili) import(ggplot2) (instead of manually copying each function - which is NOT a good way to do this) |7de4df9| 
|  NAMESPACE  |  1 +
|  R/ggdend.R | 32 +++++++++++++++++++-------------
|  2 files changed, 20 insertions(+), 13 deletions(-)

* 2016-06-12(Tal Galili) New function: find_k - Find the (estimated) number of clusters for a dendrogram using average silhouette width |5b6a666| 
|  DESCRIPTION   |  5 ++--
|  NAMESPACE     |  3 +++
|  NEWS          |  9 +++++--
|  R/find_k.R    | 81 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/find_k.Rd | 52 ++++++++++++++++++++++++++++++++++++
|  5 files changed, 146 insertions(+), 4 deletions(-)

* 2016-06-12(Tal Galili) allow NEWS.md to be listed on CRAN |dbfd35c| 
|  .Rbuildignore | 1 -
|  1 file changed, 1 deletion(-)

* 2016-05-26(Tal Galili) would this help codecov to work?! |6a0d6f8| 
|  .travis.yml | 8 +++++---
|  1 file changed, 5 insertions(+), 3 deletions(-)

* 2016-05-26(Tal Galili) http -> https |68350b2| 
|  DESCRIPTION |  4 ++--
|  README.md   | 15 ++++++++-------
|  2 files changed, 10 insertions(+), 9 deletions(-)

* 2016-05-25(Tal Galili) Update Startup Message |b529c5f| 
|  R/ggdend.R |  2 +-
|  R/zzz.R    | 49 +++++++++++++++++++++++++++++++++----------------
|  2 files changed, 34 insertions(+), 17 deletions(-)

* 2016-05-23(Tal Galili) Fix (as is done now in dplyr): Warning: replacing previous import 'dendextend::%>%' by 'plotly::%>%' when loading 'heatmaply' |f97c47b| 
|  NAMESPACE        |  1 +
|  R/magrittr.R     | 24 ++----------------------
|  man/pipe.Rd      | 33 ---------------------------------
|  man/reexports.Rd | 16 ++++++++++++++++
|  4 files changed, 19 insertions(+), 55 deletions(-)

* 2016-05-08(Tal Galili) more info on the statistical use of E_FM and V_FM |08351a2| 
|  vignettes/introduction.Rmd | 15 +++++++++++++++
|  1 file changed, 15 insertions(+)

* 2016-04-25(Tal Galili) Use test_check instead of test_package |7af67a3| 
|  tests/test-all.R | 13 +++++++++++--
|  1 file changed, 11 insertions(+), 2 deletions(-)

* 2016-04-25(Tal Galili) check if the tests now work (if I place them in the tests\\testthat |362e0b0| 
|  tests/test-all.R | 29 ++++++++++++++++++-----------
|  1 file changed, 18 insertions(+), 11 deletions(-)

* 2016-04-24(Tal Galili) alternative name of Baker's Gamma |270dd40| 
|  R/cor_bakers_gamma.R    | 3 ++-
|  man/cor_bakers_gamma.Rd | 3 ++-
|  man/entanglement.Rd     | 2 +-
|  3 files changed, 5 insertions(+), 3 deletions(-)

* 2016-04-24(Tal Galili) ^ instead of ** |884c01d| 
|  R/entanglement.R | 6 +++---
|  1 file changed, 3 insertions(+), 3 deletions(-)

* 2016-03-24(Tal Galili) update documentation of the functions' location. |1325bbb| 
|  man/fac2num.Rd       | 2 +-
|  man/is.dendlist.Rd   | 2 +-
|  man/is.dendrogram.Rd | 2 +-
|  man/is.hclust.Rd     | 2 +-
|  man/is.phylo.Rd      | 2 +-
|  5 files changed, 5 insertions(+), 5 deletions(-)

* 2016-03-17(Tal Galili) Move is.X style functions to a new file: is.functions.R |2b533fe| 
|  DESCRIPTION           |  4 +--
|  NEWS                  |  9 +++++
|  R/cutree.dendrogram.R | 52 ----------------------------
|  R/dendlist.R          | 15 ---------
|  R/is.functions.R      | 90 +++++++++++++++++++++++++++++++++++++++++++++++++
|  5 files changed, 101 insertions(+), 69 deletions(-)

* 2016-02-10(Tal Galili) until tests\\testthat will work. |dd25ff2| 
|  tests/test-all.R | 8 ++++++--
|  1 file changed, 6 insertions(+), 2 deletions(-)

* 2016-02-10(Tal Galili) 1.1.8 bump |6e490e0| 
|  DESCRIPTION | 2 +-
|  NEWS        | 5 +++++
|  2 files changed, 6 insertions(+), 1 deletion(-)

* 2016-02-10(Tal Galili) some updates |634511f| 
|  TODO | 34 ----------------------------------
|  1 file changed, 34 deletions(-)

* 2016-02-10(Tal Galili) ideas |90a4627| 
|  TODO | 51 ++++++++++++++++++++++++++++++++++++++++++++++++++-
|  1 file changed, 50 insertions(+), 1 deletion(-)

* 2016-02-10(Tal Galili) Added "tryCatch" to deal with the tests issue. + updated changelog and NEWS |3f2c1a2| 
|  ChangeLog        | 366 +++++++++++++++++++++++++++++++++++++++++++++++++++++
|  NEWS             |   2 +-
|  NEWS.md          |  47 +++++++
|  tests/test-all.R |   7 +-
|  4 files changed, 419 insertions(+), 3 deletions(-)

* 2016-02-10(Tal Galili) another fix for the warning. |3708e45| 
|  tests/testthat/test-cutree.dendrogram.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2016-02-10(Tal Galili) Added  rmarkdown in Suggests of DESCRIPTION |881733a| 
|  DESCRIPTION | 3 ++-
|  NEWS        | 7 +++++++
|  2 files changed, 9 insertions(+), 1 deletion(-)

* 2016-02-10(Tal Galili) typo |77ccd5f| 
|  R/zzz.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2016-02-10(Tal Galili) Tests fixed to deal with the new R's ability to run as.hclust on dendrogram with ties. |f0ee811| 
|  DESCRIPTION                             | 4 ++--
|  NEWS                                    | 1 +
|  R/cutree.dendrogram.R                   | 2 +-
|  tests/testthat/test-cutree.dendrogram.R | 9 ++++++++-
|  4 files changed, 12 insertions(+), 4 deletions(-)

* 2016-02-10(Tal Galili) Moved `inst/tests/` to `tests/testthat/` |b4c7fbc| 
|  NEWS                                                    | 7 +++++++
|  tests/test-all.R                                        | 2 +-
|  {inst/tests => tests/testthat}/test-attr_access.R       | 0
|  {inst/tests => tests/testthat}/test-bk_method.R         | 0
|  {inst/tests => tests/testthat}/test-branches_attr_by.R  | 0
|  {inst/tests => tests/testthat}/test-common_subtrees.R   | 0
|  {inst/tests => tests/testthat}/test-cor_bakers_gamma.R  | 0
|  {inst/tests => tests/testthat}/test-cor_cophenetic.R    | 0
|  {inst/tests => tests/testthat}/test-cut_lower_fun.R     | 0
|  {inst/tests => tests/testthat}/test-cutree.dendrogram.R | 0
|  {inst/tests => tests/testthat}/test-dendlist.R          | 0
|  {inst/tests => tests/testthat}/test-distinct_edges.R    | 0
|  {inst/tests => tests/testthat}/test-entanglement.R      | 0
|  {inst/tests => tests/testthat}/test-general.R           | 0
|  {inst/tests => tests/testthat}/test-ggdend.R            | 0
|  {inst/tests => tests/testthat}/test-labels-assign.R     | 0
|  {inst/tests => tests/testthat}/test-labels_colors.R     | 0
|  {inst/tests => tests/testthat}/test-nleaves.R           | 0
|  {inst/tests => tests/testthat}/test-rect.dendrogram.R   | 0
|  {inst/tests => tests/testthat}/test-rotate.R            | 0
|  {inst/tests => tests/testthat}/test-set.dendrogram.R    | 0
|  {inst/tests => tests/testthat}/test-trim.R              | 0
|  {inst/tests => tests/testthat}/test-unbranch.R          | 0
|  {inst/tests => tests/testthat}/test-untangle.R          | 0
|  24 files changed, 8 insertions(+), 1 deletion(-)

* 2016-01-06(Tal Galili) Adding Gregory Jefferis as an author (thanks to his work on dendroextras, which was later reused in the dendextend package) |818aa14| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 6 ++++--
|  2 files changed, 6 insertions(+), 4 deletions(-)

* 2016-01-05(Tal Galili) remove sort_cluster_numbers from another place... |d42be6f| 
|  R/color_branches.R                         | 3 +--
|  R/cutree.dendrogram.R                      | 2 +-
|  inst/tests/test-cutree.dendrogram.R        | 8 ++++----
|  man/color_branches.Rd                      | 3 +--
|  vignettes/disabled/dendextend-tutorial.rnw | 4 ++--
|  5 files changed, 9 insertions(+), 11 deletions(-)

* 2016-01-05(Tal Galili) Fix #18 by removing the sort_cluster_numbers parameter. |287b1fd| 
|  DESCRIPTION           |  4 ++--
|  NEWS                  |  7 +++++++
|  R/color_branches.R    |  8 ++++----
|  R/colored_bars.R      |  4 ++--
|  R/cutree.dendrogram.R | 21 ++++++---------------
|  man/color_branches.Rd |  4 ++--
|  man/cutree-methods.Rd | 12 ------------
|  7 files changed, 23 insertions(+), 37 deletions(-)

* 2016-01-02(Tal Galili) Add legend to a SO example |655a0aa| 
|  vignettes/FAQ.Rmd | 5 ++++-
|  1 file changed, 4 insertions(+), 1 deletion(-)

* 2016-01-02(Tal Galili) Added many description elements in .Rd files. |d10d082| 
|  NEWS                                | 10 +++++++---
|  R/attr_access.R                     |  5 +++++
|  R/bk_method.R                       |  3 ++-
|  R/color_branches.R                  |  7 +++++--
|  R/colored_bars.R                    |  6 ++++--
|  R/cor_bakers_gamma.R                |  1 +
|  R/cor_cophenetic.R                  |  3 ++-
|  R/cutree.dendrogram.R               |  5 +++++
|  R/dendextend_options.R              |  2 ++
|  R/dendlist.R                        |  2 ++
|  R/dist_long.R                       |  1 +
|  R/distinct_edges.R                  |  3 ++-
|  R/get_nodes_xy.R                    |  3 ++-
|  R/labels.R                          |  1 +
|  R/labels_colors.R                   |  2 ++
|  R/nleaves.R                         |  1 +
|  R/prune.R                           |  5 +++--
|  R/pvclust.R                         |  6 ++++--
|  R/unbranch.R                        |  7 ++++++-
|  man/all_unique.Rd                   |  3 +++
|  man/assign_dendextend_options.Rd    |  3 +++
|  man/bakers_gamma_for_2_k_matrix.Rd  |  3 +++
|  man/color_branches.Rd               |  3 ++-
|  man/colored_bars.Rd                 |  6 ++++--
|  man/dist_long.Rd                    |  3 +++
|  man/distinct_edges.Rd               |  5 ++++-
|  man/get_branches_heights.Rd         |  3 +++
|  man/get_childrens_heights.Rd        |  3 +++
|  man/get_leaves_attr.Rd              |  3 +++
|  man/get_leaves_nodePar.Rd           |  3 +++
|  man/get_nodes_xy.Rd                 |  5 ++++-
|  man/get_root_branches_attr.Rd       |  3 +++
|  man/heights_per_k.dendrogram.Rd     |  4 ++++
|  man/is.dendlist.Rd                  |  3 +++
|  man/is.dendrogram.Rd                |  3 +++
|  man/is.hclust.Rd                    |  3 +++
|  man/is.phylo.Rd                     |  3 +++
|  man/is_null_list.Rd                 |  3 +++
|  man/labels_cex.Rd                   |  3 +++
|  man/labels_colors.Rd                |  3 +++
|  man/leaf_Colors.Rd                  |  2 +-
|  man/order.hclust.Rd                 |  3 +++
|  man/prune_leaf.Rd                   |  5 ++++-
|  man/pvclust_show_signif.Rd          |  5 ++++-
|  man/pvclust_show_signif_gradient.Rd |  5 ++++-
|  man/raise.dendrogram.Rd             |  3 +++
|  man/sort_2_clusters_vectors.Rd      |  5 ++++-
|  man/sort_dist_mat.Rd                |  5 ++++-
|  man/unbranch.Rd                     |  3 +++
|  man/unclass_dend.Rd                 |  3 +++
|  50 files changed, 156 insertions(+), 27 deletions(-)

* 2016-01-01(Tal Galili) change update to set in the document |758eb9b| 
|  R/colored_bars.R    | 10 +++++-----
|  man/colored_bars.Rd |  2 +-
|  2 files changed, 6 insertions(+), 6 deletions(-)

* 2016-01-01(Tal Galili) having colored_bars more robust to various types of vectors. And updated the introduction vignette to use sort_by_labels_order properly in the example. |f0f96c5| 
|  R/colored_bars.R           | 6 ++++--
|  vignettes/introduction.Rmd | 4 +++-
|  2 files changed, 7 insertions(+), 3 deletions(-)

* 2016-01-01(Tal Galili) Updated the vignette (and removed the check in colored_bars for matrix/vector) |8aa9e78| 
|  DESCRIPTION       |  2 +-
|  R/colored_bars.R  |  5 +++--
|  vignettes/FAQ.Rmd | 46 ++++++++++++++++++++++++++++++++++++++++++++++
|  3 files changed, 50 insertions(+), 3 deletions(-)

* 2016-01-01(Tal Galili) colored_bars - updated example (a new mtcars example) |a89df04| 
|  R/colored_bars.R    | 39 +++++++++++++++++++++++++++
|  man/colored_bars.Rd | 73 +++++++++++++++++++++++++++++++++++++++++----------
|  2 files changed, 98 insertions(+), 14 deletions(-)

* 2016-01-01(Tal Galili) colored_bars - Fixed many bugs (in the horiz string location, and in the display of multiple bars) |b394170| 
|  R/colored_bars.R | 23 ++++++++++-------------
|  1 file changed, 10 insertions(+), 13 deletions(-)

* 2016-01-01(Tal Galili) Fixes to the bars' positions for horiz = TRUE |6cf4e2e| 
|  R/colored_bars.R | 10 +++++-----
|  1 file changed, 5 insertions(+), 5 deletions(-)

* 2016-01-01(Tal Galili) colored_bars - Major corrections to the way the bars are located automatically (it is now positioned underneath the labels automatically!) |ce47da4| 
|  R/colored_bars.R | 226 +++++++++++++++++++++++++++++++++++------------------
|  1 file changed, 152 insertions(+), 74 deletions(-)

* 2016-01-01(Tal Galili) rxoygen2 edit |ccbbf4f| 
|  NAMESPACE                                  |  2 +-
|  R/dendextend_options.R                     |  8 +--
|  R/rotate.R                                 |  2 +-
|  man/Bk.Rd                                  | 19 +++---
|  man/Bk_permutations.Rd                     | 19 +++---
|  man/Bk_plot.Rd                             | 37 +++++------
|  man/DendSer.dendrogram.Rd                  |  4 +-
|  man/FM_index.Rd                            | 17 ++---
|  man/FM_index_R.Rd                          | 13 ++--
|  man/FM_index_permutation.Rd                |  9 +--
|  man/FM_index_profdpm.Rd                    | 15 +++--
|  man/all.equal.dendrogram.Rd                |  9 +--
|  man/all_couple_rotations_at_k.Rd           |  5 +-
|  man/all_unique.Rd                          |  7 +-
|  man/as.dendlist.Rd                         |  4 +-
|  man/as.phylo.dendrogram.Rd                 |  8 +--
|  man/as_hclust_fixed.Rd                     | 10 +--
|  man/assign_dendextend_options.Rd           |  5 +-
|  man/assign_values_to_branches_edgePar.Rd   |  7 +-
|  man/assign_values_to_leaves_edgePar.Rd     |  6 +-
|  man/assign_values_to_leaves_nodePar.Rd     | 10 +--
|  man/assign_values_to_nodes_nodePar.Rd      | 22 ++++---
|  man/bakers_gamma_for_2_k_matrix.Rd         |  5 +-
|  man/branches_attr_by_clusters.Rd           | 15 +++--
|  man/branches_attr_by_labels.Rd             | 16 ++---
|  man/circlize_dendrogram.Rd                 |  9 +--
|  man/click_rotate.Rd                        |  7 +-
|  man/collapse_branch.Rd                     |  7 +-
|  man/color_branches.Rd                      | 56 ++++++++--------
|  man/color_labels.Rd                        | 14 ++--
|  man/color_unique_labels.Rd                 |  3 +-
|  man/common_subtrees_clusters.Rd            |  5 +-
|  man/cor.dendlist.Rd                        |  9 +--
|  man/cor_FM_index.Rd                        |  4 +-
|  man/cor_bakers_gamma.Rd                    | 36 ++++++-----
|  man/cor_common_nodes.Rd                    |  8 ++-
|  man/cor_cophenetic.Rd                      | 40 ++++++------
|  man/count_terminal_nodes.Rd                | 10 +--
|  man/cut_lower_fun.Rd                       |  8 ++-
|  man/cutree-methods.Rd                      | 79 +++++++++++-----------
|  man/cutree_1h.dendrogram.Rd                | 18 +++---
|  man/cutree_1k.dendrogram.Rd                | 30 +++++----
|  man/d3dendro_options.Rd                    |  8 +--
|  man/d3dendrogram.Rd                        |  8 +--
|  man/dend_diff.Rd                           | 14 ++--
|  man/dendextend-package.Rd                  |  2 +-
|  man/dendextend_labels.dendrogram.Rd        |  4 +-
|  man/dendextend_options.Rd                  |  4 +-
|  man/dendlist.Rd                            |  8 ++-
|  man/dist.dendlist.Rd                       | 14 ++--
|  man/dist_long.Rd                           |  6 +-
|  man/distinct_edges.Rd                      |  7 +-
|  man/duplicate_leaf.Rd                      |  4 +-
|  man/entanglement.Rd                        | 27 ++++----
|  man/fac2num.Rd                             |  4 +-
|  man/fix_members_attr.dendrogram.Rd         |  5 +-
|  man/flatten.dendrogram.Rd                  |  4 +-
|  man/flip_leaves.Rd                         |  3 +-
|  man/get_branches_heights.Rd                |  7 +-
|  man/get_childrens_heights.Rd               | 10 +--
|  man/get_leaves_attr.Rd                     | 21 +++---
|  man/get_leaves_branches_attr.Rd            |  8 ++-
|  man/get_leaves_branches_col.Rd             | 12 ++--
|  man/get_leaves_edgePar.Rd                  |  5 +-
|  man/get_leaves_nodePar.Rd                  |  8 +--
|  man/get_nodes_attr.Rd                      | 29 +++++----
|  man/get_nodes_xy.Rd                        | 17 ++---
|  man/get_root_branches_attr.Rd              |  7 +-
|  man/ggdend.Rd                              | 43 ++++++------
|  man/hang.dendrogram.Rd                     | 13 ++--
|  man/heights_per_k.dendrogram.Rd            | 17 ++---
|  man/highlight_distinct_edges.Rd            | 28 ++++----
|  man/identify.dendrogram.Rd                 | 23 +++----
|  man/intersect_trees.Rd                     |  5 +-
|  man/is.dendlist.Rd                         |  5 +-
|  man/is.dendrogram.Rd                       |  5 +-
|  man/is.hclust.Rd                           |  5 +-
|  man/is.natural.number.Rd                   |  3 +-
|  man/is.phylo.Rd                            |  5 +-
|  man/is_null_list.Rd                        |  7 +-
|  man/khan.Rd                                | 40 ++++++------
|  man/labels-assign.Rd                       | 22 +++----
|  man/labels_cex.Rd                          |  8 +--
|  man/labels_colors.Rd                       | 11 ++--
|  man/ladderize.Rd                           |  8 ++-
|  man/leaf_Colors.Rd                         |  5 +-
|  man/lowest_common_branch.Rd                |  4 +-
|  man/match_order_by_labels.Rd               |  4 +-
|  man/match_order_dendrogram_by_old_order.Rd | 12 ++--
|  man/na_locf.Rd                             |  8 ++-
|  man/nleaves.Rd                             | 16 ++---
|  man/nnodes.Rd                              |  4 +-
|  man/noded_with_condition.Rd                |  9 +--
|  man/order.dendrogram-assign.Rd             |  5 +-
|  man/order.hclust.Rd                        | 15 ++---
|  man/partition_leaves.Rd                    |  4 +-
|  man/pipe.Rd                                |  8 +--
|  man/plot_horiz.dendrogram.Rd               | 26 ++++----
|  man/prune.Rd                               |  2 +-
|  man/prune_common_subtrees.dendlist.Rd      |  6 +-
|  man/prune_leaf.Rd                          |  7 +-
|  man/pvclust_show_signif.Rd                 | 11 ++--
|  man/pvclust_show_signif_gradient.Rd        | 15 ++---
|  man/raise.dendrogram.Rd                    |  5 +-
|  man/rank_branches.Rd                       | 13 ++--
|  man/rank_order.dendrogram.Rd               |  6 +-
|  man/rank_values_with_clusters.Rd           |  5 +-
|  man/rect.dendrogram.Rd                     | 33 +++++-----
|  man/remove_branches_edgePar.Rd             |  4 +-
|  man/remove_leaves_nodePar.Rd               |  4 +-
|  man/remove_nodes_nodePar.Rd                |  4 +-
|  man/rllply.Rd                              | 10 +--
|  man/rotate.Rd                              | 61 ++++++++---------
|  man/rotate_DendSer.Rd                      |  2 +-
|  man/sample.dendrogram.Rd                   | 16 +++--
|  man/set.Rd                                 | 97 ++++++++++++++--------------
|  man/shuffle.Rd                             |  8 ++-
|  man/sort_2_clusters_vectors.Rd             | 10 ++-
|  man/sort_dist_mat.Rd                       |  5 +-
|  man/sort_levels_values.Rd                  | 16 +++--
|  man/tanglegram.Rd                          | 46 ++++++-------
|  man/theme_dendro.Rd                        |  4 +-
|  man/unbranch.Rd                            |  5 +-
|  man/unclass_dend.Rd                        | 13 ++--
|  man/untangle.Rd                            | 12 ++--
|  man/untangle_DendSer.Rd                    |  2 +-
|  man/untangle_random_search.Rd              | 17 ++---
|  man/untangle_step_rotate_1side.Rd          | 23 +++----
|  man/untangle_step_rotate_2side.Rd          | 19 +++---
|  man/which_leaf.Rd                          |  6 +-
|  man/which_node.Rd                          |  7 +-
|  131 files changed, 891 insertions(+), 834 deletions(-)

* 2015-12-31(Tal Galili) colored_bars - Fix the default position of the bars when dend is provided. |28eb04d| 
|  NEWS             |  5 ++++-
|  R/colored_bars.R | 14 +++++++++-----
|  2 files changed, 13 insertions(+), 6 deletions(-)

* 2015-12-31(Tal Galili) Fix the example in the documentation of `colored_bars` |d49f883| 
|  DESCRIPTION         |  5 +++--
|  NEWS                |  7 +++++++
|  R/colored_bars.R    |  8 ++++----
|  man/colored_bars.Rd | 26 ++++++++++++++------------
|  4 files changed, 28 insertions(+), 18 deletions(-)

* 2015-11-07(Tal Galili) ::: instead of :: (does it work?) |c80aa2e| 
|  R/dendextend_options.R | 8 ++++----
|  1 file changed, 4 insertions(+), 4 deletions(-)

* 2015-11-07(Tal Galili) ... not used |2454971| 
|  R/labels_colors.R          | 2 +-
|  man/color_unique_labels.Rd | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2015-11-07(Tal Galili) color_unique_labels  - a function to Color unique labels in a dendrogram |3d385af| 
|  DESCRIPTION                |  4 ++--
|  NAMESPACE                  |  1 +
|  NEWS                       |  9 +++++++++
|  R/labels_colors.R          | 48 ++++++++++++++++++++++++++++++++++++++++++++
|  man/color_unique_labels.Rd | 30 +++++++++++++++++++++++++++
|  5 files changed, 90 insertions(+), 2 deletions(-)

* 2015-11-07(Tal Galili) update citation. (bioinformatics paper is published :) ) |5751356| 
|  DESCRIPTION   | 2 +-
|  inst/CITATION | 4 ++--
|  2 files changed, 3 insertions(+), 3 deletions(-)

* 2015-10-31(Tal Galili) ignore caching and an old tutorial |8f58f47| 
|  .Rbuildignore    | 2 ++
|  dendextend.Rproj | 1 +
|  2 files changed, 3 insertions(+)

* 2015-10-31(Tal Galili) # Use ylim to deal with long labels in ggplot2 |50eb921| 
|  R/ggdend.R    | 8 ++++++++
|  man/ggdend.Rd | 8 ++++++++
|  2 files changed, 16 insertions(+)

* 2015-10-30(Tal Galili) update changelog and NEWS |4ab0bcc| 
|  ChangeLog | 71 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  NEWS.md   | 17 +++++++++++++++
|  R/zzz.R   |  2 +-
|  3 files changed, 89 insertions(+), 1 deletion(-)

* 2015-10-30(Tal Galili) update citations |483b935| 
|  DESCRIPTION   | 4 ++--
|  NEWS          | 5 ++++-
|  inst/CITATION | 4 ++--
|  3 files changed, 8 insertions(+), 5 deletions(-)

* 2015-10-01(Tal Galili) added counter badges |b53cba4| 
|  README.md | 2 ++
|  1 file changed, 2 insertions(+)

* 2015-09-20(Tal Galili) rect.dendrogram and identify.dendrogram - gain the stop_if_out parameter. The defaults for this parameter makes the error of "Error in rect.dendrogram(x, k = k, x = X$x, cluster = cluster[, k - 1],  : k must be between 2 and 10" - to become less common (since it replaces it with a warning). |9b0ea47| 
|  DESCRIPTION                |  4 ++--
|  NEWS                       |  4 +++-
|  R/rect.dendrogram.R        | 28 ++++++++++++++++++++++------
|  man/identify.dendrogram.Rd |  6 +++++-
|  man/rect.dendrogram.Rd     |  7 ++++++-
|  5 files changed, 38 insertions(+), 11 deletions(-)

* 2015-09-06(Tal Galili) as.ggdend.dendrogram - can now handle different label heights. (for example, the ones produces when using hang.dendrogram) |6548b02| 
|  DESCRIPTION | 2 +-
|  NEWS        | 4 ++--
|  R/ggdend.R  | 2 ++
|  3 files changed, 5 insertions(+), 3 deletions(-)

* 2015-09-03(Tal Galili) Fix 2 warnings |0e05202| 
|  R/labels.R           | 18 +-----------------
|  man/labels-assign.Rd | 19 +------------------
|  2 files changed, 2 insertions(+), 35 deletions(-)

* 2015-09-03(Tal Galili) Removed functions labels.matrix and labels<-.matrix, in order to avoid conflicts with arules (and since these functions are not really used in other parts of the package)- reported by Maja Alicja. |ebcae92| 
|  DESCRIPTION                     |   2 +-
|  NAMESPACE                       |   2 -
|  NEWS                            |   3 +-
|  R/labels.R                      | 111 ++++++++++++++++++--------------------
|  inst/tests/test-labels-assign.R |  43 ++++++++-------
|  man/labels-assign.Rd            |   5 --
|  6 files changed, 79 insertions(+), 87 deletions(-)

* 2015-08-28(Tal Galili) intersect_trees - return dendlist() and a warning if there are no shared labels between the two trees. |9de3f36| 
|  DESCRIPTION | 2 +-
|  NEWS        | 5 ++++-
|  R/prune.R   | 5 +++++
|  3 files changed, 10 insertions(+), 2 deletions(-)

* 2015-08-14(Tal Galili) Basic test for as.ggdend |f1ab77f| 
|  inst/tests/test-ggdend.R | 29 +++++++++++++++++++++++++++++
|  1 file changed, 29 insertions(+)

* 2015-08-14(Tal Galili) as.ggdend.dendrogram - fix "Error in FUN(X[[i]], ...) : subscript out of bounds" problem for some (more) trees. Fixes bug #12 |15ce942| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 8 ++++++++
|  R/ggdend.R  | 6 ++++--
|  3 files changed, 14 insertions(+), 4 deletions(-)

* 2015-07-30(Tal Galili) Remove d3heatmap example so to reduce package size |81c707d| 
|  vignettes/Cluster_Analysis.Rmd | 6 +++---
|  1 file changed, 3 insertions(+), 3 deletions(-)

* 2015-07-30(Tal Galili) reduce sizes of files (for CRAN) |c62be8e| 
|  ...ts - enhanced with the dendextend package.html | 191 +++++------
|  inst/ignored/Introduction to dendextend.html      | 356 +++++++++++++-------
|  vignettes/Cluster_Analysis.Rmd                    |   2 +-
|  vignettes/FAQ.Rmd                                 |   6 +-
|  vignettes/introduction.Rmd                        |   2 +-
|  5 files changed, 310 insertions(+), 247 deletions(-)

* 2015-07-30(Tal Galili) misc |c85c6ee| 
|  ChangeLog | 187 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  NEWS.md   |  46 +++++++++++++++
|  2 files changed, 233 insertions(+)

* 2015-07-30(Tal Galili) Added an example for using NMF::aheatmap |9d75974| 
|  DESCRIPTION                |  1 +
|  vignettes/introduction.Rmd | 26 ++++++++++++++++++++++++--
|  2 files changed, 25 insertions(+), 2 deletions(-)

* 2015-07-30(Tal Galili) Added a link to the paper from the DESCRIPTION |5d3763e| 
|  DESCRIPTION | 3 ++-
|  1 file changed, 2 insertions(+), 1 deletion(-)

* 2015-07-30(Tal Galili) Added a CITATION file |086d89e| 
|  DESCRIPTION   |  2 +-
|  NEWS          |  6 +++++-
|  inst/CITATION | 19 +++++++++++++++++++
|  3 files changed, 25 insertions(+), 2 deletions(-)

* 2015-07-17(Tal Galili) Another step towards 1.1.0 (but not there yet...) |5d141ea| 
|  DESCRIPTION | 2 +-
|  NEWS        | 6 ++++--
|  2 files changed, 5 insertions(+), 3 deletions(-)

* 2015-07-17(Tal Galili) minor typo fixes and doc-inter-linking |abcc402| 
|  R/untangle.R                      | 11 ++++++++++-
|  man/set.Rd                        |  3 +++
|  man/untangle.Rd                   |  1 +
|  man/untangle_step_rotate_1side.Rd |  2 +-
|  man/untangle_step_rotate_2side.Rd |  8 ++++++++
|  5 files changed, 23 insertions(+), 2 deletions(-)

* 2015-07-17(Tal Galili) Adding a d3heatmap example |c5de02c| 
|  ...ta sets - enhanced with the dendextend package.html | 16 ++++++++++++++++
|  vignettes/Cluster_Analysis.Rmd                         | 14 ++++++++++++++
|  2 files changed, 30 insertions(+)

* 2015-07-17(Tal Galili) Updated FAQ HTML file. |cc851f6| 
|  inst/ignored/Frequently asked questions.html | 143 +++++++++++++++++++++----
|  1 file changed, 123 insertions(+), 20 deletions(-)

* 2015-07-17(Tal Galili) Rename vignette files |2dd4fcd| 
|  README.md                                                           | 4 ++--
|  ...quantly asked questions.html => Frequently asked questions.html} | 0
|  ...on famous data sets - enhanced with the dendextend package.html} | 0
|  3 files changed, 2 insertions(+), 2 deletions(-)

* 2015-07-17(Tal Galili) added a circular example of Iris |4848a5d| 
|  vignettes/Cluster_Analysis.Rmd | 18 ++++++++++++++++--
|  1 file changed, 16 insertions(+), 2 deletions(-)

* 2015-07-17(Tal Galili) implemented various fixes |5455bdc| 
|  ...ts - enhanced with the dendextend package.html | 240 +++++++++++---------
|  1 file changed, 131 insertions(+), 109 deletions(-)

* 2015-07-16(Tal Galili) Various fixes to spelling and grammatical mistakes |e9ea9f9| 
|  vignettes/Cluster_Analysis.Rmd | 137 +++++++++++++++++++--------------------
|  vignettes/FAQ.Rmd              |  16 ++---
|  2 files changed, 76 insertions(+), 77 deletions(-)

* 2015-07-15(Tal Galili) set - added "branches_k_lty" parameter |a81ca28| 
|  DESCRIPTION        |  4 ++--
|  NEWS               |  5 ++++-
|  R/color_branches.R | 13 +++++++++++++
|  R/set.dendrogram.R | 13 ++++++++++---
|  man/set.Rd         |  4 +++-
|  5 files changed, 32 insertions(+), 7 deletions(-)

* 2015-07-15(Tal Galili) Mention other names for the circlized dendrogram plot. |1d8a78b| 
|  R/circlize.R               | 3 +++
|  man/circlize_dendrogram.Rd | 3 +++
|  2 files changed, 6 insertions(+)

* 2015-07-15(Tal Galili) switch URL order |7bac0fe| 
|  DESCRIPTION | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2015-07-15(Tal Galili) explain proper citation of circlize function. |636c15f| 
|  R/circlize.R               | 3 ++-
|  man/circlize_dendrogram.Rd | 3 ++-
|  2 files changed, 4 insertions(+), 2 deletions(-)

* 2015-07-14(Tal Galili) as.ggdend.dendrogram - fix "Error in FUN(X[[i]], ...) : subscript out of bounds" problem for some trees. |418cc2c| 
|  DESCRIPTION | 2 +-
|  NEWS        | 5 ++++-
|  R/ggdend.R  | 2 +-
|  3 files changed, 6 insertions(+), 3 deletions(-)

* 2015-07-11(Tal Galili) seealso linking |4b0d157| 
|  R/color_branches.R    | 3 ++-
|  man/color_branches.Rd | 3 ++-
|  2 files changed, 4 insertions(+), 2 deletions(-)

* 2015-07-11(Tal Galili) Another SO question |07abbc3| 
|  vignettes/FAQ.Rmd | 34 ++++++++++++++++++++++++++++++++++
|  1 file changed, 34 insertions(+)

* 2015-07-11(Tal Galili) fix "graphical parameter "mfrow" has the wrong length" |edb9613| 
|  vignettes/introduction.Rmd | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-07-11(Tal Galili) inte-linking and misc |fe50082| 
|  R/attr_access.R                | 2 +-
|  R/labels_colors.R              | 2 +-
|  man/get_leaves_branches_col.Rd | 2 +-
|  man/labels_colors.Rd           | 2 +-
|  4 files changed, 4 insertions(+), 4 deletions(-)

* 2015-07-11(Tal Galili) Fix "Error: Vignette 'FAQ.Rmd' is non-ASCII but has no declared encoding" (thanks to Duncan Murdoch :) ) |22c9e44| 
|  R/zzz.R           | 3 +++
|  vignettes/FAQ.Rmd | 4 ++--
|  2 files changed, 5 insertions(+), 2 deletions(-)

* 2015-07-11(Tal Galili) Added 2 new SO questions to FAQ |7f9a3ae| 
|  vignettes/FAQ.Rmd          | 56 +++++++++++++++++++++++++++++++++++++++++++-
|  vignettes/introduction.Rmd |  1 +
|  2 files changed, 56 insertions(+), 1 deletion(-)

* 2015-07-11(Tal Galili) more links |84ae6d0| 
|  R/color_branches.R   | 3 ++-
|  R/labels_colors.R    | 3 +++
|  man/color_labels.Rd  | 3 ++-
|  man/labels_colors.Rd | 5 +++++
|  4 files changed, 12 insertions(+), 2 deletions(-)

* 2015-07-10(Tal Galili) circlize_dendrogram - a function for creating radial dendrogram plots! (based on the circlize package) |8b080d7| 
|  DESCRIPTION                |   8 ++-
|  NAMESPACE                  |   1 +
|  NEWS                       |   1 +
|  R/circlize.R               | 141 +++++++++++++++++++++++++++++++++++++++++++
|  README.md                  |   9 +++
|  man/circlize_dendrogram.Rd |  79 ++++++++++++++++++++++++
|  vignettes/FAQ.Rmd          |  29 +++++++++
|  vignettes/introduction.Rmd |  54 +++++++++++++++++
|  8 files changed, 320 insertions(+), 2 deletions(-)

* 2015-07-10(Tal Galili) Added labels_cex |da35752| 
|  NAMESPACE         |  2 ++
|  NEWS              |  1 +
|  R/labels_colors.R | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/labels_cex.Rd | 42 ++++++++++++++++++++++++++++++++++++++++++
|  4 files changed, 95 insertions(+)

* 2015-07-10(Tal Galili) Added labels_col as an alias of labels_colors |01ba9e6| 
|  NAMESPACE            | 1 +
|  NEWS                 | 8 +++++++-
|  R/labels_colors.R    | 6 +++++-
|  man/labels_colors.Rd | 3 +++
|  4 files changed, 16 insertions(+), 2 deletions(-)

* 2015-07-05(Tal Galili) assign_values_to_nodes_nodePar - can now handle NA with a character string vector in value. Fixes #10 |9ceadb1| 
|  DESCRIPTION                           | 4 ++--
|  NEWS                                  | 7 +++++++
|  R/attr_access.R                       | 9 ++++++++-
|  man/assign_values_to_nodes_nodePar.Rd | 7 +++++++
|  vignettes/introduction.Rmd            | 2 +-
|  5 files changed, 25 insertions(+), 4 deletions(-)

* 2015-06-28(Tal Galili) update DESCRIPTION to 1.0.2 |64bc90f| 
|  DESCRIPTION | 2 +-
|  NEWS        | 4 ++++
|  2 files changed, 5 insertions(+), 1 deletion(-)

* 2015-06-28(Tal Galili) A new minimal quick introduction vignette |7ee0812| 
|  vignettes/Quick_Introduction.Rmd | 127 +++++++++++++++++++++++++++++++++++++
|  1 file changed, 127 insertions(+)

* 2015-06-28(Tal Galili) fix typo |ffc2c00| 
|  DESCRIPTION       | 2 +-
|  vignettes/FAQ.Rmd | 4 ++--
|  2 files changed, 3 insertions(+), 3 deletions(-)

* 2015-06-28(Tal Galili) ggplot.ggdend - added offset_labels |578e70f| 
|  NEWS          | 7 +++++++
|  R/ggdend.R    | 9 +++++++--
|  man/ggdend.Rd | 5 ++++-
|  3 files changed, 18 insertions(+), 3 deletions(-)

* 2015-06-28(Tal Galili) Added import to NAMESPACE: graphics, grDevices |0148a92| 
|  DESCRIPTION            | 9 +++++----
|  NAMESPACE              | 2 ++
|  NEWS                   | 8 ++++++++
|  R/dendextend-package.R | 2 ++
|  4 files changed, 17 insertions(+), 4 deletions(-)

* 2015-06-27(Tal Galili) misc |f6890d6| 
|  ChangeLog | 19 +++++++++++++++++++
|  1 file changed, 19 insertions(+)

* 2015-06-27(Tal Galili) fix url |6b6bafd| 
|  inst/ignored/Introduction to dendextend.html | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-06-27(Tal Galili) fix dpi to get smaller vignettes |f53c729| 
|  vignettes/Cluster_Analysis.Rmd | 2 +-
|  vignettes/introduction.Rmd     | 4 ++--
|  2 files changed, 3 insertions(+), 3 deletions(-)

* 2015-06-27(Tal Galili) fix: prune.hclust: no visible binding for global variable 'x' unbranch.hclust: no visible binding for global variable 'x' |30804af| 
|  R/prune.R    | 2 +-
|  R/unbranch.R | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2015-06-27(Tal Galili) updated for 1.0.0. |69c26b4| 
|  ChangeLog | 316 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  NEWS.md   |  18 +++-
|  2 files changed, 333 insertions(+), 1 deletion(-)

* 2015-06-27(Tal Galili) update date |a85432c| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-06-27(Tal Galili) object -> dend  for: shuffle |ec62d71| 
|  NEWS           |  2 +-
|  R/untangle.R   | 30 +++++++++++++++---------------
|  man/shuffle.Rd | 12 ++++++------
|  3 files changed, 22 insertions(+), 22 deletions(-)

* 2015-06-27(Tal Galili) x -> dend  for: unbranch |541d5ef| 
|  NEWS            |  2 +-
|  R/unbranch.R    | 26 +++++++++++++-------------
|  man/unbranch.Rd | 10 +++++-----
|  3 files changed, 19 insertions(+), 19 deletions(-)

* 2015-06-27(Tal Galili) tree1/tree2 -> dend1/dend2  for: tanglegram |5517d9b| 
|  NEWS              |   2 +-
|  R/tanglegram.R    | 136 ++++++++++++++++++++++++++--------------------------
|  man/tanglegram.Rd |  14 +++---
|  3 files changed, 76 insertions(+), 76 deletions(-)

* 2015-06-27(Tal Galili) x -> dend  for: prune |8660626| 
|  NEWS              |  2 +-
|  R/prune.R         | 94 ++++++++++++++++++++++++++---------------------------
|  man/prune.Rd      | 12 +++----
|  man/prune_leaf.Rd |  4 +--
|  4 files changed, 56 insertions(+), 56 deletions(-)

* 2015-06-27(Tal Galili) intersect_trees x1/x2 -> dend1/dend2 |e87987d| 
|  NEWS                   |  3 +--
|  R/prune.R              | 22 +++++++++++-----------
|  man/intersect_trees.Rd |  6 +++---
|  3 files changed, 15 insertions(+), 16 deletions(-)

* 2015-06-27(Tal Galili) object -> dend  for: labels_colors |a306bb1| 
|  NEWS                 |  1 +
|  R/labels_colors.R    | 28 ++++++++++++++--------------
|  man/labels_colors.Rd |  6 +++---
|  3 files changed, 18 insertions(+), 17 deletions(-)

* 2015-06-27(Tal Galili) x -> dend  for: get_nodes_xy |3f50252| 
|  NEWS                | 2 +-
|  R/get_nodes_xy.R    | 6 ++++--
|  man/get_nodes_xy.Rd | 4 ++--
|  3 files changed, 7 insertions(+), 5 deletions(-)

* 2015-06-27(Tal Galili) tree1/tree2 -> dend1/dend2  for: untangle_random_search |9fa317f| 
|  NEWS                          |  2 +-
|  R/untangle.R                  | 32 ++++++++++++++++----------------
|  man/untangle_random_search.Rd |  6 +++---
|  3 files changed, 20 insertions(+), 20 deletions(-)

* 2015-06-27(Tal Galili) tree1/tree2 -> dend1/dend2  for: entanglement |5610519| 
|  NEWS                |  2 +-
|  R/entanglement.R    | 88 +++++++++++++++++++++++++--------------------------
|  man/entanglement.Rd | 14 ++++----
|  3 files changed, 52 insertions(+), 52 deletions(-)

* 2015-06-27(Tal Galili) y to dend2 |2e653c5| 
|  R/distinct_edges.R              | 34 +++++++++++++++++-----------------
|  man/dend_diff.Rd                |  4 ++--
|  man/distinct_edges.Rd           |  6 +++---
|  man/highlight_distinct_edges.Rd |  4 ++--
|  4 files changed, 24 insertions(+), 24 deletions(-)

* 2015-06-27(Tal Galili) x -> dend  for: dend_diff, dist.dendlist, distinct_edges, highlight_distinct_edges, partition_leaves |1da678e| 
|  NEWS                            |  2 +-
|  R/distinct_edges.R              | 94 +++++++++++++++++++--------------------
|  man/dend_diff.Rd                |  8 ++--
|  man/dist.dendlist.Rd            |  4 +-
|  man/distinct_edges.Rd           |  6 +--
|  man/highlight_distinct_edges.Rd | 10 ++---
|  man/partition_leaves.Rd         |  4 +-
|  7 files changed, 64 insertions(+), 64 deletions(-)

* 2015-06-27(Tal Galili) tree -> dend  for: cutree_1h.dendrogram, cutree_1k.dendrogram, heights_per_k.dendrogram |7ec15a4| 
|  NEWS                            |  2 +-
|  R/cutree.dendrogram.R           | 95 ++++++++++++++++++++-------------------
|  man/cutree_1h.dendrogram.Rd     |  6 +--
|  man/cutree_1k.dendrogram.Rd     |  4 +-
|  man/heights_per_k.dendrogram.Rd |  4 +-
|  5 files changed, 57 insertions(+), 54 deletions(-)

* 2015-06-27(Tal Galili) tree -> dend  for: dendextend_cut_lower_fun |d13b9c6| 
|  NEWS                 |  2 +-
|  R/cut_lower_fun.R    | 24 ++++++++++++------------
|  man/cut_lower_fun.Rd | 10 +++++-----
|  3 files changed, 18 insertions(+), 18 deletions(-)

* 2015-06-27(Tal Galili) tree1/tree2 -> dend1/dend2  for: cor_cophenetic |4c987d3| 
|  NEWS                  |  2 +-
|  R/cor_cophenetic.R    | 40 ++++++++++++++++++++--------------------
|  man/cor_cophenetic.Rd | 10 +++++-----
|  3 files changed, 26 insertions(+), 26 deletions(-)

* 2015-06-27(Tal Galili) cor_bakers_gamma: tree1/2 -> dend1/2 |9641738| 
|  NEWS                               |  2 +-
|  R/cor_bakers_gamma.R               | 76 ++++++++++++++++++------------------
|  man/bakers_gamma_for_2_k_matrix.Rd |  6 +--
|  man/cor_bakers_gamma.Rd            | 12 +++---
|  4 files changed, 48 insertions(+), 48 deletions(-)

* 2015-06-27(Tal Galili)       * x -> dend  for: cor.dendlist       * tree1/tree2 -> dend1/dend2  for: cor_FM_index, cor_common_nodes |b62be29| 
|  NEWS                    |  2 ++
|  R/cor.dendlist.R        | 38 +++++++++++++++++++-------------------
|  man/cor.dendlist.Rd     |  6 +++---
|  man/cor_FM_index.Rd     |  6 +++---
|  man/cor_common_nodes.Rd |  6 +++---
|  5 files changed, 30 insertions(+), 28 deletions(-)

* 2015-06-27(Tal Galili) bug fix (renaming object to dend) |952667f| 
|  R/branches_attr_by.R | 2 +-
|  R/distinct_edges.R   | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2015-06-27(Tal Galili) tree -> dend  for:                color_branches, color_labels_by_labels, color_labels, get_branches_heights, dendextend_get_branches_heights |7fd2a2c| 
|  NEWS                         |   2 +
|  R/attr_access.R              |  16 +++----
|  R/color_branches.R           | 100 ++++++++++++++++++++---------------------
|  R/set.dendrogram.R           |   6 +--
|  man/color_branches.Rd        |  10 ++---
|  man/color_labels.Rd          |   6 +--
|  man/get_branches_heights.Rd  |   4 +-
|  man/rank_order.dendrogram.Rd |   2 +-
|  8 files changed, 74 insertions(+), 72 deletions(-)

* 2015-06-27(Tal Galili) object -> dend  for: |95856ed| 
|  NEWS                                     |  13 +-
|  R/ape.R                                  |   1 +
|  R/attr_access.R                          | 194 ++++++++++++++---------------
|  inst/tests/test-attr_access.R            |   2 +-
|  man/assign_values_to_branches_edgePar.Rd |  12 +-
|  man/assign_values_to_leaves_edgePar.Rd   |  10 +-
|  man/assign_values_to_leaves_nodePar.Rd   |   6 +-
|  man/assign_values_to_nodes_nodePar.Rd    |   4 +-
|  man/get_leaves_attr.Rd                   |   4 +-
|  man/get_leaves_branches_attr.Rd          |   4 +-
|  man/get_leaves_branches_col.Rd           |   4 +-
|  man/get_leaves_edgePar.Rd                |   4 +-
|  man/get_leaves_nodePar.Rd                |   4 +-
|  man/get_nodes_attr.Rd                    |   4 +-
|  man/remove_branches_edgePar.Rd           |   4 +-
|  man/remove_leaves_nodePar.Rd             |   4 +-
|  man/remove_nodes_nodePar.Rd              |   4 +-
|  17 files changed, 145 insertions(+), 133 deletions(-)

* 2015-06-27(Tal Galili) roxygen 4.1.1 |b1723fe| 
|  NAMESPACE                                  | 2 +-
|  man/Bk.Rd                                  | 2 +-
|  man/Bk_permutations.Rd                     | 2 +-
|  man/Bk_plot.Rd                             | 2 +-
|  man/DendSer.dendrogram.Rd                  | 2 +-
|  man/FM_index.Rd                            | 2 +-
|  man/FM_index_R.Rd                          | 2 +-
|  man/FM_index_permutation.Rd                | 2 +-
|  man/FM_index_profdpm.Rd                    | 2 +-
|  man/all.equal.dendrogram.Rd                | 2 +-
|  man/all_couple_rotations_at_k.Rd           | 2 +-
|  man/all_unique.Rd                          | 2 +-
|  man/as.dendlist.Rd                         | 2 +-
|  man/as.phylo.dendrogram.Rd                 | 2 +-
|  man/as_hclust_fixed.Rd                     | 2 +-
|  man/assign_dendextend_options.Rd           | 2 +-
|  man/assign_values_to_branches_edgePar.Rd   | 2 +-
|  man/assign_values_to_leaves_edgePar.Rd     | 2 +-
|  man/assign_values_to_leaves_nodePar.Rd     | 2 +-
|  man/assign_values_to_nodes_nodePar.Rd      | 2 +-
|  man/bakers_gamma_for_2_k_matrix.Rd         | 2 +-
|  man/branches_attr_by_clusters.Rd           | 2 +-
|  man/branches_attr_by_labels.Rd             | 2 +-
|  man/click_rotate.Rd                        | 2 +-
|  man/collapse_branch.Rd                     | 2 +-
|  man/color_branches.Rd                      | 2 +-
|  man/color_labels.Rd                        | 2 +-
|  man/colored_bars.Rd                        | 2 +-
|  man/common_subtrees_clusters.Rd            | 2 +-
|  man/cor.dendlist.Rd                        | 2 +-
|  man/cor_FM_index.Rd                        | 2 +-
|  man/cor_bakers_gamma.Rd                    | 2 +-
|  man/cor_common_nodes.Rd                    | 2 +-
|  man/cor_cophenetic.Rd                      | 2 +-
|  man/count_terminal_nodes.Rd                | 2 +-
|  man/cut_lower_fun.Rd                       | 2 +-
|  man/cutree-methods.Rd                      | 2 +-
|  man/cutree_1h.dendrogram.Rd                | 2 +-
|  man/cutree_1k.dendrogram.Rd                | 2 +-
|  man/d3dendro_options.Rd                    | 2 +-
|  man/d3dendrogram.Rd                        | 2 +-
|  man/dend_diff.Rd                           | 2 +-
|  man/dendextend-package.Rd                  | 2 +-
|  man/dendextend_labels.dendrogram.Rd        | 2 +-
|  man/dendextend_options.Rd                  | 2 +-
|  man/dendlist.Rd                            | 2 +-
|  man/dist.dendlist.Rd                       | 2 +-
|  man/dist_long.Rd                           | 2 +-
|  man/distinct_edges.Rd                      | 2 +-
|  man/duplicate_leaf.Rd                      | 2 +-
|  man/entanglement.Rd                        | 2 +-
|  man/fac2num.Rd                             | 2 +-
|  man/fix_members_attr.dendrogram.Rd         | 2 +-
|  man/flatten.dendrogram.Rd                  | 2 +-
|  man/flip_leaves.Rd                         | 2 +-
|  man/get_branches_heights.Rd                | 2 +-
|  man/get_childrens_heights.Rd               | 2 +-
|  man/get_leaves_attr.Rd                     | 2 +-
|  man/get_leaves_branches_attr.Rd            | 2 +-
|  man/get_leaves_branches_col.Rd             | 2 +-
|  man/get_leaves_edgePar.Rd                  | 2 +-
|  man/get_leaves_nodePar.Rd                  | 2 +-
|  man/get_nodes_attr.Rd                      | 2 +-
|  man/get_nodes_xy.Rd                        | 2 +-
|  man/get_root_branches_attr.Rd              | 2 +-
|  man/ggdend.Rd                              | 2 +-
|  man/hang.dendrogram.Rd                     | 2 +-
|  man/heights_per_k.dendrogram.Rd            | 2 +-
|  man/highlight_distinct_edges.Rd            | 2 +-
|  man/identify.dendrogram.Rd                 | 2 +-
|  man/intersect_trees.Rd                     | 2 +-
|  man/is.dendlist.Rd                         | 2 +-
|  man/is.dendrogram.Rd                       | 2 +-
|  man/is.hclust.Rd                           | 2 +-
|  man/is.natural.number.Rd                   | 2 +-
|  man/is.phylo.Rd                            | 2 +-
|  man/is_null_list.Rd                        | 2 +-
|  man/khan.Rd                                | 2 +-
|  man/labels-assign.Rd                       | 2 +-
|  man/labels_colors.Rd                       | 2 +-
|  man/ladderize.Rd                           | 2 +-
|  man/leaf_Colors.Rd                         | 2 +-
|  man/lowest_common_branch.Rd                | 2 +-
|  man/match_order_by_labels.Rd               | 2 +-
|  man/match_order_dendrogram_by_old_order.Rd | 2 +-
|  man/na_locf.Rd                             | 2 +-
|  man/nleaves.Rd                             | 2 +-
|  man/nnodes.Rd                              | 2 +-
|  man/noded_with_condition.Rd                | 2 +-
|  man/order.dendrogram-assign.Rd             | 2 +-
|  man/order.hclust.Rd                        | 2 +-
|  man/partition_leaves.Rd                    | 2 +-
|  man/pipe.Rd                                | 2 +-
|  man/plot_horiz.dendrogram.Rd               | 2 +-
|  man/prune.Rd                               | 2 +-
|  man/prune_common_subtrees.dendlist.Rd      | 2 +-
|  man/prune_leaf.Rd                          | 2 +-
|  man/pvclust_show_signif.Rd                 | 2 +-
|  man/pvclust_show_signif_gradient.Rd        | 2 +-
|  man/raise.dendrogram.Rd                    | 2 +-
|  man/rank_branches.Rd                       | 2 +-
|  man/rank_order.dendrogram.Rd               | 2 +-
|  man/rank_values_with_clusters.Rd           | 2 +-
|  man/rect.dendrogram.Rd                     | 2 +-
|  man/remove_branches_edgePar.Rd             | 2 +-
|  man/remove_leaves_nodePar.Rd               | 2 +-
|  man/remove_nodes_nodePar.Rd                | 2 +-
|  man/rllply.Rd                              | 2 +-
|  man/rotate.Rd                              | 2 +-
|  man/rotate_DendSer.Rd                      | 2 +-
|  man/sample.dendrogram.Rd                   | 2 +-
|  man/shuffle.Rd                             | 2 +-
|  man/sort_2_clusters_vectors.Rd             | 2 +-
|  man/sort_dist_mat.Rd                       | 2 +-
|  man/sort_levels_values.Rd                  | 2 +-
|  man/tanglegram.Rd                          | 2 +-
|  man/theme_dendro.Rd                        | 2 +-
|  man/unbranch.Rd                            | 2 +-
|  man/unclass_dend.Rd                        | 2 +-
|  man/untangle.Rd                            | 2 +-
|  man/untangle_DendSer.Rd                    | 2 +-
|  man/untangle_random_search.Rd              | 2 +-
|  man/untangle_step_rotate_1side.Rd          | 2 +-
|  man/untangle_step_rotate_2side.Rd          | 2 +-
|  man/which_leaf.Rd                          | 2 +-
|  man/which_node.Rd                          | 2 +-
|  126 files changed, 126 insertions(+), 126 deletions(-)

* 2015-06-27(Tal Galili) object -> dend |8a2f94a| 
|  R/set.dendrogram.R | 80 ++++++++++++++++++++++++++--------------------------
|  man/set.Rd         | 16 +++++------
|  2 files changed, 48 insertions(+), 48 deletions(-)

* 2015-06-24(Tal Galili) Added d3heatmap example to vignette + as suggests to DESCRIPTION |f8a4926| 
|  DESCRIPTION                |  1 +
|  vignettes/introduction.Rmd | 33 ++++++++++++++++++++++++++++++++-
|  2 files changed, 33 insertions(+), 1 deletion(-)

* 2015-06-23(Tal Galili) moved assign_dendextend_options to ".onLoad" - this now allows the use of dendextend::some_func |bf35c68| 
|  DESCRIPTION            |  2 +-
|  NEWS                   |  3 ++-
|  R/dendextend_options.R | 45 +++++++++++++++++++++++++++++++++++++++++++--
|  R/zzz.R                | 17 ++++++++++++++---
|  vignettes/FAQ.Rmd      | 13 +++++++++++++
|  5 files changed, 73 insertions(+), 7 deletions(-)

* 2015-06-07(Tal Galili) Added VignetteIndexEntry information (and Sys.Date) |5adda4c| 
|  vignettes/Cluster_Analysis.Rmd | 6 +++++-
|  vignettes/FAQ.Rmd              | 5 +++++
|  vignettes/introduction.Rmd     | 1 +
|  3 files changed, 11 insertions(+), 1 deletion(-)

* 2015-06-07(Tal Galili) Update instructions on viewing the vignette |4ca1df8| 
|  R/zzz.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-06-06(Tal Galili) Better format. |89a8aee| 
|  README.md                                         |  2 +-
|  ...ction.html => Introduction to dendextend.html} | 34 ++++++++++-----------
|  vignettes/introduction.Rmd                        |  4 +--
|  3 files changed, 20 insertions(+), 20 deletions(-)

* 2015-06-06(Tal Galili) misc |b8c68cd| 
|  ChangeLog | 892 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  NEWS.md   |  14 +-
|  2 files changed, 900 insertions(+), 6 deletions(-)

* 2015-06-06(Tal Galili) Fix "CRAN URL not in canonical form" |59b2397| 
|  DESCRIPTION                    |  2 +-
|  R/bk_method.R                  |  2 +-
|  R/colored_bars.R               |  2 +-
|  R/distinct_edges.R             |  2 +-
|  R/ggdendro.R                   |  2 +-
|  R/magrittr.R                   |  4 ++--
|  R/pvclust.R                    |  2 +-
|  README.md                      |  2 +-
|  inst/ignored/introduction.html | 12 ++++++------
|  man/colored_bars.Rd            |  2 +-
|  vignettes/introduction.Rmd     | 12 ++++++------
|  11 files changed, 22 insertions(+), 22 deletions(-)

* 2015-06-06(Tal Galili) Fix " \usage lines wider than 90 characters:" |36a9a84| 
|  R/cor_cophenetic.R    | 4 +++-
|  man/cor_cophenetic.Rd | 4 +++-
|  2 files changed, 6 insertions(+), 2 deletions(-)

* 2015-06-06(Tal Galili) Fix doc problems in cor_cophenetic |f2cd040| 
|  R/cor_cophenetic.R    | 4 ++--
|  man/cor_cophenetic.Rd | 4 ++--
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2015-06-06(Tal Galili) Fix cor_cophenetic.dendlist method |35ce2ce| 
|  R/cor_cophenetic.R | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2015-06-06(Tal Galili) Updated html with the khan analysis |19ca6e7| 
|  ...ts - enhanced with the dendextend package.html | 80 +++++++++++++++++++--
|  1 file changed, 76 insertions(+), 4 deletions(-)

* 2015-06-06(Tal Galili) Added the "khan" dataset analysis. |02db42c| 
|  NEWS                           |   2 +-
|  vignettes/Cluster_Analysis.Rmd | 128 +++++++++++++++++++++++++++++++++++++++
|  2 files changed, 129 insertions(+), 1 deletion(-)

* 2015-06-06(Tal Galili) Added nleaves.dendlist |5ef24b1| 
|  NAMESPACE      |  1 +
|  NEWS           |  1 +
|  R/nleaves.R    | 13 ++++++++++++-
|  man/nleaves.Rd |  5 ++++-
|  4 files changed, 18 insertions(+), 2 deletions(-)

* 2015-06-06(Tal Galili) added - prune_common_subtrees.dendlist - Prune trees to their common subtrees |86b8eb9| 
|  NAMESPACE                             |  1 +
|  NEWS                                  |  2 +-
|  R/prune.R                             | 33 +++++++++++++++++++++++++++++++++
|  man/prune_common_subtrees.dendlist.Rd | 27 +++++++++++++++++++++++++++
|  4 files changed, 62 insertions(+), 1 deletion(-)

* 2015-06-06(Tal Galili) cor_cophenetic - changed method to method_coef (so it could be updated when using cor.dendlist) |f2bd51b| 
|  NEWS                  |  2 +-
|  R/cor_cophenetic.R    | 10 +++++-----
|  man/cor_cophenetic.Rd |  2 +-
|  3 files changed, 7 insertions(+), 7 deletions(-)

* 2015-06-06(Tal Galili) untangle now has a new "labels" method, and it is now the default. |712bcd6| 
|  NEWS            |  1 +
|  R/untangle.R    | 21 ++++++++++++++++-----
|  man/untangle.Rd |  4 ++--
|  3 files changed, 19 insertions(+), 7 deletions(-)

* 2015-06-06(Tal Galili) clean code a bit from comments |becc43e| 
|  R/untangle.R | 557 ++++++++++++++++++++++++++++-----------------------------
|  1 file changed, 273 insertions(+), 284 deletions(-)

* 2015-06-06(Tal Galili) Adding Bk_plot to see also of Bk |674a498| 
|  R/bk_method.R | 2 +-
|  man/Bk.Rd     | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2015-06-06(Tal Galili) Generated by roxygen2 (4.1.1.9000) |7acec1b| 
|  NAMESPACE                                  | 2 +-
|  man/Bk.Rd                                  | 2 +-
|  man/Bk_permutations.Rd                     | 2 +-
|  man/Bk_plot.Rd                             | 2 +-
|  man/DendSer.dendrogram.Rd                  | 2 +-
|  man/FM_index.Rd                            | 2 +-
|  man/FM_index_R.Rd                          | 2 +-
|  man/FM_index_permutation.Rd                | 2 +-
|  man/FM_index_profdpm.Rd                    | 2 +-
|  man/all.equal.dendrogram.Rd                | 2 +-
|  man/all_couple_rotations_at_k.Rd           | 2 +-
|  man/all_unique.Rd                          | 2 +-
|  man/as.dendlist.Rd                         | 2 +-
|  man/as.phylo.dendrogram.Rd                 | 2 +-
|  man/as_hclust_fixed.Rd                     | 2 +-
|  man/assign_dendextend_options.Rd           | 2 +-
|  man/assign_values_to_branches_edgePar.Rd   | 2 +-
|  man/assign_values_to_leaves_edgePar.Rd     | 2 +-
|  man/assign_values_to_leaves_nodePar.Rd     | 2 +-
|  man/assign_values_to_nodes_nodePar.Rd      | 2 +-
|  man/bakers_gamma_for_2_k_matrix.Rd         | 2 +-
|  man/branches_attr_by_clusters.Rd           | 2 +-
|  man/branches_attr_by_labels.Rd             | 2 +-
|  man/click_rotate.Rd                        | 2 +-
|  man/collapse_branch.Rd                     | 2 +-
|  man/color_branches.Rd                      | 2 +-
|  man/color_labels.Rd                        | 2 +-
|  man/colored_bars.Rd                        | 2 +-
|  man/common_subtrees_clusters.Rd            | 2 +-
|  man/cor.dendlist.Rd                        | 2 +-
|  man/cor_FM_index.Rd                        | 2 +-
|  man/cor_bakers_gamma.Rd                    | 2 +-
|  man/cor_common_nodes.Rd                    | 2 +-
|  man/cor_cophenetic.Rd                      | 2 +-
|  man/count_terminal_nodes.Rd                | 2 +-
|  man/cut_lower_fun.Rd                       | 2 +-
|  man/cutree-methods.Rd                      | 2 +-
|  man/cutree_1h.dendrogram.Rd                | 2 +-
|  man/cutree_1k.dendrogram.Rd                | 2 +-
|  man/d3dendro_options.Rd                    | 2 +-
|  man/d3dendrogram.Rd                        | 2 +-
|  man/dend_diff.Rd                           | 2 +-
|  man/dendextend-package.Rd                  | 2 +-
|  man/dendextend_labels.dendrogram.Rd        | 2 +-
|  man/dendextend_options.Rd                  | 2 +-
|  man/dendlist.Rd                            | 2 +-
|  man/dist.dendlist.Rd                       | 2 +-
|  man/dist_long.Rd                           | 2 +-
|  man/distinct_edges.Rd                      | 2 +-
|  man/duplicate_leaf.Rd                      | 2 +-
|  man/entanglement.Rd                        | 2 +-
|  man/fac2num.Rd                             | 2 +-
|  man/fix_members_attr.dendrogram.Rd         | 2 +-
|  man/flatten.dendrogram.Rd                  | 2 +-
|  man/flip_leaves.Rd                         | 2 +-
|  man/get_branches_heights.Rd                | 2 +-
|  man/get_childrens_heights.Rd               | 2 +-
|  man/get_leaves_attr.Rd                     | 2 +-
|  man/get_leaves_branches_attr.Rd            | 2 +-
|  man/get_leaves_branches_col.Rd             | 2 +-
|  man/get_leaves_edgePar.Rd                  | 2 +-
|  man/get_leaves_nodePar.Rd                  | 2 +-
|  man/get_nodes_attr.Rd                      | 2 +-
|  man/get_nodes_xy.Rd                        | 2 +-
|  man/get_root_branches_attr.Rd              | 2 +-
|  man/ggdend.Rd                              | 2 +-
|  man/hang.dendrogram.Rd                     | 2 +-
|  man/heights_per_k.dendrogram.Rd            | 2 +-
|  man/highlight_distinct_edges.Rd            | 2 +-
|  man/identify.dendrogram.Rd                 | 2 +-
|  man/intersect_trees.Rd                     | 2 +-
|  man/is.dendlist.Rd                         | 2 +-
|  man/is.dendrogram.Rd                       | 2 +-
|  man/is.hclust.Rd                           | 2 +-
|  man/is.natural.number.Rd                   | 2 +-
|  man/is.phylo.Rd                            | 2 +-
|  man/is_null_list.Rd                        | 2 +-
|  man/labels-assign.Rd                       | 2 +-
|  man/labels_colors.Rd                       | 2 +-
|  man/ladderize.Rd                           | 2 +-
|  man/leaf_Colors.Rd                         | 2 +-
|  man/lowest_common_branch.Rd                | 2 +-
|  man/match_order_by_labels.Rd               | 2 +-
|  man/match_order_dendrogram_by_old_order.Rd | 2 +-
|  man/na_locf.Rd                             | 2 +-
|  man/nleaves.Rd                             | 2 +-
|  man/nnodes.Rd                              | 2 +-
|  man/noded_with_condition.Rd                | 2 +-
|  man/order.dendrogram-assign.Rd             | 2 +-
|  man/order.hclust.Rd                        | 2 +-
|  man/partition_leaves.Rd                    | 2 +-
|  man/pipe.Rd                                | 2 +-
|  man/plot_horiz.dendrogram.Rd               | 2 +-
|  man/prune.Rd                               | 2 +-
|  man/prune_leaf.Rd                          | 2 +-
|  man/pvclust_show_signif.Rd                 | 2 +-
|  man/pvclust_show_signif_gradient.Rd        | 2 +-
|  man/raise.dendrogram.Rd                    | 2 +-
|  man/rank_branches.Rd                       | 2 +-
|  man/rank_order.dendrogram.Rd               | 2 +-
|  man/rank_values_with_clusters.Rd           | 2 +-
|  man/rect.dendrogram.Rd                     | 2 +-
|  man/remove_branches_edgePar.Rd             | 2 +-
|  man/remove_leaves_nodePar.Rd               | 2 +-
|  man/remove_nodes_nodePar.Rd                | 2 +-
|  man/rllply.Rd                              | 2 +-
|  man/rotate.Rd                              | 2 +-
|  man/rotate_DendSer.Rd                      | 2 +-
|  man/sample.dendrogram.Rd                   | 2 +-
|  man/set.Rd                                 | 2 +-
|  man/shuffle.Rd                             | 2 +-
|  man/sort_2_clusters_vectors.Rd             | 2 +-
|  man/sort_dist_mat.Rd                       | 2 +-
|  man/sort_levels_values.Rd                  | 2 +-
|  man/tanglegram.Rd                          | 2 +-
|  man/theme_dendro.Rd                        | 2 +-
|  man/unbranch.Rd                            | 2 +-
|  man/unclass_dend.Rd                        | 2 +-
|  man/untangle.Rd                            | 2 +-
|  man/untangle_DendSer.Rd                    | 2 +-
|  man/untangle_random_search.Rd              | 2 +-
|  man/untangle_step_rotate_1side.Rd          | 2 +-
|  man/untangle_step_rotate_2side.Rd          | 2 +-
|  man/which_leaf.Rd                          | 2 +-
|  man/which_node.Rd                          | 2 +-
|  125 files changed, 125 insertions(+), 125 deletions(-)

* 2015-06-06(Tal Galili) Adding the khan dataset to the package. |56baf12| 
|  DESCRIPTION   |   3 +-
|  NEWS          |   6 ++--
|  R/data.R      | 104 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  data/khan.rda | Bin 0 -> 114677 bytes
|  man/khan.Rd   |  80 +++++++++++++++++++++++++++++++++++++++++++
|  5 files changed, 189 insertions(+), 4 deletions(-)

* 2015-06-06(Tal Galili) more links |e14dc3a| 
|  README.md | 6 ++----
|  1 file changed, 2 insertions(+), 4 deletions(-)

* 2015-06-06(Tal Galili) update links to the newer vignettes |b56e833| 
|  README.md                      |  6 ++++--
|  vignettes/Cluster_Analysis.Rmd | 14 ++++++++++++++
|  2 files changed, 18 insertions(+), 2 deletions(-)

* 2015-06-06(Tal Galili) got "codecov.io" to work. |a4e4443| 
|  README.md | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-06-05(Tal Galili) adding covr (to try to get some code coverage) |112fca3| 
|  DESCRIPTION | 3 ++-
|  1 file changed, 2 insertions(+), 1 deletion(-)

* 2015-06-05(Tal Galili) update travis.yml - Change lang to r (and some more things), and see if it still works. |21e5d93| 
|  .travis.yml | 31 ++++++-------------------------
|  1 file changed, 6 insertions(+), 25 deletions(-)

* 2015-05-24(Tal Galili) Date |e9dfd54| 
|  DESCRIPTION | 2 +-
|  NEWS        | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2015-05-24(Tal Galili) Update news since version 0.18.3 |424cd2b| 
|  NEWS.md | 105 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 105 insertions(+)

* 2015-05-24(Tal Galili) fix typos |7cb02c6| 
|  vignettes/introduction.Rmd | 12 ++++++------
|  1 file changed, 6 insertions(+), 6 deletions(-)

* 2015-05-24(Tal Galili) updated vignettes to have smaller dpi (so that the file sizes will be more reasonable) |39e3c21| 
|  vignettes/Cluster_Analysis.Rmd |  6 +++---
|  vignettes/FAQ.Rmd              | 15 +++++++++++++++
|  vignettes/introduction.Rmd     |  8 ++++----
|  3 files changed, 22 insertions(+), 7 deletions(-)

* 2015-05-24(Tal Galili) html versions of the vignettes |a2204c5| 
|  inst/ignored/Frequantly asked questions.html      | 325 +++++++++++
|  ...ts - enhanced with the dendextend package.html | 574 ++++++++++++++++++++
|  inst/ignored/introduction.html                    | 412 ++++----------
|  3 files changed, 1014 insertions(+), 297 deletions(-)

* 2015-05-24(Tal Galili) misc |4718cb5| 
|  vignettes/Cluster_Analysis.Rmd | 1 +
|  1 file changed, 1 insertion(+)

* 2015-05-24(Tal Galili) Fix typos |6334236| 
|  vignettes/Cluster_Analysis.Rmd | 24 ++++++++++++------------
|  1 file changed, 12 insertions(+), 12 deletions(-)

* 2015-05-24(Tal Galili) Added "animals - Attributes of Animals" section to cluster_analysis.Rmd |5dd94fc| 
|  NEWS                           |   1 +
|  vignettes/Cluster_Analysis.Rmd | 115 +++++++++++++++++++++++++++++++++++++++
|  2 files changed, 116 insertions(+)

* 2015-05-24(Tal Galili) cor_FM_index - Correlation of FM_index for some k (similar to Bk actually). This is added to cor.dendlist |58eeedc| 
|  NAMESPACE           |  1 +
|  NEWS                |  3 +++
|  R/cor.dendlist.R    | 59 +++++++++++++++++++++++++++++++++++++++++++++------
|  man/cor.dendlist.Rd | 10 +++++----
|  man/cor_FM_index.Rd | 39 ++++++++++++++++++++++++++++++++++
|  5 files changed, 101 insertions(+), 11 deletions(-)

* 2015-05-24(Tal Galili) added "cluster" as suggest |b6b1d35| 
|  DESCRIPTION | 3 ++-
|  1 file changed, 2 insertions(+), 1 deletion(-)

* 2015-05-24(Tal Galili) Vignette - added the votes.repub analysis (Votes for Republican Candidate in Presidential Elections) |9ddce80| 
|  vignettes/Cluster_Analysis.Rmd | 205 ++++++++++++++++++++++++++++++++++++++-
|  1 file changed, 200 insertions(+), 5 deletions(-)

* 2015-05-24(Tal Galili) exclude any cache folder in vignette or git |fbd747b| 
|  .Rbuildignore | 1 +
|  .gitignore    | 2 +-
|  2 files changed, 2 insertions(+), 1 deletion(-)

* 2015-05-24(Tal Galili) remove un-needed new line (cat("\n")) |062c9c4| 
|  inst/tests/test-distinct_edges.R | 2 +-
|  inst/tests/test-entanglement.R   | 2 +-
|  inst/tests/test-ggdend.R         | 2 +-
|  3 files changed, 3 insertions(+), 3 deletions(-)

* 2015-05-24(Tal Galili) added a link to cor_common_nodes from cor.dendlist |4844174| 
|  R/cor.dendlist.R    | 3 ++-
|  man/cor.dendlist.Rd | 3 ++-
|  2 files changed, 4 insertions(+), 2 deletions(-)

* 2015-05-24(Tal Galili) untangle_random_search/untangle_step_rotate_2side/untangle_best_k_to_rotate_by_2side_backNforth - |c9129c6| 
|  NEWS         | 3 ++-
|  R/untangle.R | 6 +++---
|  2 files changed, 5 insertions(+), 4 deletions(-)

* 2015-05-24(Tal Galili) Added Iris analysis to cluster_analysis.Rmd |e444b56| 
|  vignettes/Cluster_Analysis.Rmd | 293 ++++++++++++++++++++++++++++++++++-----
|  1 file changed, 261 insertions(+), 32 deletions(-)

* 2015-05-24(Tal Galili) misc |e404aa9| 
|  R/color_branches.R | 4 +++-
|  R/tanglegram.R     | 1 +
|  R/zzz.R            | 3 +++
|  man/tanglegram.Rd  | 3 ++-
|  4 files changed, 9 insertions(+), 2 deletions(-)

* 2015-05-24(Tal Galili) a warning for a common bug that happened. |6a16ace| 
|  R/branches_attr_by.R | 4 ++++
|  1 file changed, 4 insertions(+)

* 2015-05-24(Tal Galili) cor_common_nodes - a new correlation measure between dendrograms. |4b2410a| 
|  NAMESPACE               |  1 +
|  NEWS                    |  1 +
|  R/cor.dendlist.R        | 60 +++++++++++++++++++++++++++++++++++++++++++----
|  man/cor.dendlist.Rd     |  6 ++---
|  man/cor_common_nodes.Rd | 43 +++++++++++++++++++++++++++++++++
|  5 files changed, 104 insertions(+), 7 deletions(-)

* 2015-05-24(Tal Galili) Moved FAQ from introduction.Rmd to FAQ.Rmd |f20096a| 
|  NEWS                       |   2 +-
|  vignettes/FAQ.Rmd          | 818 +++++++++++++++++++++++++++++++++++++++++++
|  vignettes/introduction.Rmd | 809 ------------------------------------------
|  3 files changed, 819 insertions(+), 810 deletions(-)

* 2015-05-24(Tal Galili) set - added "rank_branches" |33e838c| 
|  NEWS               | 2 ++
|  R/set.dendrogram.R | 3 +++
|  man/set.Rd         | 1 +
|  3 files changed, 6 insertions(+)

* 2015-05-24(Tal Galili) tanglegram - new parameter: faster. |728deab| 
|  NEWS              |  4 +++-
|  R/tanglegram.R    | 10 ++++++++++
|  man/tanglegram.Rd |  4 ++++
|  3 files changed, 17 insertions(+), 1 deletion(-)

* 2015-05-24(Tal Galili) moved lines to their right place. |085aff4| 
|  NEWS | 12 ++++++------
|  1 file changed, 6 insertions(+), 6 deletions(-)

* 2015-05-24(Tal Galili) move a line around. |aba3dfb| 
|  R/tanglegram.R | 5 ++++-
|  1 file changed, 4 insertions(+), 1 deletion(-)

* 2015-05-24(Tal Galili) untangle.dendlist - now preserve the names in the dendlist |cf5a1ae| 
|  NEWS         | 4 +++-
|  R/untangle.R | 4 ++++
|  2 files changed, 7 insertions(+), 1 deletion(-)

* 2015-05-24(Tal Galili) Added MASS (for using parcoord in the examples) |6f34c1a| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-05-24(Tal Galili) dendlist - added the `which` parameter (for indicating which elements in the dendlist to pick out) |f6edbbc| 
|  NEWS            |  1 +
|  R/dendlist.R    | 18 +++++++++++++++---
|  man/dendlist.Rd | 11 +++++++----
|  3 files changed, 23 insertions(+), 7 deletions(-)

* 2015-05-24(Tal Galili) untangle.dendlist - can now return a dendlist with more than two elements. |9fe8e48| 
|  NEWS            |  1 +
|  R/untangle.R    | 13 ++++++++++++-
|  man/untangle.Rd |  3 +++
|  3 files changed, 16 insertions(+), 1 deletion(-)

* 2015-05-24(Tal Galili) ladderize - added the `which` parameter (for indicating which elements in the dendlist to ladderize) |4f93598| 
|  NEWS             |  1 +
|  R/rotate.R       | 14 ++++++++++----
|  man/ladderize.Rd |  6 +++++-
|  3 files changed, 16 insertions(+), 5 deletions(-)

* 2015-05-24(Tal Galili) remove the warning when creating an empty dendlist |532fb37| 
|  NEWS                       |  2 +-
|  R/dendlist.R               |  2 +-
|  inst/tests/test-dendlist.R | 25 ++++++++++++++-----------
|  3 files changed, 16 insertions(+), 13 deletions(-)

* 2015-05-23(Tal Galili) Rename file to be "cluster analysis" |aa156c6| 
|  vignettes/{Iris_Analysis.Rmd => Cluster_Analysis.Rmd} | 15 +++++++++++++++
|  1 file changed, 15 insertions(+)

* 2015-05-23(Tal Galili) Moved the "Iris analysis" from the introduction vignette to a seperate Rmd file. |25ed06f| 
|  vignettes/Iris_Analysis.Rmd | 88 +++++++++++++++++++++++++++++++++++++++++++
|  vignettes/introduction.Rmd  | 83 ----------------------------------------
|  2 files changed, 88 insertions(+), 83 deletions(-)

* 2015-05-23(Tal Galili) Added some explenations of the tanglegram when used with the coloring of the branches and lines. |8c639f4| 
|  vignettes/introduction.Rmd | 54 ++++++++++++++++++++++++++++++++++++++------
|  1 file changed, 47 insertions(+), 7 deletions(-)

* 2015-05-23(Tal Galili) Added tests for rank_values_with_clusters |b6660a5| 
|  NEWS                              |  2 +-
|  inst/tests/test-common_subtrees.R | 49 +++++++++++++++++++++++++++++++++++++
|  2 files changed, 50 insertions(+), 1 deletion(-)

* 2015-05-23(Tal Galili) added context |0e3ae60| 
|  inst/tests/test-dendlist.R | 3 +++
|  1 file changed, 3 insertions(+)

* 2015-05-23(Tal Galili) Decided this will be version 1.0.0 and not 0.19.0 |25c19e1| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 2 +-
|  2 files changed, 3 insertions(+), 3 deletions(-)

* 2015-05-23(Tal Galili) Fix "common_subtrees_color_branches" to make sure everyone are using the same colors. |36f22d3| 
|  R/tanglegram.R    | 75 ++++++++++++++++++++++++++++++++++-------------------
|  man/tanglegram.Rd | 10 ++++---
|  2 files changed, 55 insertions(+), 30 deletions(-)

* 2015-05-23(Tal Galili) color_branches - now uses branches_attr_by_clusters with "all" labels needing to fit a group for the branches to be colors. |9e27f28| 
|  R/color_branches.R | 3 ++-
|  1 file changed, 2 insertions(+), 1 deletion(-)

* 2015-05-23(Tal Galili)    * branches_attr_by_clusters -       * can now accept a vector of values with the length of the labels.       * new parameter "branches_changed_have_which_labels" - allows the user the decide if the change in parameters will be for branches with all/any of the labels (useful for tanglegram - since we would like to color common subtrees with all of the labels, not just any.) |b2fd1d0| 
|  NEWS                             |  4 +++
|  R/branches_attr_by.R             | 70 ++++++++++++++++++++++++++++++++------
|  man/branches_attr_by_clusters.Rd | 16 +++++++--
|  3 files changed, 77 insertions(+), 13 deletions(-)

* 2015-05-23(Tal Galili) Added rank_values_with_clusters - Rank a vector based on clusters (important for various functions.) |97787ac| 
|  NAMESPACE                        |  1 +
|  NEWS                             |  2 +-
|  R/common_subtrees.R              | 52 ++++++++++++++++++++++++++++++++++----
|  man/rank_values_with_clusters.Rd | 37 +++++++++++++++++++++++++++
|  4 files changed, 86 insertions(+), 6 deletions(-)

* 2015-05-22(Tal Galili) Fix: ggplot.ggdend: no visible global function definition for |ff33554| 
|  R/ggdend.R | 1 +
|  1 file changed, 1 insertion(+)

* 2015-05-22(Tal Galili) Fix: Codoc mismatches from documentation object 'ggdend': |7161cd7| 
|  R/ggdend.R    | 6 ++++--
|  man/ggdend.Rd | 5 ++++-
|  2 files changed, 8 insertions(+), 3 deletions(-)

* 2015-05-22(Tal Galili) fix: \examples lines wider than 100 characters: |ca11269| 
|  R/attr_access.R                          | 4 +++-
|  man/assign_values_to_branches_edgePar.Rd | 4 +++-
|  2 files changed, 6 insertions(+), 2 deletions(-)

* 2015-05-22(Tal Galili) added test for ggdend |d00f01a| 
|  inst/tests/test-ggdend.R | 50 ++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 50 insertions(+)

* 2015-05-22(Tal Galili) added get_nodes_attr test |788def3| 
|  inst/tests/test-attr_access.R | 13 +++++++++++++
|  1 file changed, 13 insertions(+)

* 2015-05-22(Tal Galili) plot.ggdend - added support to plot nodes |bd2e1a9| 
|  NEWS       |  4 +++-
|  R/ggdend.R | 28 +++++++++++++++++++++++++++-
|  2 files changed, 30 insertions(+), 2 deletions(-)

* 2015-05-22(Tal Galili) Fix ggdend to now deal with edgePar and nodePar being lists. (now the vignette doesn't crash) |d20f2d0| 
|  R/ggdend.R | 57 ++++++++++++++++++++++++++++++++++++++++++++++++---------
|  1 file changed, 48 insertions(+), 9 deletions(-)

* 2015-05-22(Tal Galili) Fix test to now account for edgePar and nodePar are lists. |2c608bf| 
|  inst/tests/test-attr_access.R      |  4 +++-
|  inst/tests/test-branches_attr_by.R | 10 ++++++++++
|  inst/tests/test-set.dendrogram.R   | 15 ++++++++-------
|  3 files changed, 21 insertions(+), 8 deletions(-)

* 2015-05-22(Tal Galili) made sure that the end of the vector in "dendextend_heights_per_k.dendrogram" will give the tree size (and not 0) as its name. |60cac76| 
|  R/cutree.dendrogram.R               |  5 +++++
|  inst/tests/test-cutree.dendrogram.R | 30 +++++++++++++++++++++++++++++-
|  2 files changed, 34 insertions(+), 1 deletion(-)

* 2015-05-22(Tal Galili) Date |f5ef241| 
|  NEWS | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-05-22(Tal Galili) Fix link |adeabab| 
|  vignettes/introduction.Rmd | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-05-22(Tal Galili) Date |5dbf21c| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-05-22(Tal Galili) Parameters are now stored as a list for (allows for branches to have colors/linetype/linewidth, some are numeric and some character): assign_values_to_branches_edgePar / assign_values_to_leaves_nodePar / assign_values_to_leaves_edgePar / assign_values_to_nodes_nodePar - the parameters are stored as a list in edgePar/nodePar (instead of a vector). Discovered thanks to Martin Maechler.  Fixes: "Error in segments(x0, y0, x1, y1, col = col, lty = lty, lwd = lwd) : invalid line type: must be length 2, 4, 6 or 8" |4bf8f20| 
|  NEWS                                     |  2 ++
|  R/attr_access.R                          | 29 +++++++++++++++++++++--------
|  inst/tests/test-branches_attr_by.R       | 23 +++++++++++++++++------
|  man/assign_values_to_branches_edgePar.Rd | 14 +++++++++++++-
|  tests/test-all.R                         | 16 ++++++++++++----
|  5 files changed, 65 insertions(+), 19 deletions(-)

* 2015-05-22(Tal Galili) Added doc to common_subtrees_clusters |a6b4cb0| 
|  NAMESPACE                       |  1 +
|  R/common_subtrees.R             | 53 +++++++++++++++++++++++----------------
|  man/common_subtrees_clusters.Rd | 44 ++++++++++++++++++++++++++++++++
|  3 files changed, 77 insertions(+), 21 deletions(-)

* 2015-05-22(Tal Galili) tanglegram - have doc match code. |d86f957| 
|  R/tanglegram.R    | 7 ++++---
|  man/tanglegram.Rd | 4 +++-
|  2 files changed, 7 insertions(+), 4 deletions(-)

* 2015-05-22(Tal Galili) Fix "color_branches: no visible binding for global variable 'cols'" |64a8bba| 
|  R/color_branches.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-05-22(Tal Galili) labels.dendrogram is now working through dendextend_options("labels.dendrogram"). The defualt is the new dendextend_labels.dendrogram (which is just stats:::labels.dendrogram), but this allows the package dendextendRcpp to change the function used by the package (without masking the function in base R) - thus making both me, and CRAN, happy :) |ae602a9| 
|  NAMESPACE                           |  1 +
|  NEWS                                |  4 +++-
|  R/dendextend_options.R              |  1 +
|  R/stats_imports.R                   | 35 +++++++++++++++++++++++++++++++++++
|  R/zzz.R                             |  4 +++-
|  man/dendextend_labels.dendrogram.Rd | 28 ++++++++++++++++++++++++++++
|  6 files changed, 71 insertions(+), 2 deletions(-)

* 2015-05-22(Tal Galili) rect.dendrogram - deals with the case we want to use k for which k+1 is not defined. |61eeded| 
|  NEWS                              |  3 ++-
|  R/rect.dendrogram.R               | 21 +++++++++++++++++++--
|  inst/tests/test-rect.dendrogram.R | 26 ++++++++++++++++++++++++++
|  man/rect.dendrogram.Rd            |  8 ++++++++
|  4 files changed, 55 insertions(+), 3 deletions(-)

* 2015-05-19(Tal Galili) tanglegram - Added new parameters: common_subtrees_color_lines and common_subtrees_color_branches to color connecting-lines and/or the dendrograms themsleves, to help detect commonly shared subtrees. |7394cba| 
|  NEWS              |  2 +-
|  R/tanglegram.R    | 72 +++++++++++++++++++++++++++++++++++++++++++++++++++--
|  man/tanglegram.Rd | 29 +++++++++++++++++++++
|  3 files changed, 100 insertions(+), 3 deletions(-)

* 2015-05-19(Tal Galili) common_subtrees_clusters - a (currently hidden) function to get clusters for labels of common subtrees between two trees. |22c3235| 
|  NEWS                  |   3 +
|  R/common_subtrees.R   | 175 ++++++++++++++++++++++++++++++++++++++++++++++++
|  man/distinct_edges.Rd |   1 +
|  tests/test-all.R      |   2 -
|  4 files changed, 179 insertions(+), 2 deletions(-)

* 2015-05-18(Tal Galili) tanglegram - turned "highlight_distinct_edges = FALSE". This is due to a bug in R that causes plot.dendrogram to crash when trying to plot a tree with both lty and some character color for the branch. |cfebab3| 
|  NEWS           | 2 +-
|  R/tanglegram.R | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2015-05-18(Tal Galili) color_branches - gained a new "cluster" parameter to allow for easy uneven coloring of branches (using branches_attr_by_clusters). This is not a new feature, as it is an attempt to have the user access more options from one place (i.e.: color_branches). |5d601b0| 
|  DESCRIPTION                      |  2 +-
|  NEWS                             |  6 ++-
|  R/branches_attr_by.R             |  2 +-
|  R/color_branches.R               | 81 ++++++++++++++++++++++++++++----------
|  man/branches_attr_by_clusters.Rd |  2 +-
|  man/color_branches.Rd            | 20 +++++++++-
|  6 files changed, 87 insertions(+), 26 deletions(-)

* 2015-05-18(Tal Galili) roxygen2 (4.0.2) -> roxygen2 (4.1.1) |81c0709| 
|  NAMESPACE                                  | 2 +-
|  man/Bk.Rd                                  | 3 ++-
|  man/Bk_permutations.Rd                     | 3 ++-
|  man/Bk_plot.Rd                             | 3 ++-
|  man/DendSer.dendrogram.Rd                  | 3 ++-
|  man/FM_index.Rd                            | 3 ++-
|  man/FM_index_R.Rd                          | 3 ++-
|  man/FM_index_permutation.Rd                | 3 ++-
|  man/FM_index_profdpm.Rd                    | 3 ++-
|  man/all.equal.dendrogram.Rd                | 3 ++-
|  man/all_couple_rotations_at_k.Rd           | 3 ++-
|  man/all_unique.Rd                          | 3 ++-
|  man/as.dendlist.Rd                         | 3 ++-
|  man/as.phylo.dendrogram.Rd                 | 3 ++-
|  man/as_hclust_fixed.Rd                     | 3 ++-
|  man/assign_dendextend_options.Rd           | 3 ++-
|  man/assign_values_to_branches_edgePar.Rd   | 3 ++-
|  man/assign_values_to_leaves_edgePar.Rd     | 3 ++-
|  man/assign_values_to_leaves_nodePar.Rd     | 3 ++-
|  man/assign_values_to_nodes_nodePar.Rd      | 3 ++-
|  man/bakers_gamma_for_2_k_matrix.Rd         | 3 ++-
|  man/branches_attr_by_clusters.Rd           | 3 ++-
|  man/branches_attr_by_labels.Rd             | 3 ++-
|  man/click_rotate.Rd                        | 3 ++-
|  man/collapse_branch.Rd                     | 3 ++-
|  man/color_branches.Rd                      | 3 ++-
|  man/color_labels.Rd                        | 3 ++-
|  man/colored_bars.Rd                        | 3 ++-
|  man/cor.dendlist.Rd                        | 3 ++-
|  man/cor_bakers_gamma.Rd                    | 3 ++-
|  man/cor_cophenetic.Rd                      | 3 ++-
|  man/count_terminal_nodes.Rd                | 3 ++-
|  man/cut_lower_fun.Rd                       | 3 ++-
|  man/cutree-methods.Rd                      | 3 ++-
|  man/cutree_1h.dendrogram.Rd                | 3 ++-
|  man/cutree_1k.dendrogram.Rd                | 3 ++-
|  man/d3dendro_options.Rd                    | 3 ++-
|  man/d3dendrogram.Rd                        | 3 ++-
|  man/dend_diff.Rd                           | 3 ++-
|  man/dendextend-package.Rd                  | 3 ++-
|  man/dendextend_options.Rd                  | 3 ++-
|  man/dendlist.Rd                            | 3 ++-
|  man/dist.dendlist.Rd                       | 3 ++-
|  man/dist_long.Rd                           | 3 ++-
|  man/distinct_edges.Rd                      | 3 ++-
|  man/duplicate_leaf.Rd                      | 3 ++-
|  man/entanglement.Rd                        | 3 ++-
|  man/fac2num.Rd                             | 3 ++-
|  man/fix_members_attr.dendrogram.Rd         | 3 ++-
|  man/flatten.dendrogram.Rd                  | 3 ++-
|  man/flip_leaves.Rd                         | 3 ++-
|  man/get_branches_heights.Rd                | 3 ++-
|  man/get_childrens_heights.Rd               | 3 ++-
|  man/get_leaves_attr.Rd                     | 3 ++-
|  man/get_leaves_branches_attr.Rd            | 3 ++-
|  man/get_leaves_branches_col.Rd             | 3 ++-
|  man/get_leaves_edgePar.Rd                  | 3 ++-
|  man/get_leaves_nodePar.Rd                  | 3 ++-
|  man/get_nodes_attr.Rd                      | 3 ++-
|  man/get_nodes_xy.Rd                        | 3 ++-
|  man/get_root_branches_attr.Rd              | 3 ++-
|  man/ggdend.Rd                              | 3 ++-
|  man/hang.dendrogram.Rd                     | 3 ++-
|  man/heights_per_k.dendrogram.Rd            | 3 ++-
|  man/highlight_distinct_edges.Rd            | 3 ++-
|  man/identify.dendrogram.Rd                 | 3 ++-
|  man/intersect_trees.Rd                     | 3 ++-
|  man/is.dendlist.Rd                         | 3 ++-
|  man/is.dendrogram.Rd                       | 3 ++-
|  man/is.hclust.Rd                           | 3 ++-
|  man/is.natural.number.Rd                   | 3 ++-
|  man/is.phylo.Rd                            | 3 ++-
|  man/is_null_list.Rd                        | 3 ++-
|  man/labels-assign.Rd                       | 3 ++-
|  man/labels_colors.Rd                       | 3 ++-
|  man/ladderize.Rd                           | 3 ++-
|  man/leaf_Colors.Rd                         | 3 ++-
|  man/lowest_common_branch.Rd                | 3 ++-
|  man/match_order_by_labels.Rd               | 3 ++-
|  man/match_order_dendrogram_by_old_order.Rd | 3 ++-
|  man/na_locf.Rd                             | 3 ++-
|  man/nleaves.Rd                             | 3 ++-
|  man/nnodes.Rd                              | 3 ++-
|  man/noded_with_condition.Rd                | 3 ++-
|  man/order.dendrogram-assign.Rd             | 3 ++-
|  man/order.hclust.Rd                        | 3 ++-
|  man/partition_leaves.Rd                    | 3 ++-
|  man/pipe.Rd                                | 3 ++-
|  man/plot_horiz.dendrogram.Rd               | 3 ++-
|  man/prune.Rd                               | 3 ++-
|  man/prune_leaf.Rd                          | 3 ++-
|  man/pvclust_show_signif.Rd                 | 3 ++-
|  man/pvclust_show_signif_gradient.Rd        | 3 ++-
|  man/raise.dendrogram.Rd                    | 3 ++-
|  man/rank_branches.Rd                       | 3 ++-
|  man/rank_order.dendrogram.Rd               | 3 ++-
|  man/rect.dendrogram.Rd                     | 3 ++-
|  man/remove_branches_edgePar.Rd             | 3 ++-
|  man/remove_leaves_nodePar.Rd               | 3 ++-
|  man/remove_nodes_nodePar.Rd                | 3 ++-
|  man/rllply.Rd                              | 3 ++-
|  man/rotate.Rd                              | 3 ++-
|  man/rotate_DendSer.Rd                      | 3 ++-
|  man/sample.dendrogram.Rd                   | 3 ++-
|  man/set.Rd                                 | 3 ++-
|  man/shuffle.Rd                             | 3 ++-
|  man/sort_2_clusters_vectors.Rd             | 3 ++-
|  man/sort_dist_mat.Rd                       | 3 ++-
|  man/sort_levels_values.Rd                  | 3 ++-
|  man/tanglegram.Rd                          | 6 ++++--
|  man/theme_dendro.Rd                        | 3 ++-
|  man/unbranch.Rd                            | 3 ++-
|  man/unclass_dend.Rd                        | 3 ++-
|  man/untangle.Rd                            | 3 ++-
|  man/untangle_DendSer.Rd                    | 3 ++-
|  man/untangle_random_search.Rd              | 3 ++-
|  man/untangle_step_rotate_1side.Rd          | 3 ++-
|  man/untangle_step_rotate_2side.Rd          | 3 ++-
|  man/which_leaf.Rd                          | 3 ++-
|  man/which_node.Rd                          | 3 ++-
|  120 files changed, 241 insertions(+), 121 deletions(-)

* 2015-05-18(Tal Galili) tanglegram - tiny clarification about color_lines |3fe5dd9| 
|  R/tanglegram.R | 1 +
|  1 file changed, 1 insertion(+)

* 2015-05-18(Tal Galili) distinct_edges - a simpler R code |47975fb| 
|  R/distinct_edges.R | 6 ++++--
|  1 file changed, 4 insertions(+), 2 deletions(-)

* 2015-05-18(Tal Galili) Fix: as.hclust.pvclust: no visible binding for global variable ‘object’ |c3ada78| 
|  R/pvclust.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-05-17(Tal Galili) Fix coveralls badge |c5fcb1c| 
|  README.md | 4 +---
|  1 file changed, 1 insertion(+), 3 deletions(-)

* 2015-05-17(Tal Galili) Added coveralls and CRAN status |6948645| 
|  .travis.yml | 4 ++++
|  NEWS        | 2 ++
|  README.md   | 3 +++
|  3 files changed, 9 insertions(+)

* 2015-05-17(Tal Galili) Added Code of conduct |fd5a95a| 
|  .Rbuildignore |  3 ++-
|  CONDUCT.md    | 25 +++++++++++++++++++++++++
|  NEWS          |  5 +++++
|  R/zzz.R       | 11 +++++++++++
|  README.md     |  6 ++++++
|  5 files changed, 49 insertions(+), 1 deletion(-)

* 2015-05-17(Tal Galili)  Fix "Objects in \usage without \alias in documentation object". For ‘prune.rpart’ and ‘sort.dendlist’. |872678a| 
|  NEWS          | 1 +
|  R/prune.R     | 1 +
|  R/rotate.R    | 1 +
|  man/prune.Rd  | 1 +
|  man/rotate.Rd | 1 +
|  5 files changed, 5 insertions(+)

* 2015-05-17(Tal Galili) as.hclust.pvclust - use "x" instead of "object", to avoid "checking S3 generic/method consistency ... WARNING" |12c1c08| 
|  NEWS        | 1 +
|  R/pvclust.R | 2 +-
|  2 files changed, 2 insertions(+), 1 deletion(-)

* 2015-05-17(Tal Galili) Fix "'::' or ':::' import not declared from: ‘rpart’" by adding rpart to DESCRIPTION. |e8a85e7| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 8 ++++++++
|  2 files changed, 10 insertions(+), 2 deletions(-)

* 2015-05-17(Tal Galili) version bump 0.18.8 |ca2a085| 
|  DESCRIPTION | 2 +-
|  NEWS        | 2 +-
|  README.md   | 4 ++--
|  3 files changed, 4 insertions(+), 4 deletions(-)

* 2015-05-17(Tal Galili) identify.dendrogram - parameter horiz now works (fixes #4) |0cf59c3| 
|  NEWS                       |  3 +++
|  R/rect.dendrogram.R        | 16 +++++++++++++---
|  man/identify.dendrogram.Rd |  6 +++++-
|  3 files changed, 21 insertions(+), 4 deletions(-)

* 2015-05-16(Tal Galili) tiny fix |117e2b2| 
|  README.md | 1 +
|  1 file changed, 1 insertion(+)

* 2015-05-16(Tal Galili) Another tweak to the install of packages |9afdd03| 
|  README.md | 10 ++++++----
|  1 file changed, 6 insertions(+), 4 deletions(-)

* 2015-05-16(Tal Galili) Simplafy github installation code a bit. |29215cb| 
|  README.md | 15 ++++-----------
|  1 file changed, 4 insertions(+), 11 deletions(-)

* 2015-05-16(Tal Galili) Added a Vectorize example (fixes #6) |df95472| 
|  R/rect.dendrogram.R    | 2 ++
|  man/rect.dendrogram.Rd | 2 ++
|  2 files changed, 4 insertions(+)

* 2015-05-16(Tal Galili) rect.dendrogram - make the heights of the rects be in the middle of the two clusters so that they would look nicer. Added prop_k_height to state which proportion of the height the rect should be (between k and k+1 heights). Also added upper_rect to allow the user to customize the exact height. (this closes issue #6) |4526d46| 
|  DESCRIPTION            |  7 ++++---
|  NEWS                   |  4 ++--
|  R/rect.dendrogram.R    | 16 +++++++++++++---
|  man/rect.dendrogram.Rd |  7 ++++++-
|  4 files changed, 25 insertions(+), 9 deletions(-)

* 2015-05-15(Tal Galili) all.equal.dendrogram - suppress warning for a dend with only 1 item, when using dendextendRcpp. |fb8515c| 
|  NEWS                            |  1 +
|  R/all.equal.R                   | 17 +++++++++++++++--
|  inst/tests/test-cut_lower_fun.R | 14 ++++++++++----
|  3 files changed, 26 insertions(+), 6 deletions(-)

* 2015-05-15(Tal Galili) Fix comments' text |1d22f77| 
|  R/cutree.dendrogram.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-05-15(Tal Galili) all.equal.dendlist - can now compare two dendlist objects to one another, and not only the dendrograms inside one dendlist. (also added new tests that all.equal.dendlist works) |c581e1b| 
|  NEWS                        |  7 +++++++
|  R/all.equal.R               | 19 +++++++++++++++++++
|  inst/tests/test-dendlist.R  | 32 +++++++++++++++++++++++++++++++-
|  man/all.equal.dendrogram.Rd |  5 +++++
|  4 files changed, 62 insertions(+), 1 deletion(-)

* 2015-05-15(Tal Galili) Test commit |6449eb7| 
|  tests/test-all.R | 3 +++
|  1 file changed, 3 insertions(+)

* 2015-05-06(Tal Galili) remove dependancy in VIGNETTE on DendSer (using require instead of library) - bump to 0.18.7 |49a073f| 
|  DESCRIPTION                |  7 +++----
|  NEWS                       |  2 ++
|  vignettes/introduction.Rmd | 30 ++++++++++++++++++------------
|  3 files changed, 23 insertions(+), 16 deletions(-)

* 2015-05-06(Tal Galili) ladderize instead of rotate_DendSer - in the example |729903b| 
|  R/set.dendrogram.R | 4 ++--
|  man/set.Rd         | 4 ++--
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2015-05-06(Tal Galili) tanglegram.dendlist - fix it when names is null to have the default be "" |8dbea82| 
|  NEWS           | 1 +
|  R/tanglegram.R | 5 ++++-
|  2 files changed, 5 insertions(+), 1 deletion(-)

* 2015-05-06(Tal Galili) untangle - added method="ladderize" |0c04568| 
|  NEWS            |  7 +++++++
|  R/untangle.R    | 11 ++++++-----
|  man/untangle.Rd |  4 ++--
|  3 files changed, 15 insertions(+), 7 deletions(-)

* 2015-04-25(Tal Galili) library corrplot added to plot cor.dendlist results. Examples added to vignette and function's example. |aea94bc| 
|  DESCRIPTION                | 3 ++-
|  NEWS                       | 3 ++-
|  R/cor.dendlist.R           | 8 +++++++-
|  man/cor.dendlist.Rd        | 8 +++++++-
|  vignettes/introduction.Rmd | 9 +++++++++
|  5 files changed, 27 insertions(+), 4 deletions(-)

* 2015-04-25(Tal Galili) tanglegram.dendlist - now gets main_left and main_right (if they are null) from the names in dendlist (if they exist) |7cc9037| 
|  NEWS              |  3 +++
|  R/tanglegram.R    | 14 +++++++++++---
|  man/tanglegram.Rd |  2 +-
|  3 files changed, 15 insertions(+), 4 deletions(-)

* 2015-04-25(Tal Galili) added example for using "get_leaves_branches_col" in "How to color the branches in heatmap.2?" |c30208f| 
|  NEWS                       | 3 +++
|  vignettes/introduction.Rmd | 8 +++++++-
|  2 files changed, 10 insertions(+), 1 deletion(-)

* 2015-04-25(Tal Galili) Fix get_leaves_branches_attr and also make it simpler. |6017490| 
|  R/attr_access.R | 12 ++++--------
|  1 file changed, 4 insertions(+), 8 deletions(-)

* 2015-04-25(Tal Galili) NEW FUNCTIONS: (version 0.18.6)    * get_leaves_edgePar - Get edgePar of dendrogram's leaves    * get_leaves_branches_attr - Get an attribute of the branches of a dendrogram's leaves    * get_leaves_branches_col - Get the colors of the branches of a dendrogram's leaves. This function is actually the point of the two other functions. It is meant to help match the color of the labels with that of the branches - after running color_branches. |139236d| 
|  DESCRIPTION                     |   4 +-
|  NAMESPACE                       |   3 +
|  NEWS                            |   8 +++
|  R/attr_access.R                 | 141 ++++++++++++++++++++++++++++++++++++++
|  man/get_leaves_branches_attr.Rd |  48 +++++++++++++
|  man/get_leaves_branches_col.Rd  |  44 ++++++++++++
|  man/get_leaves_edgePar.Rd       |  45 ++++++++++++
|  man/get_leaves_nodePar.Rd       |   1 +
|  8 files changed, 292 insertions(+), 2 deletions(-)

* 2015-04-22(Tal Galili) use color_branches instead of set (easier for people - I would guess) |ade1635| 
|  vignettes/introduction.Rmd | 6 ++++--
|  1 file changed, 4 insertions(+), 2 deletions(-)

* 2015-04-22(Tal Galili) VIGNETTE added: "How to color the branches in heatmap.2?" |6127035| 
|  DESCRIPTION                |   4 +-
|  NEWS                       |   7 +
|  vignettes/introduction.Rmd | 632 +++++++++++++++++++++++++++++++++++++++++++
|  3 files changed, 641 insertions(+), 2 deletions(-)

* 2015-03-05(Tal Galili) s |17f6568| 
|  README.md | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-03-05(Tal Galili) Added TOC to readme.md |4d083c0| 
|  README.md | 12 +++++++++++-
|  1 file changed, 11 insertions(+), 1 deletion(-)

* 2015-02-14(Tal Galili) Update vignette on github |e0ecc5a| 
|  inst/ignored/introduction.html | 1875 ++++++++++++++++++--------------------
|  1 file changed, 866 insertions(+), 1009 deletions(-)

* 2015-02-14(Tal Galili) moved to knitr::docco_linear (and some fixes to figures height) |6de5e7b| 
|  vignettes/introduction.Rmd | 10 +++++-----
|  1 file changed, 5 insertions(+), 5 deletions(-)

* 2015-02-07(Tal Galili) as.hclust.pvclust |1c3ce5b| 
|  NAMESPACE   |  1 +
|  NEWS        |  1 +
|  R/pvclust.R | 11 ++++++++++-
|  3 files changed, 12 insertions(+), 1 deletion(-)

* 2015-02-07(Tal Galili) Added sort.dendlist |e90a0cd| 
|  DESCRIPTION   |  4 ++--
|  NAMESPACE     |  1 +
|  NEWS          |  1 +
|  R/rotate.R    | 11 +++++++++++
|  man/rotate.Rd |  2 ++
|  5 files changed, 17 insertions(+), 2 deletions(-)

* 2015-02-07(Tal Galili) prune.rpart added |3ae7031| 
|  NAMESPACE    |  1 +
|  NEWS         | 10 ++++++++++
|  R/prune.R    |  8 ++++++++
|  man/prune.Rd |  2 ++
|  4 files changed, 21 insertions(+)

* 2015-01-31(Tal Galili) Bump to 0.18.3 |86adb2a| 
|  ChangeLog | 13 +++++++++++++
|  R/zzz.R   |  2 +-
|  2 files changed, 14 insertions(+), 1 deletion(-)

* 2015-01-31(Tal Galili) require -> requireNamespace |6dcc805| 
|  .Rbuildignore   | 2 +-
|  R/bk_method.R   | 2 +-
|  R/rainbow_fun.R | 2 +-
|  3 files changed, 3 insertions(+), 3 deletions(-)

* 2015-01-31(Tal Galili) update NEWS.md and changelog |e8b9e78| 
|  ChangeLog | 42 ++++++++++++++++++++++++++++++++++++++++++
|  NEWS      |  2 +-
|  NEWS.md   | 20 ++++++++++++++++++++
|  R/zzz.R   |  2 +-
|  4 files changed, 64 insertions(+), 2 deletions(-)

* 2015-01-31(Tal Galili) Fix "Please use :: or requireNamespace() instead." by commenting out all "library", since using "::" is enough! |fc73295| 
|  NEWS                  |   6 +
|  R/DendSer.R           |   2 +-
|  R/ape.R               |   8 +-
|  R/cutree.dendrogram.R |  42 +++---
|  R/ggdend.R            |   4 +-
|  R/ggdendro.R          |   2 +-
|  R/nleaves.R           |   4 +-
|  R/prune.R             |   2 +-
|  R/rotate.R            |   4 +-
|  R/set.dendrogram.R    |   2 +-
|  R/unbranch.R          |   2 +-
|  R/untangle.R          | 358 ++++++++++++++++++++++++------------------------
|  R/zzz.R               |   2 +-
|  13 files changed, 222 insertions(+), 216 deletions(-)

* 2015-01-31(Tal Galili) Fix "title case" for the package's Title in the DESCRIPTION |ccf93c3| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 5 +++++
|  2 files changed, 7 insertions(+), 2 deletions(-)

* 2015-01-31(Tal Galili) Fix "No package encoding and non-ASCII characters in the following R files" |bba4e4c| 
|  R/ggdend.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-01-31(Tal Galili) Minor doc fix for `collapse_branch` |2f3019b| 
|  DESCRIPTION            | 2 +-
|  NEWS                   | 9 +++++++++
|  R/unbranch.R           | 3 ++-
|  man/collapse_branch.Rd | 3 ++-
|  4 files changed, 14 insertions(+), 3 deletions(-)

* 2015-01-31(Tal Galili) Update NEWS.md and changelog |e0ef4b5| 
|  ChangeLog | 39 +++++++++++++++++++++++++++++++++++++++
|  NEWS.md   | 29 +++++++++++++++++++++++++++++
|  2 files changed, 68 insertions(+)

* 2015-01-31(Tal Galili) collapse_branch to vignette |4cafe05| 
|  NEWS                       |  8 +++++++-
|  vignettes/introduction.Rmd | 17 +++++++++++++++++
|  2 files changed, 24 insertions(+), 1 deletion(-)

* 2015-01-31(Tal Galili) Add ladderize to collapse_branch example |f7043c6| 
|  R/rotate.R             | 2 +-
|  R/unbranch.R           | 8 +++++---
|  man/collapse_branch.Rd | 7 ++++---
|  man/rotate.Rd          | 2 +-
|  4 files changed, 11 insertions(+), 8 deletions(-)

* 2015-01-31(Tal Galili) ###VIGNETTE - new sections!    * Quick functions for FAQ       * How to colour the labels of a dendrogram by an additional factor variable       * How to color a dendrogram's branches/labels based on cluster (i.e.: cutree result)       * Change dendrogram's labels       * Larger font for leaves in a dendrogram       * How to view attributes of a dendrogram    * rotate - explain about sort    * ggplot2 integration (!)    * Comparing trees:       * dend_diff       * all.equal       * dist.dendlist       * cor.dendlist |84335e7| 
|  NEWS                       |  15 +++
|  vignettes/introduction.Rmd | 305 +++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 320 insertions(+)

* 2015-01-31(Tal Galili) `ggplot.ggdend` - support theme = NULL |d94efb6| 
|  NEWS          | 2 +-
|  R/ggdend.R    | 9 ++++++---
|  man/ggdend.Rd | 5 +++--
|  3 files changed, 10 insertions(+), 6 deletions(-)

* 2015-01-31(Tal Galili) Minor .Rd fixes. |d69de40| 
|  R/ggdend.R    | 4 ++--
|  man/ggdend.Rd | 4 ++--
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2015-01-31(Tal Galili) `sort.dendrogram` - added a new parameter: type = c("labels", "nodes"), to use `ladderize` for sorting |2d4fe25| 
|  DESCRIPTION   |  4 ++--
|  NEWS          |  8 ++++++++
|  R/rotate.R    | 17 +++++++++++++++--
|  man/rotate.Rd | 11 ++++++++++-
|  4 files changed, 35 insertions(+), 5 deletions(-)

* 2015-01-30(Tal Galili) cheatsheet? |1f2c862| 
|  TODO | 5 +++++
|  1 file changed, 5 insertions(+)

* 2015-01-30(Tal Galili) Updated ChangeLog and NEWS.md |d3b1613| 
|  ChangeLog | 674 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
|  NEWS.md   | 102 +++++++++
|  2 files changed, 768 insertions(+), 8 deletions(-)

* 2015-01-30(Tal Galili) Fix package date. |10d25e2| 
|  DESCRIPTION | 2 +-
|  NEWS        | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2015-01-29(Tal Galili) Fix various doc errors. |369cce9| 
|  R/rotate.R       | 19 ++++++++++---------
|  man/ladderize.Rd |  6 +++---
|  man/rotate.Rd    |  8 ++++----
|  3 files changed, 17 insertions(+), 16 deletions(-)

* 2015-01-29(Tal Galili) Fix "ggplot.ggdend: no visible global function definition for ‘aes_string’" error |f5b34b7| 
|  R/ggdend.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-01-29(Tal Galili) `ladderize` - Ladderize a Tree (reorganizes the internal structure of the tree to get the ladderized effect when plotted) |9120507| 
|  NAMESPACE        |   4 ++
|  NEWS             |   1 +
|  R/rotate.R       | 116 +++++++++++++++++++++++++++++++++++++++++++++++++++--
|  man/ladderize.Rd |  47 ++++++++++++++++++++++
|  man/rotate.Rd    |   4 +-
|  5 files changed, 167 insertions(+), 5 deletions(-)

* 2015-01-29(Tal Galili) Use aes_string instead of aes! |70ab17c| 
|  R/ggdend.R | 13 ++++++++-----
|  1 file changed, 8 insertions(+), 5 deletions(-)

* 2015-01-29(Tal Galili) Fix as.ggdend - to get the col/cex of the labels correctly. |174e12f| 
|  R/ggdend.R | 7 +++++--
|  1 file changed, 5 insertions(+), 2 deletions(-)

* 2015-01-29(Tal Galili) Fix "Missing link or links in documentation object" error |e8713e5| 
|  R/ape.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-01-29(Tal Galili) Fix "lines wider than 100 characters:" error |a035228| 
|  R/distinct_edges.R              | 4 +++-
|  man/as.phylo.dendrogram.Rd      | 2 +-
|  man/highlight_distinct_edges.Rd | 4 +++-
|  3 files changed, 7 insertions(+), 3 deletions(-)

* 2015-01-29(Tal Galili) Fix many "no visible global function definition for ..." errors. |c028b06| 
|  R/ggdend.R    | 42 ++++++++++++++++++++++++++++++++----------
|  man/ggdend.Rd | 18 ++++++++++--------
|  2 files changed, 42 insertions(+), 18 deletions(-)

* 2015-01-29(Tal Galili) Fix theme_dendro: no visible global function definition for 'element_text' |4e30954| 
|  R/ggdendro.R | 5 ++++-
|  1 file changed, 4 insertions(+), 1 deletion(-)

* 2015-01-29(Tal Galili) fix collapse_branch: no visible binding for global variable ‘dend_node’ |c51c27e| 
|  R/unbranch.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-01-29(Tal Galili) Fix Codoc mismatches in prepare.ggdend |c87b7d8| 
|  R/ggdend.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-01-29(Tal Galili) ggplot.ggdend: leaf_labels -> labels |5f6e090| 
|  R/ggdend.R | 8 ++++----
|  1 file changed, 4 insertions(+), 4 deletions(-)

* 2015-01-29(Tal Galili) DESCRIPTION: Moved ape and ggplot2 to "Suggests" packages - so that I could refer to them in the vignette/help pages. |9f54d6a| 
|  DESCRIPTION | 7 ++++---
|  1 file changed, 4 insertions(+), 3 deletions(-)

* 2015-01-29(Tal Galili) Rename dist_fun.R to dist_long.R |6ed91cc| 
|  NEWS                          | 1 +
|  R/{dist_fun.R => dist_long.R} | 0
|  R/unbranch.R                  | 1 +
|  3 files changed, 2 insertions(+)

* 2015-01-29(Tal Galili) `collapse_branch` - simplifies a tree with branches lower than some tollerance level |691c490| 
|  NAMESPACE              |  1 +
|  NEWS                   |  1 +
|  R/unbranch.R           | 90 ++++++++++++++++++++++++++++++++++++++++++++++++
|  man/collapse_branch.Rd | 38 ++++++++++++++++++++
|  4 files changed, 130 insertions(+)

* 2015-01-29(Tal Galili) Fix "Error in plot.xy(xy.coords(x, y), type = type, ...) : " when dend has graphical parameters. |480b0fc| 
|  R/ggdendro.R | 16 ++++++++++++++++
|  1 file changed, 16 insertions(+)

* 2015-01-29(Tal Galili) Fix: Error in eval(expr, envir, enclos) : object 'cex' not found In addition: Warning message: In is.na(data$labels$cex) :   is.na() applied to non-(list or vector) of type 'NULL' |50ab05a| 
|  R/ggdend.R | 22 +++++++++++++++++-----
|  1 file changed, 17 insertions(+), 5 deletions(-)

* 2015-01-29(Tal Galili) `remove_nodes_nodePar` - as the name implies... |3584e7c| 
|  NAMESPACE                   |  1 +
|  NEWS                        |  2 ++
|  R/attr_access.R             | 37 ++++++++++++++++++++++++++++++++++++-
|  man/remove_nodes_nodePar.Rd | 33 +++++++++++++++++++++++++++++++++
|  4 files changed, 72 insertions(+), 1 deletion(-)

* 2015-01-28(Tal Galili) fix namespace issues (using S3 for a non-imported package is NOT wise, and results in the main function not seeing the new S3 function implemented...) |bc5c1ee| 
|  NAMESPACE     |  4 ++--
|  R/ggdend.R    | 14 ++++++++------
|  man/ggdend.Rd |  4 ++--
|  3 files changed, 12 insertions(+), 10 deletions(-)

* 2015-01-28(Tal Galili) Added theme_dendro as the default theme for ggplot.ggdend |0dfc218| 
|  R/ggdend.R    | 16 +++++++---------
|  man/ggdend.Rd |  4 +++-
|  2 files changed, 10 insertions(+), 10 deletions(-)

* 2015-01-28(Tal Galili) Organize NEWS |c41aeba| 
|  NEWS | 31 +++++++++++++++++--------------
|  1 file changed, 17 insertions(+), 14 deletions(-)

* 2015-01-28(Tal Galili) Importing `theme_dendro` from the ggdendro package |d4f6552| 
|  NAMESPACE           |  1 +
|  R/ggdend.R          |  2 +-
|  R/ggdendro.R        | 32 ++++++++++++++++++++++++++++++++
|  man/ggdend.Rd       |  3 +++
|  man/theme_dendro.Rd | 24 ++++++++++++++++++++++++
|  5 files changed, 61 insertions(+), 1 deletion(-)

* 2015-01-28(Tal Galili) Mention ggplot2 -> plot.ly in the ggdend doc. |5340107| 
|  R/ggdend.R    | 22 ++++++++++++++++++++--
|  man/ggdend.Rd | 22 ++++++++++++++++++++--
|  2 files changed, 40 insertions(+), 4 deletions(-)

* 2015-01-27(Tal Galili) `prepare.ggdend` - fills a ggdend object with various default values (to be later used when plotted)  (this function was extrected from ggplot.ggdend) |5fffec4| 
|  NAMESPACE     |  1 +
|  NEWS          |  1 +
|  R/ggdend.R    | 82 +++++++++++++++++++++++++++++++++------------------------
|  man/ggdend.Rd | 24 ++++++++++++-----
|  4 files changed, 67 insertions(+), 41 deletions(-)

* 2015-01-27(Tal Galili) Thanks to Andrie de Vries, dendextend now enhances ggplot2 :) |13647d4| 
|  DESCRIPTION | 7 +++++--
|  1 file changed, 5 insertions(+), 2 deletions(-)

* 2015-01-27(Tal Galili) Adding documentation to ggdend and friends! |64a21a9| 
|  NAMESPACE     |   5 +++
|  NEWS          |   3 +-
|  R/ggdend.R    | 121 ++++++++++++++++++++++++++++++++++++++++++++++++++------
|  man/ggdend.Rd |  99 ++++++++++++++++++++++++++++++++++++++++++++++
|  4 files changed, 216 insertions(+), 12 deletions(-)

* 2015-01-27(Tal Galili) Added a working (at least partially) version of ggplot.ggdend |e54200a| 
|  R/ggdend.R | 246 +++++++++++++++++++++++++++++++++++++++++++++++++----------
|  1 file changed, 205 insertions(+), 41 deletions(-)

* 2015-01-27(Tal Galili) `as.ggdend.dendrogram` - turns a dendrogram to the ggdend class, ready to be plotted with ggplot2. |9cc9761| 
|  NEWS       |   2 +
|  R/ggdend.R | 241 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 243 insertions(+)

* 2015-01-27(Tal Galili) `get_leaves_nodePar` - a new function that Get's the nodePar of dendrogram's leaves (designed to help with as.ggdend) |57192cd| 
|  NAMESPACE                     |  1 +
|  NEWS                          |  2 +-
|  R/attr_access.R               | 45 +++++++++++++++++++++++++++++++++++++++++
|  inst/tests/test-attr_access.R | 22 ++++++++++++++++++++
|  man/get_leaves_nodePar.Rd     | 40 ++++++++++++++++++++++++++++++++++++
|  5 files changed, 109 insertions(+), 1 deletion(-)

* 2015-01-27(Tal Galili) Added the file ggdendro.R with the dendrogram_data function (imported from the ggdendro package) |08d69d6| 
|  NEWS         |   3 ++
|  R/ggdendro.R | 165 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 168 insertions(+)

* 2015-01-26(Tal Galili) renamed imports_stats.R to stats_imports.R |27068c4| 
|  NEWS                                   | 1 +
|  R/{imports_stats.R => stats_imports.R} | 0
|  2 files changed, 1 insertion(+)

* 2015-01-26(Tal Galili) cor.dendlist and dist.dendlist - their matrix now includes dend names in col/row names. |951968a| 
|  R/cor.dendlist.R     | 4 +++-
|  R/distinct_edges.R   | 5 ++++-
|  man/cor.dendlist.Rd  | 2 +-
|  man/dist.dendlist.Rd | 2 +-
|  4 files changed, 9 insertions(+), 4 deletions(-)

* 2015-01-26(Tal Galili) Add ggdendro example for creating a radial plot :) |efaf335| 
|  R/ape.R                    | 12 ++++++++++++
|  man/as.phylo.dendrogram.Rd | 19 ++++++++++++++++++-
|  2 files changed, 30 insertions(+), 1 deletion(-)

* 2015-01-26(Tal Galili) export as.phylo.dendrogram in a way that actually works... |c8b69de| 
|  NAMESPACE                  |  1 +
|  NEWS                       |  2 +-
|  R/ape.R                    | 47 +++++++++++++++++++++++++++++++++++++++++---
|  R/noded_with_condition.R   |  2 +-
|  man/as.phylo.dendrogram.Rd | 35 +++++++++++++++++++++++++++++++++
|  man/which_node.Rd          |  1 +
|  6 files changed, 83 insertions(+), 5 deletions(-)

* 2015-01-26(Tal Galili) get_nodes_attr with id example |d2464f6| 
|  vignettes/introduction.Rmd | 1 +
|  1 file changed, 1 insertion(+)

* 2015-01-26(Tal Galili) Fix "Error in missing(id) : 'missing' can only be used for arguments" in get_nodes_attr |e912cc3| 
|  R/attr_access.R | 8 +++++---
|  1 file changed, 5 insertions(+), 3 deletions(-)

* 2015-01-26(Tal Galili) magrittr is imported there is no longer a need for "library(magrittr)" in examples. |8210261| 
|  R/branches_attr_by.R           | 1 -
|  R/dist_fun.R                   | 1 -
|  R/get_nodes_xy.R               | 1 -
|  R/noded_with_condition.R       | 2 --
|  R/set.dendrogram.R             | 1 -
|  man/branches_attr_by_labels.Rd | 1 -
|  man/dist_long.Rd               | 1 -
|  man/get_nodes_xy.Rd            | 1 -
|  man/noded_with_condition.Rd    | 1 -
|  man/set.Rd                     | 1 -
|  man/which_leaf.Rd              | 1 -
|  11 files changed, 12 deletions(-)

* 2015-01-26(Tal Galili) `which_node` - a new function which finds Which node is common to a group of labels |fbaef43| 
|  NAMESPACE                |  1 +
|  NEWS                     |  2 ++
|  R/noded_with_condition.R | 46 ++++++++++++++++++++++++++++++++++++++++++++++
|  man/which_node.Rd        | 43 +++++++++++++++++++++++++++++++++++++++++++
|  4 files changed, 92 insertions(+)

* 2015-01-26(Tal Galili) update `get_nodes_attr` - added the "id" parameter (to get attributes of only a subset of id's) |de61889| 
|  NEWS                          |  1 +
|  R/attr_access.R               | 26 +++++++++++++++++++++++---
|  inst/tests/test-attr_access.R |  5 +++++
|  man/get_nodes_attr.Rd         |  8 +++++++-
|  4 files changed, 36 insertions(+), 4 deletions(-)

* 2015-01-26(Tal Galili) Rename `get_branches_attr` to be `get_root_branches_attr` |3e38822| 
|  NAMESPACE                                               |  2 +-
|  NEWS                                                    |  2 +-
|  R/attr_access.R                                         |  4 ++--
|  R/unbranch.R                                            | 12 ++++++------
|  inst/tests/test-unbranch.R                              |  6 +++---
|  man/assign_values_to_branches_edgePar.Rd                |  2 +-
|  man/{get_branches_attr.Rd => get_root_branches_attr.Rd} | 12 ++++++------
|  man/remove_branches_edgePar.Rd                          |  2 +-
|  8 files changed, 21 insertions(+), 21 deletions(-)

* 2015-01-26(Tal Galili) minor docs update and version bump |5ac4ac6| 
|  DESCRIPTION                     | 4 ++--
|  R/distinct_edges.R              | 1 -
|  man/dend_diff.Rd                | 2 ++
|  man/highlight_distinct_edges.Rd | 1 -
|  4 files changed, 4 insertions(+), 4 deletions(-)

* 2015-01-26(Tal Galili) Made dend_diff work with dendlist |4fd37af| 
|  NAMESPACE          |  2 ++
|  NEWS               |  2 +-
|  R/distinct_edges.R | 46 ++++++++++++++++++++++++++++++++++++++++++----
|  man/dend_diff.Rd   | 19 +++++++++++++++----
|  4 files changed, 60 insertions(+), 9 deletions(-)

* 2015-01-26(Tal Galili) Made highlight_distinct_edges work with dendlist (and added a nice iris example) |edcae3a| 
|  NAMESPACE                       |  2 ++
|  NEWS                            |  2 +-
|  R/distinct_edges.R              | 51 +++++++++++++++++++++++++++++++++++++--
|  man/highlight_distinct_edges.Rd | 34 +++++++++++++++++++++++---
|  4 files changed, 82 insertions(+), 7 deletions(-)

* 2015-01-25(Tal Galili) `cutree_1h.dendrogram` and `cutree_1k.dendrogram` - will now create clusters as the number of items if k==nleaves(tree) or if h<0. This is both consistent with stats::hclust, but it also "makes sense" (since this is well defined for ANY tree) |7afd28e| 
|  NEWS                                |  1 +
|  R/cutree.dendrogram.R               | 21 ++++++++++++++++++++-
|  inst/tests/test-cut_lower_fun.R     |  9 +++++++++
|  inst/tests/test-cutree.dendrogram.R | 33 ++++++++++++++++++++++++---------
|  inst/tests/test-distinct_edges.R    |  1 +
|  5 files changed, 55 insertions(+), 10 deletions(-)

* 2015-01-25(Tal Galili) `cutree` - now produces warnings if it returns 0's. i.e.: when it can't cut the tree based on the required parameter. (following isue #5 reported by grafab) |fce5319| 
|  NEWS                                |  2 +-
|  R/cutree.dendrogram.R               | 13 ++++++++++---
|  inst/tests/test-cutree.dendrogram.R | 24 ++++++++++++++++++++++++
|  man/cutree-methods.Rd               |  7 ++++++-
|  4 files changed, 41 insertions(+), 5 deletions(-)

* 2015-01-25(Tal Galili) Various doc .Rd fixes. |45b21e0| 
|  NAMESPACE                       |  1 -
|  R/ape.R                         |  2 +-
|  R/distinct_edges.R              | 12 ++++++------
|  R/tanglegram.R                  |  1 +
|  man/dend_diff.Rd                |  2 +-
|  man/distinct_edges.Rd           |  2 +-
|  man/highlight_distinct_edges.Rd |  6 +++---
|  man/partition_leaves.Rd         |  2 +-
|  man/tanglegram.Rd               |  1 +
|  9 files changed, 15 insertions(+), 14 deletions(-)

* 2015-01-25(Tal Galili) `tanglegram` - a new highlight_distinct_edges parameter (default is TRUE) |7a7e758| 
|  NEWS              | 1 +
|  R/tanglegram.R    | 6 ++++++
|  man/tanglegram.Rd | 2 ++
|  3 files changed, 9 insertions(+)

* 2015-01-25(Tal Galili) New function: all.equal.dendrogram/all.equal.dendlist - Global Comparison of two (or more) dendrograms |8edaa3b| 
|  NAMESPACE                   |   2 +
|  NEWS                        |   1 +
|  R/all.equal.R               | 157 ++++++++++++++++++++++++++++++++++++++++++
|  man/all.equal.dendrogram.Rd |  65 +++++++++++++++++
|  4 files changed, 225 insertions(+)

* 2015-01-25(Tal Galili) `labels<-.dendrogram` - no longer forces as.character conversion |6a6223b| 
|  NEWS                             | 1 +
|  R/labels.R                       | 3 ++-
|  inst/tests/test-set.dendrogram.R | 5 ++++-
|  3 files changed, 7 insertions(+), 2 deletions(-)

* 2015-01-25(Tal Galili) minor test fix |0b8b076| 
|  inst/tests/test-distinct_edges.R | 11 ++++++++---
|  1 file changed, 8 insertions(+), 3 deletions(-)

* 2015-01-25(Tal Galili) use ave instead of ward in hclust (make sure the change to ward.D will no longer cause issues) |a220126| 
|  inst/tests/test-unbranch.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-01-25(Tal Galili) New functions (with doc and tests):    * partition_leaves - A list with labels for each subtree (edge)    * distinct_edges - Finds the edges present in the first tree but not in the second    * highlight_distinct_edges - Highlight distint edges in a tree (compared to another one)    * dend_diff - Plots two trees side by side, highlighting edges unique to each tree in red.    * dist.dendlist - Topological Distances Between Two dendrograms (currently only the Robinson-Foulds distance) |05b4ebc| 
|  NAMESPACE                        |   5 +
|  NEWS                             |  17 ++-
|  R/distinct_edges.R               | 291 +++++++++++++++++++++++++++++++++++++
|  inst/tests/test-distinct_edges.R |  39 +++++
|  man/dend_diff.Rd                 |  42 ++++++
|  man/dist.dendlist.Rd             |  38 +++++
|  man/distinct_edges.Rd            |  36 +++++
|  man/highlight_distinct_edges.Rd  |  49 +++++++
|  man/partition_leaves.Rd          |  43 ++++++
|  9 files changed, 559 insertions(+), 1 deletion(-)

* 2015-01-25(Tal Galili) Small document update to assign_values_to_branches_edgePar |330ed91| 
|  R/attr_access.R                          | 3 ++-
|  man/assign_values_to_branches_edgePar.Rd | 3 ++-
|  2 files changed, 4 insertions(+), 2 deletions(-)

* 2015-01-25(Tal Galili) cor.dendlist - Correlation matrix between a list of trees. |a3d8371| 
|  NAMESPACE           |  1 +
|  NEWS                |  2 ++
|  R/cor.dendlist.R    | 77 +++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/cor.dendlist.Rd | 43 ++++++++++++++++++++++++++++
|  4 files changed, 123 insertions(+)

* 2015-01-24(Tal Galili) A new phylo method for `labels` and `labels<-` |f51e36a| 
|  DESCRIPTION          |  2 +-
|  NAMESPACE            |  2 ++
|  NEWS                 |  7 ++++++-
|  R/labels.R           | 38 ++++++++++++++++++++++++++++++++++++++
|  man/labels-assign.Rd |  6 ++++++
|  5 files changed, 53 insertions(+), 2 deletions(-)

* 2015-01-24(Tal Galili) `nleaves.phylo` - no longer require conversion to a dendrogram in order to compute. |8b5dad4| 
|  R/nleaves.R | 5 ++++-
|  1 file changed, 4 insertions(+), 1 deletion(-)

* 2015-01-21(Tal Galili) 1) new file ape.R - to which I moved `as.dendrogram.phylo` and `as.phylo.dendrogram` functions to. |e94bd9b| 
|  DESCRIPTION      |  4 ++--
|  NAMESPACE        |  1 +
|  NEWS             |  7 +++++++
|  R/ape.R          | 42 ++++++++++++++++++++++++++++++++++++++++++
|  R/nleaves.R      | 22 ----------------------
|  tests/test-all.R |  2 ++
|  6 files changed, 54 insertions(+), 24 deletions(-)

* 2014-12-08(Tal Galili) Bump to 0.17.6 |a4d0561| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 8 ++++++++
|  2 files changed, 10 insertions(+), 2 deletions(-)

* 2014-12-08(Tal Galili) roxygen2 from 4.0.1 to 4.0.2 |b46267b| 
|  man/Bk.Rd                                  |  2 +-
|  man/Bk_permutations.Rd                     |  2 +-
|  man/Bk_plot.Rd                             |  2 +-
|  man/DendSer.dendrogram.Rd                  |  2 +-
|  man/FM_index.Rd                            |  2 +-
|  man/FM_index_R.Rd                          |  2 +-
|  man/FM_index_permutation.Rd                |  2 +-
|  man/FM_index_profdpm.Rd                    |  2 +-
|  man/all_couple_rotations_at_k.Rd           |  2 +-
|  man/all_unique.Rd                          |  2 +-
|  man/as.dendlist.Rd                         |  2 +-
|  man/as_hclust_fixed.Rd                     |  2 +-
|  man/assign_dendextend_options.Rd           |  2 +-
|  man/assign_values_to_branches_edgePar.Rd   |  2 +-
|  man/assign_values_to_leaves_edgePar.Rd     |  2 +-
|  man/assign_values_to_leaves_nodePar.Rd     |  2 +-
|  man/assign_values_to_nodes_nodePar.Rd      |  2 +-
|  man/bakers_gamma_for_2_k_matrix.Rd         |  2 +-
|  man/branches_attr_by_clusters.Rd           |  2 +-
|  man/branches_attr_by_labels.Rd             |  2 +-
|  man/click_rotate.Rd                        |  6 +++---
|  man/color_branches.Rd                      |  2 +-
|  man/color_labels.Rd                        |  8 ++++----
|  man/colored_bars.Rd                        |  2 +-
|  man/cor_bakers_gamma.Rd                    |  6 +++---
|  man/cor_cophenetic.Rd                      |  6 +++---
|  man/count_terminal_nodes.Rd                |  2 +-
|  man/cut_lower_fun.Rd                       |  2 +-
|  man/cutree-methods.Rd                      |  6 +++---
|  man/cutree_1h.dendrogram.Rd                | 10 +++++-----
|  man/cutree_1k.dendrogram.Rd                |  2 +-
|  man/d3dendro_options.Rd                    |  2 +-
|  man/d3dendrogram.Rd                        |  2 +-
|  man/dendextend-package.Rd                  |  2 +-
|  man/dendextend_options.Rd                  |  2 +-
|  man/dendlist.Rd                            |  2 +-
|  man/duplicate_leaf.Rd                      |  2 +-
|  man/entanglement.Rd                        |  6 +++---
|  man/fac2num.Rd                             |  2 +-
|  man/fix_members_attr.dendrogram.Rd         |  2 +-
|  man/flatten.dendrogram.Rd                  |  2 +-
|  man/flip_leaves.Rd                         |  2 +-
|  man/get_branches_attr.Rd                   |  2 +-
|  man/get_branches_heights.Rd                |  2 +-
|  man/get_childrens_heights.Rd               |  2 +-
|  man/get_leaves_attr.Rd                     |  2 +-
|  man/get_nodes_attr.Rd                      |  2 +-
|  man/get_nodes_xy.Rd                        |  2 +-
|  man/hang.dendrogram.Rd                     |  2 +-
|  man/heights_per_k.dendrogram.Rd            |  2 +-
|  man/identify.dendrogram.Rd                 |  2 +-
|  man/intersect_trees.Rd                     |  2 +-
|  man/is.dendlist.Rd                         |  2 +-
|  man/is.dendrogram.Rd                       |  2 +-
|  man/is.hclust.Rd                           |  2 +-
|  man/is.natural.number.Rd                   |  2 +-
|  man/is.phylo.Rd                            |  2 +-
|  man/is_null_list.Rd                        |  2 +-
|  man/labels-assign.Rd                       |  6 +++---
|  man/labels_colors.Rd                       |  2 +-
|  man/leaf_Colors.Rd                         |  2 +-
|  man/lowest_common_branch.Rd                |  2 +-
|  man/match_order_by_labels.Rd               |  2 +-
|  man/match_order_dendrogram_by_old_order.Rd |  2 +-
|  man/na_locf.Rd                             |  2 +-
|  man/nleaves.Rd                             |  6 +++---
|  man/nnodes.Rd                              |  2 +-
|  man/noded_with_condition.Rd                |  2 +-
|  man/order.dendrogram-assign.Rd             |  2 +-
|  man/order.hclust.Rd                        |  2 +-
|  man/pipe.Rd                                |  2 +-
|  man/plot_horiz.dendrogram.Rd               |  2 +-
|  man/prune.Rd                               |  6 +++---
|  man/prune_leaf.Rd                          |  2 +-
|  man/pvclust_show_signif.Rd                 |  2 +-
|  man/pvclust_show_signif_gradient.Rd        |  2 +-
|  man/raise.dendrogram.Rd                    |  2 +-
|  man/rank_branches.Rd                       |  2 +-
|  man/rank_order.dendrogram.Rd               |  2 +-
|  man/rect.dendrogram.Rd                     |  6 +++---
|  man/remove_branches_edgePar.Rd             |  2 +-
|  man/remove_leaves_nodePar.Rd               |  2 +-
|  man/rllply.Rd                              |  2 +-
|  man/rotate.Rd                              |  6 +++---
|  man/rotate_DendSer.Rd                      |  2 +-
|  man/sample.dendrogram.Rd                   |  2 +-
|  man/set.Rd                                 |  6 +++---
|  man/shuffle.Rd                             |  6 +++---
|  man/sort_2_clusters_vectors.Rd             |  2 +-
|  man/sort_dist_mat.Rd                       |  2 +-
|  man/sort_levels_values.Rd                  |  2 +-
|  man/tanglegram.Rd                          |  6 +++---
|  man/unbranch.Rd                            |  6 +++---
|  man/unclass_dend.Rd                        |  2 +-
|  man/untangle.Rd                            |  6 +++---
|  man/untangle_DendSer.Rd                    |  2 +-
|  man/untangle_random_search.Rd              |  2 +-
|  man/untangle_step_rotate_1side.Rd          |  2 +-
|  man/untangle_step_rotate_2side.Rd          |  2 +-
|  man/which_leaf.Rd                          |  2 +-
|  100 files changed, 137 insertions(+), 137 deletions(-)

* 2014-12-08(Tal Galili) dist_long - Turns a dist object to a "long" table. |a5fee75| 
|  NAMESPACE        |  4 +++-
|  R/dist_fun.R     | 63 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/dist_long.Rd | 28 ++++++++++++++++++++++++
|  3 files changed, 94 insertions(+), 1 deletion(-)

* 2014-12-08(Tal Galili) Update text (per request by CRAN) |46697aa| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-12-08(Tal Galili) text editing |5afb4dd| 
|  vignettes/introduction.Rmd | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-10-04(Tal Galili) Ignore ^\.travis.yml$ when building the package. |45cba35| 
|  .Rbuildignore | 3 ++-
|  1 file changed, 2 insertions(+), 1 deletion(-)

* 2014-10-04(Tal Galili) Adding .travis.yml |6e17ba3| 
|  .travis.yml | 24 ++++++++++++++++++++++++
|  README.md   |  3 +++
|  2 files changed, 27 insertions(+)

* 2014-09-22(Tal Galili) VIGNETTE - fix several typos and grammatical mistakes. |7e41e50| 
|  NAMESPACE                  |  2 +-
|  NEWS                       |  3 +++
|  TODO                       | 61 ++++++++++++++++++++++++++++++++++++++++++++
|  vignettes/introduction.Rmd | 26 +++++++++----------
|  4 files changed, 78 insertions(+), 14 deletions(-)

* 2014-09-22(Tal Galili) Fixing - \usage lines wider than 90 characters |fff3e9f| 
|  NEWS                    | 3 ++-
|  R/cor_bakers_gamma.R    | 6 ++++--
|  man/cor_bakers_gamma.Rd | 6 ++++--
|  3 files changed, 10 insertions(+), 5 deletions(-)

* 2014-09-22(Tal Galili) Several bug fixes to the docs. |45bf641| 
|  NAMESPACE               |  2 +-
|  NEWS                    | 11 ++++++++
|  R/cor_bakers_gamma.R    | 18 ++++++++++++-
|  R/dendlist.R            | 64 +++++++++++++++++++++++++++++++----------------
|  R/set.dendrogram.R      |  1 +
|  man/cor_bakers_gamma.Rd | 13 ++++++++--
|  man/dendlist.Rd         | 14 +++++++++++
|  man/plot.dendlist.Rd    | 34 -------------------------
|  man/set.Rd              |  1 +
|  9 files changed, 98 insertions(+), 60 deletions(-)

* 2014-09-22(Tal Galili) Fixing tests as well. (with as.hclust for sub dends. |bf0fd2b| 
|  NEWS                                |  2 +-
|  inst/tests/test-cutree.dendrogram.R | 86 +++++++++++++++++------------------
|  inst/tests/test-labels-assign.R     |  3 +-
|  3 files changed, 46 insertions(+), 45 deletions(-)

* 2014-09-22(Tal Galili) `order.dendrogram<-` - commenting off an example which (as of R 3.1.1-patched) produces an error (as it should). |4a672fa| 
|  DESCRIPTION                    |  4 ++--
|  NEWS                           | 10 ++++++++++
|  R/labels.R                     |  4 ++--
|  R/zzz.R                        |  1 +
|  man/order.dendrogram-assign.Rd |  4 ++--
|  5 files changed, 17 insertions(+), 6 deletions(-)

* 2014-09-20(Tal Galili) Added set.data.table - informs the user of the conflict in "set" between dendextend and data.table. |e167228| 
|  DESCRIPTION        |  5 +++--
|  NAMESPACE          |  1 +
|  NEWS               |  2 ++
|  R/set.dendrogram.R | 10 ++++++++++
|  man/set.Rd         |  2 ++
|  5 files changed, 18 insertions(+), 2 deletions(-)

* 2014-09-20(Tal Galili) added sessionInfo to VIGNETTE |f34c02a| 
|  NEWS                       | 8 ++++++++
|  vignettes/introduction.Rmd | 8 ++++++++
|  2 files changed, 16 insertions(+)

* 2014-08-26(Tal Galili) full name credit. |16ee14d| 
|  NEWS | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-08-26(Tal Galili) link to the bug report, and thanked varmara. |0e10459| 
|  NEWS | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-08-26(Tal Galili) color_labels - now can handle the coloring of labels when the function is without k and h, but that it is not possible to cut the tree to nleaves items (due to several leaves with 0 height). This is done by not doing any cutting in such cases, and just directly using labels_colors. (added tests) |734fe99| 
|  DESCRIPTION                     |  4 ++--
|  NEWS                            |  7 +++++++
|  R/color_branches.R              |  8 ++++++--
|  inst/tests/test-labels_colors.R | 35 +++++++++++++++++++++++++++++++++++
|  man/color_labels.Rd             |  3 ---
|  5 files changed, 50 insertions(+), 7 deletions(-)

* 2014-08-25(Tal Galili) Version 0.17.2 (updated NEWS DESCRIPTION, etc) |fa1dba2| 
|  DESCRIPTION |  4 ++--
|  NEWS        |  7 +++++--
|  NEWS.md     | 19 +++++++++++++++++--
|  TODO        | 11 ++++++++++-
|  4 files changed, 34 insertions(+), 7 deletions(-)

* 2014-08-25(Tal Galili) Add to introduction.Rmd how to install the package from github. |0ecf3af| 
|  README.md                  |  6 +-----
|  vignettes/introduction.Rmd | 40 ++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 41 insertions(+), 5 deletions(-)

* 2014-08-25(Tal Galili) Added the function assign_values_to_leaves_edgePar |8ff1d61| 
|  NAMESPACE                              |  1 +
|  R/attr_access.R                        | 92 +++++++++++++++++++++++++++++++-
|  man/assign_values_to_leaves_edgePar.Rd | 52 ++++++++++++++++++
|  3 files changed, 144 insertions(+), 1 deletion(-)

* 2014-08-23(Tal Galili) capitalize R Core Team |48b8f6d| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-08-23(Tal Galili) Added cor_bakers_gamma.dendlist |08e0276| 
|  NAMESPACE            | 1 +
|  NEWS                 | 6 +++++-
|  R/cor_bakers_gamma.R | 7 +++++++
|  TODO                 | 3 +++
|  4 files changed, 16 insertions(+), 1 deletion(-)

* 2014-08-23(Tal Galili) VIGNETTE Fix some typos and mistakes |33316b3| 
|  NEWS                       | 11 +++++++++--
|  vignettes/introduction.Rmd |  8 ++++----
|  2 files changed, 13 insertions(+), 6 deletions(-)

* 2014-08-19(Tal Galili) more editing, and thanks. |d47c870| 
|  NEWS    |  1 +
|  R/zzz.R | 29 +++++++++++++++++------------
|  2 files changed, 18 insertions(+), 12 deletions(-)

* 2014-08-19(Tal Galili) compacted ‘dendextend-tutorial.pdf’ from 725Kb to 551Kb |5944f4e| 
|  DESCRIPTION                      |   2 +-
|  NEWS                             |  15 +++++++++++++
|  NEWS.md                          |  15 +++++++++++++
|  R/zzz.R                          |  42 ++++++++++++++++++++++++++++++++++---
|  inst/doc/dendextend-tutorial.pdf | Bin 754947 -> 564592 bytes
|  5 files changed, 70 insertions(+), 4 deletions(-)

* 2014-08-19(Tal Galili) updated |6c952e3| 
|  ChangeLog | 37 +++++++++++++++++++++++++++++++++++++
|  NEWS.md   |  4 ++++
|  2 files changed, 41 insertions(+)

* 2014-08-19(Tal Galili) Have the package build the vignette. |8653ed9| 
|  DESCRIPTION | 1 +
|  NEWS        | 1 +
|  2 files changed, 2 insertions(+)

* 2014-08-19(Tal Galili) Update the location of vignettes on github. |ec66fa0| 
|  README.md | 7 ++++---
|  1 file changed, 4 insertions(+), 3 deletions(-)

* 2014-08-19(Tal Galili) Fixed introduction.html to not overlap the bounderies of the code area. |7d47c9e| 
|  vignettes/introduction.Rmd | 37 ++++++++++++++++++++++++-------------
|  1 file changed, 24 insertions(+), 13 deletions(-)

* 2014-08-19(Tal Galili) Created a copy of "introduction.html" in inst/ignored (so people could see it on github) |0a1195a| 
|  .Rbuildignore                  |    7 +-
|  NEWS                           |    2 +-
|  inst/ignored/introduction.html | 1543 ++++++++++++++++++++++++++++++++++++++
|  3 files changed, 1549 insertions(+), 3 deletions(-)

* 2014-08-19(Tal Galili) Moved dendextend-tutorial.rnw to vignettes\disabled - so it is still there, but not compiled. Also moved dendextend-tutorial.pdf to inst\doc - so there is a copy of this older vignette, but without needed to run it with all the benchmarks... (it is also compressed) |5558f2c| 
|  NEWS                                             |    3 +
|  R/zzz.R                                          |    7 +-
|  inst/doc/dendextend-tutorial.pdf                 |  Bin 0 -> 754947 bytes
|  vignettes/dendextend-tutorial.pdf                | 9793 --------------------
|  vignettes/{ => disabled}/dendextend-tutorial.rnw |    2 +-
|  5 files changed, 8 insertions(+), 9797 deletions(-)

* 2014-08-19(Tal Galili) erased file |a97af45| 
|  R/dendlist - Copy.R | 275 --------------------------------------------------
|  1 file changed, 275 deletions(-)

* 2014-08-19(Tal Galili) Update NEWS.md and ChangeLog before CRAN release. for 0.17.0 |4e47159| 
|  ChangeLog | 74 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  NEWS.md   | 11 ++++++---
|  2 files changed, 82 insertions(+), 3 deletions(-)

* 2014-08-19(Tal Galili) Moved ggdendro, labeltodendro, dendroextras, ape to "Enhances:" in DESCRIPTION. (include fixing tests, and adding library - so to through errors in case the package is not available) |992d09d| 
|  DESCRIPTION              | 11 ++++++-----
|  NAMESPACE                |  1 -
|  NEWS                     |  2 +-
|  R/DendSer.R              |  2 +-
|  R/bk_method.R            |  2 +-
|  R/dendextend-package.R   |  2 +-
|  R/nleaves.R              |  6 +++---
|  R/prune.R                |  2 +-
|  R/pvclust.R              |  2 +-
|  R/rotate.R               |  2 +-
|  R/unbranch.R             |  2 +-
|  inst/tests/test-rotate.R |  2 +-
|  12 files changed, 18 insertions(+), 18 deletions(-)

* 2014-08-19(Tal Galili) Added spaces to docs |d4ce41a| 
|  man/as.dendlist.Rd | 22 ----------------------
|  1 file changed, 22 deletions(-)

* 2014-08-19(Tal Galili) new function: `rainbow_fun` - uses rainbow_hcl, or rainbow (if colorspace is not available) |f71d025| 
|  DESCRIPTION          |   2 +-
|  NEWS                 |   9 +-
|  R/branches_attr_by.R |   4 +-
|  R/color_branches.R   |  14 +--
|  R/colored_bars.R     |   1 +
|  R/dendlist - Copy.R  | 275 +++++++++++++++++++++++++++++++++++++++++++++++++
|  R/labels_colors.R    |   4 +-
|  R/rainbow_fun.R      |  33 ++++++
|  man/as.dendlist.Rd   |  22 ++++
|  man/colored_bars.Rd  |   1 +
|  10 files changed, 345 insertions(+), 20 deletions(-)

* 2014-08-19(Tal Galili) Break lines which were too long. |fd1f130| 
|  R/pvclust.R                         | 8 ++++++--
|  man/pvclust_show_signif.Rd          | 4 +++-
|  man/pvclust_show_signif_gradient.Rd | 4 +++-
|  3 files changed, 12 insertions(+), 4 deletions(-)

* 2014-08-19(Tal Galili) Added warn = dendextend_options("warn") to docs |94bd5f4| 
|  R/cutree.dendrogram.R | 5 +++--
|  man/cutree-methods.Rd | 5 +++--
|  2 files changed, 6 insertions(+), 4 deletions(-)

* 2014-08-19(Tal Galili) edgeText is not needed here. |9a4441e| 
|  R/get_nodes_xy.R | 8 ++++----
|  1 file changed, 4 insertions(+), 4 deletions(-)

* 2014-08-19(Tal Galili) laply -> lapply , and some tree to dend fixes. |4167e7b| 
|  R/untangle.R | 10 +++++-----
|  1 file changed, 5 insertions(+), 5 deletions(-)

* 2014-08-18(Tal Galili) paramters to parameters |b4097c8| 
|  DESCRIPTION                | 2 +-
|  vignettes/introduction.Rmd | 8 ++++----
|  2 files changed, 5 insertions(+), 5 deletions(-)

* 2014-08-18(Tal Galili) The following files are already in R: 'jss.bst', 'jss.cls' and I remove them from the package. |954508e| 
|  .Rbuildignore | 2 ++
|  1 file changed, 2 insertions(+)

* 2014-08-18(Tal Galili) all.unique to all_unique in the example. |a100582| 
|  R/color_branches.R | 10 +++++-----
|  man/all_unique.Rd  | 10 +++++-----
|  2 files changed, 10 insertions(+), 10 deletions(-)

* 2014-08-18(Tal Galili) Update various files |6bc8a22| 
|  .Rbuildignore        |   5 +-
|  ChangeLog            | 404 +++++++++++++++++++++++++++++++++++++++++++++++++
|  DESCRIPTION          |   2 +-
|  NEWS.md              |  52 +++++++
|  TODO                 |   8 +
|  vignettes/.gitignore |   3 +-
|  6 files changed, 470 insertions(+), 4 deletions(-)

* 2014-08-18(Tal Galili) cutree.hclust - added a dummy parameter |786c408| 
|  R/cutree.dendrogram.R | 1 +
|  1 file changed, 1 insertion(+)

* 2014-08-18(Tal Galili) Added a dendextendRcpp section. (and removed the not-working ggdendro section) |3d381da| 
|  vignettes/introduction.Rmd | 38 ++++++--------------------------------
|  1 file changed, 6 insertions(+), 32 deletions(-)

* 2014-08-18(Tal Galili) `cutree.dendrogram` - added a parameter (NA_to_0L) to control it. Also, make `Bk` work with cutree(NA_to_0L = FALSE) |b33a2a7| 
|  NEWS                  | 3 ++-
|  R/bk_method.R         | 4 ++--
|  R/cutree.dendrogram.R | 6 +++++-
|  man/cutree-methods.Rd | 4 ++++
|  4 files changed, 13 insertions(+), 4 deletions(-)

* 2014-08-18(Tal Galili) vignettes: Cophenetic correlation and Bk plots. |9cdc2d5| 
|  vignettes/introduction.Rmd | 133 ++++++++++++++++++++++++++++++++++++++++++-
|  1 file changed, 131 insertions(+), 2 deletions(-)

* 2014-08-18(Tal Galili) vignettes: Correlation measures - Baker's Gamma Index |b12f2df| 
|  vignettes/introduction.Rmd | 68 ++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 68 insertions(+)

* 2014-08-18(Tal Galili) vignettes: tanglegram |6666a97| 
|  vignettes/introduction.Rmd | 139 +++++++++++++++++++++++++++++++++++++++++--
|  1 file changed, 135 insertions(+), 4 deletions(-)

* 2014-08-18(Tal Galili) Fixing how the tests are printed by adding cat("\n") |6d5169c| 
|  inst/tests/test-entanglement.R | 3 +++
|  1 file changed, 3 insertions(+)

* 2014-08-18(Tal Galili) Test in set.dendrogram needed - dendextend_options("warn", TRUE) |576f951| 
|  inst/tests/test-set.dendrogram.R | 23 ++++++++++++++++++-----
|  1 file changed, 18 insertions(+), 5 deletions(-)

* 2014-08-18(Tal Galili) Test for Color recycling needed - dendextend_options("warn", TRUE) |006168a| 
|  inst/tests/test-labels_colors.R | 2 ++
|  1 file changed, 2 insertions(+)

* 2014-08-18(Tal Galili) Rename all.unique to all_unique |3411cc2| 
|  NAMESPACE                            |  3 ++-
|  NEWS                                 |  4 ++--
|  R/color_branches.R                   | 27 ++++++++++++++++++++-------
|  inst/tests/test-general.R            |  9 +++++----
|  man/{all.unique.Rd => all_unique.Rd} |  6 +++---
|  5 files changed, 32 insertions(+), 17 deletions(-)

* 2014-08-18(Tal Galili) `cutree.dendrogram` - replaces NA values with 0L - adjust the tests. |49a4bd8| 
|  NEWS                                | 2 +-
|  inst/tests/test-cutree.dendrogram.R | 8 ++++----
|  2 files changed, 5 insertions(+), 5 deletions(-)

* 2014-08-18(Tal Galili)    * `untangle_step_rotate_1side` - added "leaves_matching_method" parameter.    * `entanglement.dendrogram` - changed the default of "leaves_matching_method" to be "labels" (slower, but safer for the user...) |f77b4b6| 
|  NEWS                              |  2 ++
|  R/entanglement.R                  |  7 ++++---
|  R/untangle.R                      | 37 ++++++++++++++++++++++++++++++-------
|  man/entanglement.Rd               |  7 ++++---
|  man/untangle_random_search.Rd     |  4 ++--
|  man/untangle_step_rotate_1side.Rd | 19 ++++++++++++++++++-
|  6 files changed, 60 insertions(+), 16 deletions(-)

* 2014-08-18(Tal Galili) tanglegram: Changed the deafult in cex_main to 2 |d02bd09| 
|  R/tanglegram.R    | 4 ++--
|  man/tanglegram.Rd | 2 +-
|  2 files changed, 3 insertions(+), 3 deletions(-)

* 2014-08-18(Tal Galili) `untangle` - has a default to method (DendSet) |424b02d| 
|  NEWS            | 1 +
|  R/untangle.R    | 9 +++++++--
|  man/untangle.Rd | 4 +++-
|  3 files changed, 11 insertions(+), 3 deletions(-)

* 2014-08-18(Tal Galili) `set.dendrogram` - added a "labels_to_char" option. |6f6f0cf| 
|  NEWS               | 1 +
|  R/set.dendrogram.R | 4 ++++
|  man/set.Rd         | 2 ++
|  3 files changed, 7 insertions(+)

* 2014-08-18(Tal Galili) vignettes: pvclust, and dendlist sections. |fe7206c| 
|  vignettes/introduction.Rmd | 72 ++++++++++++++++++++++++++++++++++++--------
|  1 file changed, 60 insertions(+), 12 deletions(-)

* 2014-08-18(Tal Galili) New function: `head.dendlist` |bd03014| 
|  NAMESPACE    |  1 +
|  NEWS         |  1 +
|  R/dendlist.R | 15 +++++++++++++++
|  3 files changed, 17 insertions(+)

* 2014-08-18(Tal Galili) update pvrect2 - if we'd ever want one with adjustable lower rects... |07866e2| 
|  R/pvclust.R | 15 ++++++++++++---
|  1 file changed, 12 insertions(+), 3 deletions(-)

* 2014-08-18(Tal Galili) Added pvrect2 - a copy of pvrect |185e6bf| 
|  R/pvclust.R | 109 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 109 insertions(+)

* 2014-08-18(Tal Galili) vignettes: "Enhancing other packages" examples for DendSer, gplots and dynamicTreeCut |69d0a52| 
|  vignettes/introduction.Rmd | 92 ++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 92 insertions(+)

* 2014-08-18(Tal Galili) Added is.infinite2 and used it so to avoid endless warnings over type coercion... |b778982| 
|  R/attr_access.R | 22 +++++++++++++++++-----
|  R/dendlist.R    |  2 +-
|  2 files changed, 18 insertions(+), 6 deletions(-)

* 2014-08-18(Tal Galili) `assign_values_to_branches_edgePar`, `assign_values_to_nodes_nodePar`, `assign_values_to_leaves_nodePar` - now ignores "Inf" also when it is a character by adding as.numeric (and not only if it is numeric!) (this might be a problem if someone would try to update a label with the name "Inf"). |a6a2a78| 
|  NEWS                             |  4 ++++
|  R/attr_access.R                  | 11 ++++++++---
|  R/branches_attr_by.R             |  2 +-
|  man/branches_attr_by_clusters.Rd |  2 +-
|  4 files changed, 14 insertions(+), 5 deletions(-)

* 2014-08-18(Tal Galili) A new test for `assign_values_to_branches_edgePar` - make sure it deals with Inf and "Inf". |9036ac1| 
|  inst/tests/test-branches_attr_by.R | 76 ++++++++++++++++++++++++++++++++++++
|  1 file changed, 76 insertions(+)

* 2014-08-17(Tal Galili) Made sure "rotate_DendSer" shows in the docs. |1409976| 
|  R/DendSer.R               | 6 +++---
|  man/DendSer.dendrogram.Rd | 2 +-
|  man/dendlist.Rd           | 2 +-
|  man/rotate_DendSer.Rd     | 2 +-
|  man/untangle_DendSer.Rd   | 2 +-
|  5 files changed, 7 insertions(+), 7 deletions(-)

* 2014-08-17(Tal Galili) Adding DendSer.R (moving functions into it) |c9f589b| 
|  NEWS         |   1 +
|  R/DendSer.R  | 130 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  R/untangle.R | 110 ------------------------------------------------
|  3 files changed, 131 insertions(+), 110 deletions(-)

* 2014-08-17(Tal Galili) vignettes: Adding extra bars and rectangles |9040574| 
|  vignettes/introduction.Rmd | 66 ++++++++++++++++++++++++++++++++++++++++++--
|  1 file changed, 64 insertions(+), 2 deletions(-)

* 2014-08-17(Tal Galili) `colored_bars` - fix for multiple bars to work. +have scale default be better for multiple bars. |2feadad| 
|  NEWS                |  3 ++-
|  R/colored_bars.R    | 28 ++++++++++++++++++++--------
|  man/colored_bars.Rd | 13 +++++++++----
|  3 files changed, 31 insertions(+), 13 deletions(-)

* 2014-08-16(Tal Galili) `rect.dendrogram` - Made sure the heights are working properly! |636a223| 
|  NEWS                |  1 +
|  R/rect.dendrogram.R | 22 +++++++++++++++-------
|  2 files changed, 16 insertions(+), 7 deletions(-)

* 2014-08-16(Tal Galili) rect.dendrogram - fix a bug with the location of the rect's (using "tree" and not "dend") |792929f| 
|  NEWS                | 2 +-
|  R/rect.dendrogram.R | 4 ++--
|  2 files changed, 3 insertions(+), 3 deletions(-)

* 2014-08-16(Tal Galili) `intersect_trees` - now returns a dendlist. |b2fa915| 
|  NEWS                   | 1 +
|  R/prune.R              | 4 ++--
|  man/intersect_trees.Rd | 2 +-
|  3 files changed, 4 insertions(+), 3 deletions(-)

* 2014-08-16(Tal Galili) Rename files: trim.R -> prune.R |83f6388| 
|  NEWS                  | 1 +
|  R/{trim.R => prune.R} | 0
|  2 files changed, 1 insertion(+)

* 2014-08-15(Tal Galili) Use "set" in order to not confuse the reader... |6e048d2| 
|  vignettes/introduction.Rmd | 30 ++++++++++++++++++++++--------
|  1 file changed, 22 insertions(+), 8 deletions(-)

* 2014-08-14(Tal Galili) Vignettes: Writing "Changing a dendrogram’s structure" |197d1fd| 
|  vignettes/introduction.Rmd | 64 ++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 64 insertions(+)

* 2014-08-14(Tal Galili) color_branches - warn of missing k only if warn=TRUE |f8677ba| 
|  R/color_branches.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-08-14(Tal Galili) vignettes: moved to dend15 and dend13. Wrote: * Setting a dendrogram's nodes/leaves (points) * Setting a dendrogram's branches |ffb1aaf| 
|  vignettes/introduction.Rmd | 226 +++++++++++++++++++++++++++++++------------
|  1 file changed, 164 insertions(+), 62 deletions(-)

* 2014-08-14(Tal Galili) `branches_attr_by_labels` now uses `dendextend_options("warn")` to decide if to print that labels were coerced into character. |a4fd3ef| 
|  NEWS                 | 1 +
|  R/branches_attr_by.R | 2 +-
|  2 files changed, 2 insertions(+), 1 deletion(-)

* 2014-08-14(Tal Galili) Fix headers. |a3e5f79| 
|  NEWS | 13 ++++++++-----
|  1 file changed, 8 insertions(+), 5 deletions(-)

* 2014-08-14(Tal Galili) `branches_attr_by_clusters` and `branches_attr_by_labels` - moved from using NA to Inf. |2f3f5df| 
|  NEWS                           |  1 +
|  R/branches_attr_by.R           | 16 ++++++++--------
|  man/branches_attr_by_labels.Rd |  4 ++--
|  3 files changed, 11 insertions(+), 10 deletions(-)

* 2014-08-14(Tal Galili) Move the function branches_attr_by_labels between two files |1e65ab0| 
|  NEWS                     |   2 +-
|  R/branches_attr_by.R     | 113 +++++++++++++++++++++++++++++++++++++++++++++
|  R/noded_with_condition.R | 101 ----------------------------------------
|  3 files changed, 114 insertions(+), 102 deletions(-)

* 2014-08-14(Tal Galili) Simplify the introduction, and use if for DESCRIPTION |4142dd9| 
|  DESCRIPTION                | 8 ++++++--
|  NEWS                       | 2 +-
|  vignettes/introduction.Rmd | 8 ++++----
|  3 files changed, 11 insertions(+), 7 deletions(-)

* 2014-08-14(Tal Galili) `colored_bars` - added defaults to make the bars be plotted bellow the labels (+allow the order of the bars to be based on the labels' order) |dc0b710| 
|  NEWS                |  1 +
|  R/colored_bars.R    | 28 ++++++++++++++++++++++++++--
|  man/colored_bars.Rd | 14 +++++++++++---
|  3 files changed, 38 insertions(+), 5 deletions(-)

* 2014-08-14(Tal Galili) `color_branches` - can now work when the labels of the tree are not unique (feature request by Heather Turner - thanks Heather :) ) |5722bcc| 
|  NEWS               |  5 +++--
|  R/color_branches.R | 13 +++++++++++++
|  2 files changed, 16 insertions(+), 2 deletions(-)

* 2014-08-14(Tal Galili) all.unique - check if all elements in a vector are unique (including tests) |0eb8327| 
|  NAMESPACE                 |  1 +
|  NEWS                      |  2 +-
|  R/color_branches.R        | 33 +++++++++++++++++++++++++++++++++
|  inst/tests/test-general.R | 14 ++++++++++++++
|  man/all.unique.Rd         | 32 ++++++++++++++++++++++++++++++++
|  5 files changed, 81 insertions(+), 1 deletion(-)

* 2014-08-14(Tal Galili) vignettes: Explaining depth-first search |b77bded| 
|  vignettes/introduction.Rmd | 153 ++++++++++++++++++++++++++++++++-----------
|  1 file changed, 115 insertions(+), 38 deletions(-)

* 2014-08-11(Tal Galili) Fix lower_rect in rect.dendrogram to work with horiz=TRUE |ac6e2f7| 
|  R/rect.dendrogram.R    | 5 ++++-
|  man/rect.dendrogram.Rd | 5 ++++-
|  2 files changed, 8 insertions(+), 2 deletions(-)

* 2014-08-11(Tal Galili) moving the date. |6d7eb14| 
|  DESCRIPTION | 2 +-
|  NEWS        | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2014-08-11(Tal Galili) `rect.dendrogram` - a new xpd and lower_rect parameters - to control how low the rect will be (for example, below or above the labels). The default is below the labels. |f7e58f6| 
|  NEWS                   |  2 +-
|  R/rect.dendrogram.R    | 32 ++++++++++++++++++++++++++++----
|  man/rect.dendrogram.Rd | 19 ++++++++++++++++---
|  3 files changed, 45 insertions(+), 8 deletions(-)

* 2014-08-10(Tal Galili) Dealing with a missing/junk attribute |12f3566| 
|  R/attr_access.R               | 5 +----
|  inst/tests/test-attr_access.R | 3 +++
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2014-08-10(Tal Galili) `get_nodes_attr` - can now return an array or a list for attributes which include a more complex structure (such as nodePar), by working with lists and adding a "simplify" parameter. |f264362| 
|  NEWS                          |  1 +
|  R/attr_access.R               | 19 +++++++++++++++++--
|  inst/tests/test-attr_access.R |  8 +++++++-
|  man/get_nodes_attr.Rd         |  6 +++++-
|  4 files changed, 30 insertions(+), 4 deletions(-)

* 2014-08-10(Tal Galili) vignettes introduction: added a first draft of explaining depth first |a99955f| 
|  vignettes/introduction.Rmd | 36 +++++++++++++++++++++++++++++++++---
|  1 file changed, 33 insertions(+), 3 deletions(-)

* 2014-08-10(Tal Galili) get_nodes_xy - Get the x-y coordiantes of a dendrogram's nodes |28b8205| 
|  DESCRIPTION         |   4 +-
|  NAMESPACE           |   1 +
|  NEWS                |   5 +
|  R/get_nodes_xy.R    | 253 ++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/get_nodes_xy.Rd |  72 ++++++++++++++
|  5 files changed, 333 insertions(+), 2 deletions(-)

* 2014-08-09(Tal Galili) Changing a dendrogram’s labels |1c2c9d5| 
|  vignettes/introduction.Rmd | 108 +++++++++++++++++++++++++++++++++++++++----
|  1 file changed, 99 insertions(+), 9 deletions(-)

* 2014-08-09(Tal Galili) set.dendrogram - if "what" is missing, return the object as is. |27836ee| 
|  NEWS               | 3 ++-
|  R/set.dendrogram.R | 5 +++++
|  2 files changed, 7 insertions(+), 1 deletion(-)

* 2014-08-09(Tal Galili) set.dendrogram - changed from using `labels_colors<-` to `color_labels` for "labels_colors" (this will now work with using k...) |69c8bcf| 
|  NEWS               | 1 +
|  R/set.dendrogram.R | 3 ++-
|  2 files changed, 3 insertions(+), 1 deletion(-)

* 2014-08-09(Tal Galili) `labels<-.dendrogram` - if value is missing, returning the dendrogram as is (this also affects `set`) |0c9d5fb| 
|  NEWS       | 2 ++
|  R/labels.R | 6 ++++++
|  2 files changed, 8 insertions(+)

* 2014-08-09(Tal Galili) `labels_colors<-` - added if(dendextend_options("warn")) |0585aae| 
|  NEWS              | 1 +
|  R/labels_colors.R | 4 ++--
|  2 files changed, 3 insertions(+), 2 deletions(-)

* 2014-08-09(Tal Galili) set.dendrogram - added nodes_pch, nodes_cex and nodes_col - using `assign_values_to_nodes_nodePar` |c638422| 
|  NEWS               |  1 +
|  R/set.dendrogram.R | 12 ++++++++++++
|  man/set.Rd         |  6 ++++++
|  3 files changed, 19 insertions(+)

* 2014-08-08(Tal Galili) Moved Iris example to the end. And added explenation in the .Rd docs of the different possible options for "what" can get in set.dendrogram. |15c19b7| 
|  vignettes/introduction.Rmd | 160 +++++++++++++++++++++++++++----------------
|  1 file changed, 101 insertions(+), 59 deletions(-)

* 2014-08-08(Tal Galili) set.dendrogram - added explenation in the .Rd docs of the different possible options for "what" |8f65726| 
|  NEWS               |  1 +
|  R/set.dendrogram.R | 21 +++++++++++++++++++++
|  man/set.Rd         | 21 +++++++++++++++++++++
|  3 files changed, 43 insertions(+)

* 2014-08-08(Tal Galili) Added a d3 .Rd |1c70916| 
|  man/d3dendro_options.Rd | 40 ++++++++++++++++++++++++++++++++++++++++
|  man/d3dendrogram.Rd     | 47 +++++++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 87 insertions(+)

* 2014-08-08(Tal Galili) Introdution vignettes - wrote a decent: tl;dr and Prerequisites (acknowledgement, iris, chaining) |b46135b| 
|  DESCRIPTION                |  29 +++++-----
|  vignettes/introduction.Rmd | 131 +++++++++++++++++++++++++++++--------------
|  2 files changed, 104 insertions(+), 56 deletions(-)

* 2014-08-08(Tal Galili) `cutree.dendrogram` - now replaces NA values with 0L |2061c3e| 
|  NEWS                  | 1 +
|  R/cutree.dendrogram.R | 3 ++-
|  2 files changed, 3 insertions(+), 1 deletion(-)

* 2014-08-08(Tal Galili) `color_branches` - now handles flat trees more gracefully. (returns them as they are) |b999388| 
|  NEWS                  |  2 +-
|  R/color_branches.R    | 17 ++++++++++++++++-
|  man/color_branches.Rd | 12 +++++++++++-
|  3 files changed, 28 insertions(+), 3 deletions(-)

* 2014-08-08(Tal Galili) Include dendextend_options("warn", TRUE) in tests. |c2f7b68| 
|  R/cutree.dendrogram.R               | 4 ++--
|  inst/tests/test-cutree.dendrogram.R | 5 ++++-
|  inst/tests/test-unbranch.R          | 3 +++
|  man/untangle_step_rotate_2side.Rd   | 4 ++--
|  4 files changed, 11 insertions(+), 5 deletions(-)

* 2014-08-08(Tal Galili) untangle_step_rotate_2side` - print_times is now dendextend_options("warn"), |0da7c3f| 
|  NEWS         | 4 +++-
|  R/untangle.R | 2 +-
|  2 files changed, 4 insertions(+), 2 deletions(-)

* 2014-08-08(Tal Galili) Update .Rd docs, now that ALL `warn` paramteres are set to dendextend_options("warn") (which is FALSE) |6f4031f| 
|  man/Bk.Rd                                |  9 +++++----
|  man/Bk_permutations.Rd                   |  7 +++++--
|  man/Bk_plot.Rd                           | 10 ++++++----
|  man/FM_index.Rd                          |  6 ++++--
|  man/FM_index_R.Rd                        |  6 ++++--
|  man/FM_index_permutation.Rd              |  7 +++++--
|  man/FM_index_profdpm.Rd                  |  6 ++++--
|  man/assign_values_to_branches_edgePar.Rd | 10 ++++------
|  man/assign_values_to_leaves_nodePar.Rd   | 11 +++++------
|  man/assign_values_to_nodes_nodePar.Rd    | 10 ++++------
|  man/color_labels.Rd                      |  7 +++++--
|  man/cor_bakers_gamma.Rd                  |  6 ++++--
|  man/cut_lower_fun.Rd                     |  8 +++++---
|  man/cutree-methods.Rd                    |  6 ++++--
|  man/cutree_1h.dendrogram.Rd              |  6 ++++--
|  man/cutree_1k.dendrogram.Rd              |  8 +++++---
|  man/dendextend_options.Rd                |  6 ++++++
|  man/get_branches_attr.Rd                 |  7 +++++--
|  man/intersect_trees.Rd                   |  8 +++++---
|  man/sort_2_clusters_vectors.Rd           |  6 ++++--
|  man/sort_levels_values.Rd                |  8 +++++---
|  man/tanglegram.Rd                        |  5 +++--
|  22 files changed, 101 insertions(+), 62 deletions(-)

* 2014-08-08(Tal Galili) ALL `warn` paramteres are no set to dendextend_options("warn") (which is FALSE) |bb759ff| 
|  NEWS                  |  6 ++++++
|  R/attr_access.R       | 30 ++++++++++++-----------------
|  R/bk_method.R         | 50 +++++++++++++++++++++++++++++++------------------
|  R/color_branches.R    | 10 ++++++----
|  R/cor_bakers_gamma.R  | 10 ++++++----
|  R/cor_cophenetic.R    |  2 +-
|  R/cut_lower_fun.R     | 10 ++++++----
|  R/cutree.dendrogram.R | 36 +++++++++++++++++++++--------------
|  R/tanglegram.R        | 11 ++++++-----
|  R/trim.R              |  8 +++++---
|  10 files changed, 102 insertions(+), 71 deletions(-)

* 2014-08-08(Tal Galili) `get_branches_attr` - change "warning" to "warn", and it now works with is.dendrogram, and no longer changes the class of something which is not a dendrogram. |73e4ad0| 
|  R/unbranch.R | 14 ++++++++------
|  1 file changed, 8 insertions(+), 6 deletions(-)

* 2014-08-08(Tal Galili) A new "warn" dendextend_options parameter. logical (FALSE). Should warning be issued? |d491d43| 
|  R/dendextend_options.R | 8 ++++++++
|  1 file changed, 8 insertions(+)

* 2014-08-08(Tal Galili) dendextend_options.R - moved `dendextend_options` functions to it. |8e33740| 
|  NEWS                   |   8 ++++
|  R/dendextend_options.R | 110 +++++++++++++++++++++++++++++++++++++++++++++++
|  R/zzz.R                |  88 -------------------------------------
|  3 files changed, 118 insertions(+), 88 deletions(-)

* 2014-08-07(Tal Galili) A new draft for introduction.Rmd Vignettes |ddc69d9| 
|  vignettes/introduction.Rmd | 187 +++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 187 insertions(+)

* 2014-08-06(Tal Galili) Added pvclust - bump to 0.16.4 |e4cca44| 
|  ChangeLog   | 120 ++++++++++++++++++++++++
|  DESCRIPTION |   5 +-
|  NEWS.md     | 297 +++++++++++++++++++++++++++++++++-------------------------
|  3 files changed, 290 insertions(+), 132 deletions(-)

* 2014-08-06(Tal Galili) NEW FUNCTIONS:    * `as.dendrogram.pvclust` - extract the hclust from a pvclust object, and turns it into a dendrogram.    * `hc2axes` - imported from pvclust, needed for text.pvclust    * `text.pvclust` - imported from pvclust, adds text to a dend plot of a pvclust result    * `pvclust_show_signif` - Shows the significant branches in a dendrogram, based on a pvclust object    * `pvclust_show_signif_gradient` - Shows the gradient of significance of branches in a dendrogram, based on a pvclust object |5677850| 
|  NAMESPACE                           |   4 +
|  NEWS                                |  16 ++
|  R/pvclust.R                         | 281 ++++++++++++++++++++++++++++++++--
|  man/pvclust_show_signif.Rd          |  65 ++++++++
|  man/pvclust_show_signif_gradient.Rd |  58 +++++++
|  5 files changed, 412 insertions(+), 12 deletions(-)

* 2014-08-06(Tal Galili) Move from is.finite to !is.infinite - so to be able to handle characters and not just numbers! |c00faa7| 
|  R/attr_access.R | 6 +++---
|  1 file changed, 3 insertions(+), 3 deletions(-)

* 2014-08-06(Tal Galili)  `assign_values_to_leaves_nodePar`, `assign_values_to_nodes_nodePar`, `assign_values_to_branches_edgePar` - If the value has `Inf` (instead of NA!) then the value will not be changed. |d44661d| 
|  R/attr_access.R                          | 16 +++++++---------
|  inst/tests/test-set.dendrogram.R         |  8 ++++----
|  man/assign_values_to_branches_edgePar.Rd |  4 +---
|  man/assign_values_to_leaves_nodePar.Rd   |  2 +-
|  man/assign_values_to_nodes_nodePar.Rd    |  6 +++---
|  5 files changed, 16 insertions(+), 20 deletions(-)

* 2014-08-06(Tal Galili) Version bump to 0.16.3 |91b0884| 
|  DESCRIPTION | 9 +++++----
|  1 file changed, 5 insertions(+), 4 deletions(-)

* 2014-08-06(Tal Galili) `assign_values_to_nodes_nodePar` - Assign values to nodePar of dendrogram's nodes |5dbfb56| 
|  NAMESPACE                              |   2 +-
|  NEWS                                   |   6 ++
|  R/attr_access.R                        | 116 +++++++++++++++++++++++++++++--
|  man/assign_values_to_leaves_nodePar.Rd |   6 +-
|  man/assign_values_to_nodes_nodePar.Rd  |  55 +++++++++++++++
|  5 files changed, 177 insertions(+), 8 deletions(-)

* 2014-08-06(Tal Galili) NEWS - updated to use header 2 and 3 instead of 1 and 2 for the markdown version. |a025624| 
|  NEWS | 271 +++++++++++++++++++++++++++++++++--------------------------------
|  1 file changed, 139 insertions(+), 132 deletions(-)

* 2014-08-06(mark) removed export directive |09030d7| 
|  R/d3dendrogram.R | 1 -
|  1 file changed, 1 deletion(-)

* 2014-08-06(mark) Added and documented global options |bfc2809| 
|  NAMESPACE        |  1 +
|  R/d3dendrogram.R | 96 ++++++++++++++++++++++++++++++++++++++++++------------
|  R/zzz.R          |  3 ++
|  3 files changed, 79 insertions(+), 21 deletions(-)

* 2014-08-06(mark) d3dendrogram accepts global options, e.g. node_fill |2d39826| 
|  R/d3dendrogram.R | 89 +++++++++++++++++++++++++++++++++++-------------------
|  1 file changed, 58 insertions(+), 31 deletions(-)

* 2014-08-06(mark) d3dendrogram now opens in (RStudio) viewer by default |10a64b3| 
|  R/d3dendrogram.R | 33 ++++++++++++++++++++++-----------
|  1 file changed, 22 insertions(+), 11 deletions(-)

* 2014-07-29(Tal Galili) require -> library (Thanks Yihui: http://yihui.name/en/2014/07/library-vs-require/) |e676951| 
|  DESCRIPTION                         |  4 +--
|  NEWS                                |  8 ++++++
|  R/as.dendrogram.randomForest.R      |  2 +-
|  R/attr_access.R                     |  6 ++---
|  R/bk_method.R                       |  4 +--
|  R/branches_attr_by.R                |  8 +++---
|  R/color_branches.R                  | 10 ++++----
|  R/colored_bars.R                    |  6 ++---
|  R/cor_bakers_gamma.R                |  4 +--
|  R/cor_cophenetic.R                  |  2 +-
|  R/cut_lower_fun.R                   |  8 +++---
|  R/cutree.dendrogram.R               | 10 ++++----
|  R/d3dendrogram.R                    |  6 ++---
|  R/nleaves.R                         |  8 +++---
|  R/noded_with_condition.R            | 12 ++++-----
|  R/pvclust.R                         |  4 +--
|  R/rotate.R                          |  6 ++---
|  R/set.dendrogram.R                  |  2 +-
|  R/trim.R                            |  2 +-
|  R/unbranch.R                        |  2 +-
|  R/untangle.R                        | 20 +++++++--------
|  R/zzz.R                             | 10 ++++----
|  TODO                                |  4 +++
|  demo/dendextend.R                   |  2 +-
|  inst/tests/test-attr_access.R       |  4 +--
|  inst/tests/test-bk_method.R         |  2 +-
|  inst/tests/test-cor_bakers_gamma.R  |  2 +-
|  inst/tests/test-cor_cophenetic.R    |  2 +-
|  inst/tests/test-cut_lower_fun.R     |  8 +++---
|  inst/tests/test-cutree.dendrogram.R |  8 +++---
|  inst/tests/test-dendlist.R          |  2 +-
|  inst/tests/test-entanglement.R      |  4 +--
|  inst/tests/test-labels-assign.R     |  2 +-
|  inst/tests/test-nleaves.R           |  2 +-
|  inst/tests/test-rotate.R            |  4 +--
|  inst/tests/test-set.dendrogram.R    | 10 ++++----
|  inst/tests/test-trim.R              |  4 +--
|  inst/tests/test-untangle.R          |  4 +--
|  man/DendSer.dendrogram.Rd           |  2 +-
|  man/FM_index.Rd                     |  2 +-
|  man/FM_index_permutation.Rd         |  2 +-
|  man/branches_attr_by_clusters.Rd    |  6 ++---
|  man/branches_attr_by_labels.Rd      |  4 +--
|  man/color_branches.Rd               |  6 ++---
|  man/cor_bakers_gamma.Rd             |  2 +-
|  man/cor_cophenetic.Rd               |  2 +-
|  man/cut_lower_fun.Rd                |  6 ++---
|  man/cutree-methods.Rd               |  2 +-
|  man/cutree_1h.dendrogram.Rd         |  2 +-
|  man/cutree_1k.dendrogram.Rd         |  2 +-
|  man/get_branches_heights.Rd         |  4 +--
|  man/get_nodes_attr.Rd               |  2 +-
|  man/heights_per_k.dendrogram.Rd     |  2 +-
|  man/na_locf.Rd                      |  4 +--
|  man/noded_with_condition.Rd         |  4 +--
|  man/rotate_DendSer.Rd               |  2 +-
|  man/set.Rd                          |  2 +-
|  man/which_leaf.Rd                   |  4 +--
|  vignettes/dendextend-tutorial.rnw   | 48 +++++++++++++++++------------------
|  59 files changed, 165 insertions(+), 153 deletions(-)

* 2014-07-26(Tal Galili) ChangeLog |2257d2c| 
|  ChangeLog | 20 ++++++++++++++++++++
|  1 file changed, 20 insertions(+)

* 2014-07-26(Tal Galili) Comment out example code that won't run. |f39d69e| 
|  NEWS.md     |   7 ++
|  R/pvclust.R | 242 +++++++++++++++++++++++++++++-----------------------------
|  2 files changed, 128 insertions(+), 121 deletions(-)

* 2014-07-26(Tal Galili) Fix: \examples lines wider than 100 characters |051eab6| 
|  DESCRIPTION                      |  2 +-
|  NEWS                             |  7 +++++++
|  R/branches_attr_by.R             |  3 ++-
|  R/noded_with_condition.R         | 30 ++++++++++++++++++++++--------
|  man/branches_attr_by_clusters.Rd |  3 ++-
|  man/branches_attr_by_labels.Rd   | 24 ++++++++++++++++++------
|  man/noded_with_condition.Rd      |  4 +++-
|  7 files changed, 55 insertions(+), 18 deletions(-)

* 2014-07-26(Tal Galili) Update NEWS and ChangeLog |9cd933b| 
|  ChangeLog | 47 +++++++++++++++++++++++++++++++++++++++++++++++
|  NEWS.md   |  8 ++++++--
|  2 files changed, 53 insertions(+), 2 deletions(-)

* 2014-07-26(Tal Galili) added a pvclust example (using a condition on p-value, and heighlighting branches based on that with lwd/col.) |cbbaae3| 
|  NEWS        |   2 +
|  R/pvclust.R | 121 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  TODO        |   1 -
|  3 files changed, 123 insertions(+), 1 deletion(-)

* 2014-07-26(Tal Galili) `na_locf` - Fill Last Observation Carried Forward |5e764d7| 
|  DESCRIPTION    |  2 +-
|  NAMESPACE      |  1 +
|  NEWS           |  4 +--
|  R/pvclust.R    | 92 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/na_locf.Rd | 57 +++++++++++++++++++++++++++++++++++
|  5 files changed, 153 insertions(+), 3 deletions(-)

* 2014-07-26(Tal Galili) `which_leaf` - a new function to tell us Which node is a leaf |3658216| 
|  NAMESPACE                |  1 +
|  NEWS                     |  1 +
|  R/noded_with_condition.R | 35 +++++++++++++++++++++++++++++++++++
|  TODO                     |  1 +
|  man/which_leaf.Rd        | 40 ++++++++++++++++++++++++++++++++++++++++
|  5 files changed, 78 insertions(+)

* 2014-07-26(Tal Galili) `assign_values_to_branches_edgePar` - allow the option to skip leaves |9ec9e1d| 
|  NEWS                                     |  1 +
|  R/attr_access.R                          | 10 ++++++++--
|  man/assign_values_to_branches_edgePar.Rd |  5 ++++-
|  3 files changed, 13 insertions(+), 3 deletions(-)

* 2014-07-26(Tal Galili) branches_attr_by_labels - if dend is not a dendrogram, we should stop and not warn! |591c3b9| 
|  R/noded_with_condition.R | 6 +++++-
|  1 file changed, 5 insertions(+), 1 deletion(-)

* 2014-07-25(Tal Galili) various doc updates. |a8863ab| 
|  ChangeLog                        | 203 +++++++++++++++++++++++++++++++++++++
|  NEWS.md                          |  60 ++++++++++-
|  R/branches_attr_by.R             |   1 +
|  TODO                             |   6 +-
|  man/branches_attr_by_clusters.Rd |   1 +
|  5 files changed, 267 insertions(+), 4 deletions(-)

* 2014-07-25(Tal Galili) Added import for "whisker" for d3dendrogram. |426bd4a| 
|  DESCRIPTION            | 1 +
|  NAMESPACE              | 1 +
|  R/d3dendrogram.R       | 3 ++-
|  R/dendextend-package.R | 1 +
|  4 files changed, 5 insertions(+), 1 deletion(-)

* 2014-07-25(Tal Galili) Updated TODO :) |82524ce| 
|  TODO | 4 ----
|  1 file changed, 4 deletions(-)

* 2014-07-25(Tal Galili) Added ref to plotDendroAndColors |81e15ee| 
|  R/branches_attr_by.R             | 3 ++-
|  R/colored_bars.R                 | 4 ++--
|  man/branches_attr_by_clusters.Rd | 3 ++-
|  man/colored_bars.Rd              | 3 ++-
|  4 files changed, 8 insertions(+), 5 deletions(-)

* 2014-07-25(Tal Galili) For now - version 0.16.0 |4c13ada| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-07-25(Tal Galili) branches_attr_by_clusters - modified the example in the docs a bit (using the original dist matrix for the cutreeDynamic). |04ffde4| 
|  R/branches_attr_by.R             | 16 +++++++++-------
|  man/branches_attr_by_clusters.Rd | 16 +++++++++-------
|  2 files changed, 18 insertions(+), 14 deletions(-)

* 2014-07-25(Tal Galili) `colored_bars` - update docs |6283ece| 
|  NEWS                | 2 +-
|  R/colored_bars.R    | 9 +++++++--
|  man/colored_bars.Rd | 3 +++
|  3 files changed, 11 insertions(+), 3 deletions(-)

* 2014-07-25(Tal Galili) `branches_attr_by_labels` - change the order of some parameters (based on how much I expect users to use each of them.) |efd8c42| 
|  NEWS                           |  1 +
|  R/noded_with_condition.R       | 11 ++++++-----
|  man/branches_attr_by_labels.Rd | 16 +++++++++-------
|  3 files changed, 16 insertions(+), 12 deletions(-)

* 2014-07-25(Tal Galili) Added branches_attr_by_clusters - This function was designed to enable the manipulation (mainly coloring) of branches, based on the results from the cutreeDynamic function (from the {dynamicTreeCut} package). |cf18ef3| 
|  NAMESPACE                        |   1 +
|  NEWS                             |   8 +-
|  R/branches_attr_by.R             | 182 +++++++++++++++++++++++++++++++++++++
|  man/branches_attr_by_clusters.Rd | 111 ++++++++++++++++++++++
|  4 files changed, 300 insertions(+), 2 deletions(-)

* 2014-07-25(Tal Galili) colored_bars - change the order of colors and dend, and allowing for dend to be missing. |4e85359| 
|  NEWS                |  4 ++++
|  R/colored_bars.R    | 19 ++++++++++++-------
|  man/colored_bars.Rd |  7 ++++---
|  3 files changed, 20 insertions(+), 10 deletions(-)

* 2014-07-25(Tal Galili) assign_values_to_branches_edgePar - now can keep existing value, if gets NA. |0c29c7b| 
|  DESCRIPTION                              | 4 ++--
|  NEWS                                     | 8 ++++++++
|  R/attr_access.R                          | 9 ++++++++-
|  R/noded_with_condition.R                 | 8 ++++++--
|  man/assign_values_to_branches_edgePar.Rd | 4 ++++
|  man/branches_attr_by_labels.Rd           | 5 +++--
|  6 files changed, 31 insertions(+), 7 deletions(-)

* 2014-07-24(talgalili) minor fixes |f0306e8| 
|  README.md | 6 ++++--
|  1 file changed, 4 insertions(+), 2 deletions(-)

* 2014-07-24(talgalili) Add options to the methods. |922befd| 
|  R/set.dendrogram.R | 3 +++
|  man/set.Rd         | 3 +++
|  2 files changed, 6 insertions(+)

* 2014-07-24(talgalili) In the docs: \dontrun { -> \dontrun{ |76e215f| 
|  R/noded_with_condition.R       | 4 ++--
|  man/branches_attr_by_labels.Rd | 2 +-
|  man/noded_with_condition.Rd    | 2 +-
|  3 files changed, 4 insertions(+), 4 deletions(-)

* 2014-07-24(talgalili) make package installation easier |859ad72| 
|  README.md | 14 ++++++++------
|  1 file changed, 8 insertions(+), 6 deletions(-)

* 2014-07-24(talgalili) Updated DESCRIPTION and NEWS to version 0.15.2 |069acdf| 
|  DESCRIPTION |  5 +++--
|  NEWS        | 11 ++++++++++-
|  2 files changed, 13 insertions(+), 3 deletions(-)

* 2014-07-24(talgalili) set.dendrogram - added new options: by_labels_branches_col, by_labels_branches_lwd, by_labels_branches_lty |0e4e414| 
|  R/set.dendrogram.R | 38 +++++++++++++++++++++++++++++++++++++-
|  man/set.Rd         | 31 ++++++++++++++++++++++++++++++-
|  2 files changed, 67 insertions(+), 2 deletions(-)

* 2014-07-24(talgalili) NEW FUNCTIONS:    * `noded_with_condition` - Find which nodes satisfies a condition    * `branches_attr_by_labels` - Change col/lwd/lty of branches matching labels condition |1c59527| 
|  NAMESPACE                      |   2 +
|  R/noded_with_condition.R       | 184 +++++++++++++++++++++++++++++++++++++++
|  man/branches_attr_by_labels.Rd |  56 ++++++++++++
|  man/noded_with_condition.Rd    |  61 +++++++++++++
|  4 files changed, 303 insertions(+)

* 2014-07-24(talgalili) Minor fixes to get the package to work. Also added some credit, and a more robust installation code to README.md (so it would work on non-Windows OS better) |53046d2| 
|  DESCRIPTION                | 3 ++-
|  README.md                  | 6 ++++--
|  dendextend.Rproj           | 2 +-
|  man/identify.dendrogram.Rd | 2 +-
|  4 files changed, 8 insertions(+), 5 deletions(-)

* 2014-07-24(talgalili) Fix malformed character. |5931a29| 
|  R/zzz.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-07-24(talgalili) Fix malformed character. |8126b0d| 
|  R/rect.dendrogram.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-07-19(Tal Galili) Added Mark van der Loo's first version of d3dendrogram |590e0d7| 
|  R/d3dendrogram.R | 198 +++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 198 insertions(+)

* 2014-07-19(Tal Galili) Added a heatmap.2 example to set.dendrogram |ce47f54| 
|  R/set.dendrogram.R | 28 ++++++++++++++++++++++++++++
|  man/set.Rd         | 28 ++++++++++++++++++++++++++++
|  2 files changed, 56 insertions(+)

* 2014-07-18(Tal Galili) `rect.dendrogram` - adding paramters for creating text under the clusters, as well as make it easier to plot lines on the rect (density = 7). props to skullkey for his help. |8706a7d| 
|  NEWS                   |  7 +++++++
|  R/rect.dendrogram.R    | 39 +++++++++++++++++++++++++++++++++++----
|  TODO                   | 12 +++++++-----
|  man/rect.dendrogram.Rd | 29 ++++++++++++++++++++++++++++-
|  4 files changed, 77 insertions(+), 10 deletions(-)

* 2014-07-16(Tal Galili) identify.dendrogram - function and docs added. (it might be a bit buggy...) |941521e| 
|  NAMESPACE                  |  1 +
|  NEWS                       |  2 ++
|  R/rect.dendrogram.R        | 78 +++++++++++++++++++++++++++++++++++++++-----
|  man/identify.dendrogram.Rd | 69 +++++++++++++++++++++++++++++++++++++++
|  4 files changed, 141 insertions(+), 9 deletions(-)

* 2014-07-16(Tal Galili) `rect.dendrogram` - just like `rect.hclust`, plus: works for dendrograms, passes `...` to rect for lwd lty etc, now has an horiz parameter! |b290b8b| 
|  NAMESPACE              |   1 +
|  NEWS                   |  11 ++--
|  R/labels.R             |   2 +-
|  R/rect.dendrogram.R    | 136 +++++++++++++++++++++++++++++++++++++++++++----
|  man/rect.dendrogram.Rd |  70 ++++++++++++++++++++++++
|  5 files changed, 206 insertions(+), 14 deletions(-)

* 2014-07-16(Tal Galili) rect.dendrogram - started working on the function. (we start with rect.hclust, and move from there) |3c8aa38| 
|  R/rect.dendrogram.R | 60 +++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 60 insertions(+)

* 2014-07-16(Tal Galili) order.hclust (new function) - Ordering of the Leaves in a hclust Dendrogram |224f9a0| 
|  NAMESPACE           |  1 +
|  NEWS                |  3 +++
|  R/dendextend.R      |  1 -
|  R/labels.R          | 28 ++++++++++++++++++++++++++++
|  man/order.hclust.Rd | 33 +++++++++++++++++++++++++++++++++
|  5 files changed, 65 insertions(+), 1 deletion(-)

* 2014-07-15(Tal Galili) Rename 2 file names from add->set (set.dendrogram.R and tests-set.dendrogram.R) |6b14d4b| 
|  DESCRIPTION                                                 |  4 ++--
|  NEWS                                                        | 10 ++++++++++
|  R/{add.dendrogram.R => set.dendrogram.R}                    |  0
|  inst/tests/{test-add.dendrogram.R => test-set.dendrogram.R} |  0
|  4 files changed, 12 insertions(+), 2 deletions(-)

* 2014-07-15(Tal Galili) Rename from "add" to "set"! |fb77b15| 
|  NAMESPACE                        |   6 +-
|  R/add.dendrogram.R               | 109 ++++++++++++++---------------
|  inst/tests/test-add.dendrogram.R |  46 ++++++-------
|  man/add.Rd                       | 137 -------------------------------------
|  man/set.Rd                       | 137 +++++++++++++++++++++++++++++++++++++
|  5 files changed, 216 insertions(+), 219 deletions(-)

* 2014-07-15(Tal Galili) Rename files - from update to add |e08cccb| 
|  NEWS                                                           | 7 ++++---
|  R/{update.dendrogram.R => add.dendrogram.R}                    | 0
|  inst/tests/{test-update.dendrogram.R => test-add.dendrogram.R} | 0
|  3 files changed, 4 insertions(+), 3 deletions(-)

* 2014-07-15(Tal Galili) Changed "update" to be "add". To make it easier to read and write... |cd72d1e| 
|  NAMESPACE                           |   5 +-
|  R/update.dendrogram.R               | 118 ++++++++++++++++-------------
|  R/zzz.R                             |   5 ++
|  inst/tests/test-update.dendrogram.R |  46 ++++++------
|  man/add.Rd                          | 137 ++++++++++++++++++++++++++++++++++
|  man/update.dendrogram.Rd            | 135 ---------------------------------
|  6 files changed, 233 insertions(+), 213 deletions(-)

* 2014-07-15(Tal Galili) update: change "with" to "value" (probably a better name for this parameter) |e9f44e6| 
|  R/update.dendrogram.R    | 34 +++++++++++++++++-----------------
|  man/update.dendrogram.Rd |  6 +++---
|  2 files changed, 20 insertions(+), 20 deletions(-)

* 2014-07-14(Tal Galili) is_null_list - making the example donotrun. Reason: I can run this only if I'd make is_null_list exported |d7cfcac| 
|  R/dendlist.R        | 4 ++++
|  TODO                | 1 +
|  man/is_null_list.Rd | 4 ++++
|  3 files changed, 9 insertions(+)

* 2014-07-14(Tal Galili) Updated some docs. |2b98871| 
|  ChangeLog    | 77 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  DESCRIPTION  |  2 +-
|  NEWS         |  2 +-
|  NEWS.md      |  8 ++++--
|  R/magrittr.R | 10 ++++++++
|  R/zzz.R      |  1 +
|  TODO         |  1 -
|  7 files changed, 96 insertions(+), 5 deletions(-)

* 2014-07-14(Tal Galili) Minor doc fixed for: cor_cophenetic, entanglement. as.phylo.dendrogram, untangle.dendlist, and labels.hclust (which required the use of @rdname) |30c5277| 
|  R/cor_cophenetic.R     |  7 +++++--
|  R/dendextend-package.R |  8 ++++++++
|  R/entanglement.R       |  6 +++---
|  R/nleaves.R            |  6 ++----
|  R/untangle.R           |  5 +++--
|  man/cor_cophenetic.Rd  |  4 +++-
|  man/entanglement.Rd    |  4 ++--
|  man/labels-assign.Rd   |  9 +++++++++
|  man/labels.hclust.Rd   | 11 -----------
|  man/shuffle.Rd         |  1 +
|  man/untangle.Rd        |  2 +-
|  11 files changed, 37 insertions(+), 26 deletions(-)

* 2014-07-14(Tal Galili) Added an internal function "zero_range" |58cf6bc| 
|  R/colored_bars.R | 19 +++++++++++++++++++
|  1 file changed, 19 insertions(+)

* 2014-07-14(Tal Galili) Change "" to `` when wrapping a function of style `fo<-`, so to have RStudio pick up on it. |bdca139| 
|  R/labels.R | 24 ++++++++++++++----------
|  1 file changed, 14 insertions(+), 10 deletions(-)

* 2014-07-14(Tal Galili) Moved {magrittr} to the "Imports" section in DESCRIPTION. And imported the %>% function from magrittr (using a trick from the dplyr package) |f2bb8be| 
|  DESCRIPTION  |  4 ++--
|  NAMESPACE    |  3 ++-
|  NEWS         |  3 +++
|  R/magrittr.R | 43 +++++++++++++++++++++++++++++++++++++++++++
|  man/pipe.Rd  | 32 ++++++++++++++++++++++++++++++++
|  5 files changed, 82 insertions(+), 3 deletions(-)

* 2014-07-14(Tal Galili) roxygen2 - Moved from using @S3method to @export (removed 45 warnings from check() ) |e036f50| 
|  NEWS                  |  3 ++-
|  R/cor_bakers_gamma.R  |  6 ++++--
|  R/cutree.dendrogram.R |  4 ++--
|  R/entanglement.R      | 12 ++++++++----
|  R/labels.R            | 12 ++++++------
|  R/nleaves.R           | 27 +++++++++++++++++----------
|  R/rotate.R            | 18 ++++++++++++------
|  R/tanglegram.R        | 12 ++++++++----
|  R/trim.R              |  9 ++++++---
|  R/unbranch.R          |  9 ++++++---
|  R/untangle.R          | 18 ++++++++++++------
|  R/update.dendrogram.R |  3 ++-
|  R/zzz.R               |  1 +
|  TODO                  |  4 ++++
|  man/labels.hclust.Rd  | 11 +++++++++++
|  15 files changed, 101 insertions(+), 48 deletions(-)

* 2014-07-14(Tal Galili) untangle.dendrogram - fix doc, and add \n to massage |0f2afed| 
|  R/untangle.R                      | 4 ++--
|  man/untangle_step_rotate_2side.Rd | 2 +-
|  2 files changed, 3 insertions(+), 3 deletions(-)

* 2014-07-14(Tal Galili) Replace expect_that with expect_equal |8a27370| 
|  inst/tests/test-labels-assign.R | 49 +++++++++++++++++++++------------------
|  1 file changed, 27 insertions(+), 22 deletions(-)

* 2014-07-14(Tal Galili) tests - add an option to stop the warnings (I know they are there, so really no point in them keep showing up...) |4862624| 
|  inst/tests/test-update.dendrogram.R | 7 +++++++
|  1 file changed, 7 insertions(+)

* 2014-07-14(Tal Galili) add ` to functions in NEWS |ece7863| 
|  NEWS    | 36 ++++++++++++++++++------------------
|  NEWS.md | 36 ++++++++++++++++++------------------
|  2 files changed, 36 insertions(+), 36 deletions(-)

* 2014-07-14(Tal Galili) Turn news to be more marked down... |b231b9b| 
|  NEWS    | 230 +++++++++++++++++++++++++++++++-------------------------------
|  NEWS.md | 230 +++++++++++++++++++++++++++++++-------------------------------
|  2 files changed, 230 insertions(+), 230 deletions(-)

* 2014-07-14(Tal Galili) update NEWS.md and changelog |5f206dd| 
|  ChangeLog | 232 ++++++++++++++++++++++++++++++++++++++++++++++++++++
|  NEWS.md   | 265 +++++++++++++++++++++++++++++++++++++++++++++++++++++++-----
|  R/zzz.R   |   4 +-
|  3 files changed, 479 insertions(+), 22 deletions(-)

* 2014-07-14(Tal Galili) Updated the README a bit. |8d6bb95| 
|  README.md | 37 +++++++------------------------------
|  1 file changed, 7 insertions(+), 30 deletions(-)

* 2014-07-14(Tal Galili) add .gitignore to not keep the cache and figure folders |5a4028c| 
|  vignettes/.gitignore | 2 ++
|  1 file changed, 2 insertions(+)

* 2014-07-14(Tal Galili) update TODO and ChangeLog |99430e2| 
|  ChangeLog | 400 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  TODO      |  25 ++++
|  2 files changed, 425 insertions(+)

* 2014-07-14(Tal Galili) Remove all extra doc files |8a3a863| 
|  inst/doc/2013-09-05_Boston-useR/.gitignore        |    4 -
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|  148 files changed, 3744 insertions(+), 19994 deletions(-)

* 2014-07-14(Tal Galili) Fix the docs of the functions in dendextend which relates to the newer dendextendRcpp (version 0.5.1): cut_lower_fun, get_branches_heights,  heights_per_k.dendrogram |a0382df| 
|  NEWS                            |  6 +++---
|  R/attr_access.R                 | 11 +++++------
|  R/cut_lower_fun.R               | 16 ++++++++--------
|  R/cutree.dendrogram.R           | 25 +++++++++++++------------
|  man/cut_lower_fun.Rd            | 16 ++++++++--------
|  man/get_branches_heights.Rd     | 11 +++++------
|  man/heights_per_k.dendrogram.Rd | 23 ++++++++++++-----------
|  7 files changed, 54 insertions(+), 54 deletions(-)

* 2014-07-13(Tal Galili) Fix typos in vignettes - thank you Bob Muenchen! |96692d2| 
|  DESCRIPTION                       | 16 +++++----
|  NEWS                              |  1 +
|  vignettes/dendextend-tutorial.bib | 10 ++++++
|  vignettes/dendextend-tutorial.rnw | 70 ++++++++++++++++++-------------------
|  4 files changed, 54 insertions(+), 43 deletions(-)

* 2014-07-13(Tal Galili) rotate_DendSer function added - and a bug was fixed in doing so. (also some credit corrections) |b045289| 
|  NAMESPACE                 |  1 +
|  NEWS                      |  2 +-
|  R/untangle.R              | 64 +++++++++++++++++++++++++++++++++++----------
|  man/DendSer.dendrogram.Rd |  8 ++++--
|  man/color_branches.Rd     |  2 +-
|  man/rotate_DendSer.Rd     | 47 +++++++++++++++++++++++++++++++++
|  man/tanglegram.Rd         |  4 +--
|  man/untangle_DendSer.Rd   |  3 ++-
|  8 files changed, 110 insertions(+), 21 deletions(-)

* 2014-07-13(Tal Galili) Vignettes - fixing spelling mistakes. |cc792b7| 
|  vignettes/dendextend-tutorial.rnw | 48 ++++++++++++++++++-------------------
|  1 file changed, 24 insertions(+), 24 deletions(-)

* 2014-07-13(Tal Galili) Update credits. |184907e| 
|  DESCRIPTION        | 8 +++++---
|  R/color_branches.R | 2 +-
|  R/tanglegram.R     | 4 ++--
|  3 files changed, 8 insertions(+), 6 deletions(-)

* 2014-07-13(Tal Galili) Minor doc changes |210cf71| 
|  R/labels.R               | 1 +
|  man/color_branches.Rd    | 1 +
|  man/labels_colors.Rd     | 4 ++++
|  man/update.dendrogram.Rd | 2 +-
|  4 files changed, 7 insertions(+), 1 deletion(-)

* 2014-07-13(Tal Galili) Added tests for update.dendrogram! |ba435a1| 
|  inst/tests/test-update.dendrogram.R | 136 ++++++++++++++++++++++++++++++++++
|  1 file changed, 136 insertions(+)

* 2014-07-13(Tal Galili) update.dendrogram - added .Rd docs :) |208af7d| 
|  NAMESPACE                |   1 +
|  R/update.dendrogram.R    | 297 ++++++++++++++++++++++-----------------------
|  man/update.dendrogram.Rd | 135 +++++++++++++++++++++
|  3 files changed, 282 insertions(+), 151 deletions(-)

* 2014-07-13(Tal Galili) tanglegram - preserve and restore previous par options (will no longer have a tiny plot in the left corner, when using a simple plot after tanglegram) |982053b| 
|  NEWS           | 4 +++-
|  R/tanglegram.R | 5 ++++-
|  2 files changed, 7 insertions(+), 2 deletions(-)

* 2014-07-12(Tal Galili) colored_bars - added docs :) |08a7118| 
|  DESCRIPTION         |   4 +-
|  NAMESPACE           |   2 +-
|  NEWS                |   2 +
|  R/colored_bars.R    | 243 +++++++++++++++++++++++++++++++-------------------
|  man/colored_bars.Rd | 116 ++++++++++++++++++++++++
|  5 files changed, 271 insertions(+), 96 deletions(-)

* 2014-07-12(Tal Galili) color_bars - adding more parameters. Made sure it can now be placed on top of a plot(dend). |a3db1f1| 
|  NAMESPACE        |   1 +
|  NEWS             |   2 +
|  R/color_bars.R   |  64 ----------------
|  R/colored_bars.R | 216 +++++++++++++++++++++++++++++++++++++++++++++++++++++
|  4 files changed, 219 insertions(+), 64 deletions(-)

* 2014-07-12(Tal Galili) color_bars - make sure to keep and reset the options |c13e95b| 
|  R/color_bars.R | 5 ++++-
|  1 file changed, 4 insertions(+), 1 deletion(-)

* 2014-07-12(Tal Galili) Rename plotHclustColors to color_bars - and made it work with dendrograms |61f854e| 
|  R/color_bars.R | 10 +++++++---
|  1 file changed, 7 insertions(+), 3 deletions(-)

* 2014-07-12(Tal Galili) plotHclustColors - first import into the package |5c5bec8| 
|  R/color_bars.R | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 57 insertions(+)

* 2014-07-11(Tal Galili) assign_values_to_branches_edgePar - value can now be different than 1 (it now also has a recycle option for the value) |fdc946e| 
|  NEWS                                     |  5 ++++-
|  R/attr_access.R                          | 24 +++++++++++++++++++++---
|  man/assign_values_to_branches_edgePar.Rd |  8 +++++++-
|  3 files changed, 32 insertions(+), 5 deletions(-)

* 2014-07-11(Tal Galili) update.dendrogram added: branches_color, branches_k_color,      branches_col, branches_lwd, branches_lty, clear_branches, clear_leaves |ee7d0c7| 
|  R/update.dendrogram.R | 68 ++++++++++++++++++++++++++++++++++++-------------
|  1 file changed, 50 insertions(+), 18 deletions(-)

* 2014-07-11(Tal Galili) `labels_colors<-` is more robust (for cases with partiel attr in nodePar). Also moved to using is.dendrogram more. |e774148| 
|  NEWS              |  5 +++--
|  R/attr_access.R   |  4 ++--
|  R/labels.R        |  1 +
|  R/labels_colors.R | 25 ++++++++++++++++++++-----
|  4 files changed, 26 insertions(+), 9 deletions(-)

* 2014-07-11(Tal Galili) Fix "is.dendlist" to use inherits instead of class |621dc3d| 
|  R/dendlist.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-07-11(Tal Galili) update.dendrogram - added options for: labels_colors, labels_cex, branches_color, hang, leaves_pch, leaves_cex, leaves_col |b29fa80| 
|  NEWS                  |  3 ++-
|  R/attr_access.R       |  8 ++++++-
|  R/labels_colors.R     |  2 ++
|  R/update.dendrogram.R | 58 +++++++++++++++++++++++++++++++++++++++++++------
|  4 files changed, 62 insertions(+), 9 deletions(-)

* 2014-07-11(Tal Galili) plot.dendlist - a wrapper for tangelgram |05d2fc8| 
|  NAMESPACE            |  3 +++
|  NEWS                 |  1 +
|  R/dendlist.R         | 34 ++++++++++++++++++++++++++++++++++
|  man/plot.dendlist.Rd | 34 ++++++++++++++++++++++++++++++++++
|  4 files changed, 72 insertions(+)

* 2014-07-11(Tal Galili) color_branches - now has a default behavior if k is missing. |f37929b| 
|  NEWS               |  5 +++--
|  R/color_branches.R | 31 ++++++++++++++++++-------------
|  2 files changed, 21 insertions(+), 15 deletions(-)

* 2014-07-11(Tal Galili) `labels_colors<-` now has a default behavior if value is missing. |928b499| 
|  NEWS              |  1 +
|  R/labels_colors.R | 11 ++++++++++-
|  2 files changed, 11 insertions(+), 1 deletion(-)

* 2014-07-11(Tal Galili) update.dendrogram - first draft of the function (implements only "labels") |7f76137| 
|  NAMESPACE             |   1 +
|  NEWS                  |   2 +
|  R/update.dendrogram.R | 131 ++++++++++++++++++++++++++++++++++++++++++++++++
|  3 files changed, 134 insertions(+)

* 2014-07-10(Tal Galili) Added cor_cophenetic.dendlist with tests and docs. |3303e4a| 
|  NAMESPACE                          |  1 +
|  R/cor_cophenetic.R                 | 26 ++++++++++++++++++---
|  inst/tests/test-cor_bakers_gamma.R |  2 +-
|  inst/tests/test-cor_cophenetic.R   | 44 ++++++++++++++++++++++++++++++++++++
|  man/cor_cophenetic.Rd              | 19 ++++++++++++----
|  5 files changed, 83 insertions(+), 9 deletions(-)

* 2014-07-10(Tal Galili) Added entanglement.dendlist to the doc |6ae315a| 
|  R/entanglement.R    | 1 +
|  man/entanglement.Rd | 1 +
|  2 files changed, 2 insertions(+)

* 2014-07-10(Tal Galili) Added match.arg for Bk_plot,  cor_cophenetic, entanglement, untangle_random_search, untangle_step_rotate_1side, and untangle_step_rotate_2side |ec129c1| 
|  NEWS                  | 1 +
|  R/bk_method.R         | 3 ++-
|  R/cor_cophenetic.R    | 7 ++++---
|  R/entanglement.R      | 3 ++-
|  R/untangle.R          | 8 +++++---
|  man/cor_cophenetic.Rd | 3 ++-
|  6 files changed, 16 insertions(+), 9 deletions(-)

* 2014-07-10(Tal Galili) Fix untangle tests: untangle_step_rotate_1side now outputs a dendlist, so we needed to extract the first element so to get the same results as before. (also added piping) |75f99af| 
|  inst/tests/test-untangle.R | 18 +++++++++---------
|  1 file changed, 9 insertions(+), 9 deletions(-)

* 2014-07-10(Tal Galili) Piping %>% some examples |1691c78| 
|  R/attr_access.R                            | 10 +++++-----
|  R/color_branches.R                         |  4 ++--
|  R/entanglement.R                           |  4 ++--
|  R/nleaves.R                                |  2 +-
|  R/sample.dendrogram.R                      |  4 ++--
|  R/tanglegram.R                             |  2 +-
|  R/untangle.R                               | 12 ++++++------
|  man/all_couple_rotations_at_k.Rd           |  2 +-
|  man/assign_values_to_branches_edgePar.Rd   |  2 +-
|  man/color_branches.Rd                      |  2 +-
|  man/duplicate_leaf.Rd                      |  2 +-
|  man/flip_leaves.Rd                         |  2 +-
|  man/leaf_Colors.Rd                         |  2 +-
|  man/match_order_by_labels.Rd               |  2 +-
|  man/match_order_dendrogram_by_old_order.Rd |  2 +-
|  man/plot_horiz.dendrogram.Rd               |  2 +-
|  man/rank_branches.Rd                       |  2 +-
|  man/rank_order.dendrogram.Rd               |  2 +-
|  man/remove_branches_edgePar.Rd             |  2 +-
|  man/remove_leaves_nodePar.Rd               |  2 +-
|  man/sample.dendrogram.Rd                   |  2 +-
|  man/shuffle.Rd                             |  2 +-
|  man/untangle_step_rotate_1side.Rd          |  2 +-
|  man/untangle_step_rotate_2side.Rd          |  4 ++--
|  24 files changed, 37 insertions(+), 37 deletions(-)

* 2014-07-10(Tal Galili) Added a TODO file |0fbee3a| 
|  NEWS | 64 -----------------------------------------------------
|  TODO | 79 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 79 insertions(+), 64 deletions(-)

* 2014-07-10(Tal Galili) Fix some spaces around "<-" |c141009| 
|  R/color_branches.R | 18 +++++++++---------
|  R/untangle.R       |  4 ++--
|  2 files changed, 11 insertions(+), 11 deletions(-)

* 2014-07-10(Tal Galili) Rename back from .b to .R |c0fd282| 
|  R/{as.dendrogram.randomForest.b => as.dendrogram.randomForest.R}        | 0
|  R/{attr_access.b => attr_access.R}                                      | 0
|  R/{bk_method.b => bk_method.R}                                          | 0
|  R/{color_branches.b => color_branches.R}                                | 0
|  R/{cor_bakers_gamma.b => cor_bakers_gamma.R}                            | 0
|  R/{cor_cophenetic.b => cor_cophenetic.R}                                | 0
|  R/{cut_lower_fun.b => cut_lower_fun.R}                                  | 0
|  R/{cutree.dendrogram.b => cutree.dendrogram.R}                          | 0
|  R/{dendextend-package.b => dendextend-package.R}                        | 0
|  R/{dendextend.b => dendextend.R}                                        | 0
|  R/{dendlist.b => dendlist.R}                                            | 0
|  R/{entanglement.b => entanglement.R}                                    | 0
|  R/{imports_stats.b => imports_stats.R}                                  | 0
|  R/{labels.b => labels.R}                                                | 0
|  R/{labels_colors.b => labels_colors.R}                                  | 0
|  R/{nleaves.b => nleaves.R}                                              | 0
|  R/{rotate.b => rotate.R}                                                | 0
|  R/{sample.dendrogram.b => sample.dendrogram.R}                          | 0
|  R/{tanglegram.b => tanglegram.R}                                        | 0
|  R/{trim.b => trim.R}                                                    | 0
|  R/{unbranch.b => unbranch.R}                                            | 0
|  R/{untangle.b => untangle.R}                                            | 0
|  R/{zzz.b => zzz.R}                                                      | 0
|  demo/{dendextend.b => dendextend.R}                                     | 0
|  ...3-09-05_Boston-useR_01_intro.b => 2013-09-05_Boston-useR_01_intro.R} | 0
|  ...ston-useR_02_dendextend.b => 2013-09-05_Boston-useR_02_dendextend.R} | 0
|  ...seR_03_untangle_iris.b => 2013-09-05_Boston-useR_03_untangle_iris.R} | 0
|  ...R_04_tree_inference.b => 2013-09-05_Boston-useR_04_tree_inference.R} | 0
|  inst/tests/{test-attr_access.b => test-attr_access.R}                   | 0
|  inst/tests/{test-bk_method.b => test-bk_method.R}                       | 0
|  inst/tests/{test-cor_bakers_gamma.b => test-cor_bakers_gamma.R}         | 0
|  inst/tests/{test-cut_lower_fun.b => test-cut_lower_fun.R}               | 0
|  inst/tests/{test-cutree.dendrogram.b => test-cutree.dendrogram.R}       | 0
|  inst/tests/{test-dendlist.b => test-dendlist.R}                         | 0
|  inst/tests/{test-entanglement.b => test-entanglement.R}                 | 0
|  inst/tests/{test-labels-assign.b => test-labels-assign.R}               | 0
|  inst/tests/{test-labels_colors.b => test-labels_colors.R}               | 0
|  inst/tests/{test-nleaves.b => test-nleaves.R}                           | 0
|  inst/tests/{test-rotate.b => test-rotate.R}                             | 0
|  inst/tests/{test-trim.b => test-trim.R}                                 | 0
|  inst/tests/{test-unbranch.b => test-unbranch.R}                         | 0
|  inst/tests/{test-untangle.b => test-untangle.R}                         | 0
|  tests/{test-all.b => test-all.R}                                        | 0
|  43 files changed, 0 insertions(+), 0 deletions(-)

* 2014-07-10(Tal Galili) rename all .r files to .b (so to allow the renaming from .r to .R on git on windows) |6145838| 
|  R/{as.dendrogram.randomForest.r => as.dendrogram.randomForest.b}        | 0
|  R/{attr_access.r => attr_access.b}                                      | 0
|  R/{bk_method.r => bk_method.b}                                          | 0
|  R/{color_branches.r => color_branches.b}                                | 0
|  R/{cor_bakers_gamma.r => cor_bakers_gamma.b}                            | 0
|  R/{cor_cophenetic.r => cor_cophenetic.b}                                | 0
|  R/{cut_lower_fun.r => cut_lower_fun.b}                                  | 0
|  R/{cutree.dendrogram.r => cutree.dendrogram.b}                          | 0
|  R/{dendextend-package.r => dendextend-package.b}                        | 0
|  R/{dendextend.r => dendextend.b}                                        | 0
|  R/{dendlist.R => dendlist.b}                                            | 0
|  R/{entanglement.r => entanglement.b}                                    | 0
|  R/{imports_stats.r => imports_stats.b}                                  | 0
|  R/{labels.r => labels.b}                                                | 0
|  R/{labels_colors.r => labels_colors.b}                                  | 0
|  R/{nleaves.r => nleaves.b}                                              | 0
|  R/{rotate.r => rotate.b}                                                | 0
|  R/{sample.dendrogram.r => sample.dendrogram.b}                          | 0
|  R/{tanglegram.r => tanglegram.b}                                        | 0
|  R/{trim.r => trim.b}                                                    | 0
|  R/{unbranch.r => unbranch.b}                                            | 0
|  R/{untangle.r => untangle.b}                                            | 0
|  R/{zzz.r => zzz.b}                                                      | 0
|  demo/{dendextend.r => dendextend.b}                                     | 0
|  ...3-09-05_Boston-useR_01_intro.R => 2013-09-05_Boston-useR_01_intro.b} | 0
|  ...ston-useR_02_dendextend.R => 2013-09-05_Boston-useR_02_dendextend.b} | 0
|  ...seR_03_untangle_iris.R => 2013-09-05_Boston-useR_03_untangle_iris.b} | 0
|  ...R_04_tree_inference.R => 2013-09-05_Boston-useR_04_tree_inference.b} | 0
|  inst/tests/{test-attr_access.r => test-attr_access.b}                   | 0
|  inst/tests/{test-bk_method.r => test-bk_method.b}                       | 0
|  inst/tests/{test-cor_bakers_gamma.r => test-cor_bakers_gamma.b}         | 0
|  inst/tests/{test-cut_lower_fun.r => test-cut_lower_fun.b}               | 0
|  inst/tests/{test-cutree.dendrogram.r => test-cutree.dendrogram.b}       | 0
|  inst/tests/{test-dendlist.R => test-dendlist.b}                         | 0
|  inst/tests/{test-entanglement.r => test-entanglement.b}                 | 0
|  inst/tests/{test-labels-assign.r => test-labels-assign.b}               | 0
|  inst/tests/{test-labels_colors.r => test-labels_colors.b}               | 0
|  inst/tests/{test-nleaves.r => test-nleaves.b}                           | 0
|  inst/tests/{test-rotate.r => test-rotate.b}                             | 0
|  inst/tests/{test-trim.r => test-trim.b}                                 | 0
|  inst/tests/{test-unbranch.r => test-unbranch.b}                         | 0
|  inst/tests/{test-untangle.r => test-untangle.b}                         | 0
|  tests/{test-all.r => test-all.b}                                        | 0
|  43 files changed, 0 insertions(+), 0 deletions(-)

* 2014-07-08(Tal Galili) .Rd files commit |1fdac74| 
|  man/Bk.Rd                                  |  65 ++++++------
|  man/Bk_permutations.Rd                     |  69 ++++++------
|  man/Bk_plot.Rd                             | 150 ++++++++++++---------------
|  man/FM_index.Rd                            |  85 +++++++--------
|  man/FM_index_R.Rd                          |  64 ++++++------
|  man/FM_index_permutation.Rd                |  36 +++----
|  man/FM_index_profdpm.Rd                    |  81 +++++++--------
|  man/all_couple_rotations_at_k.Rd           |  29 +++---
|  man/as_hclust_fixed.Rd                     |  18 ++--
|  man/assign_dendextend_options.Rd           |   1 +
|  man/assign_values_to_branches_edgePar.Rd   |  16 ++-
|  man/assign_values_to_leaves_nodePar.Rd     |  29 +++---
|  man/bakers_gamma_for_2_k_matrix.Rd         |  16 ++-
|  man/click_rotate.Rd                        |  10 +-
|  man/color_branches.Rd                      |  90 +++++++---------
|  man/color_labels.Rd                        |  53 ++++------
|  man/cor_bakers_gamma.Rd                    |  90 +++++++---------
|  man/cor_cophenetic.Rd                      |  63 ++++++-----
|  man/count_terminal_nodes.Rd                |  26 ++---
|  man/cut_lower_fun.Rd                       |  34 +++---
|  man/cutree-methods.Rd                      | 142 ++++++++++++-------------
|  man/cutree_1h.dendrogram.Rd                |  35 +++----
|  man/cutree_1k.dendrogram.Rd                |  59 +++++------
|  man/dendextend-package.Rd                  |   4 +-
|  man/dendextend_options.Rd                  |  16 +--
|  man/dendlist.Rd                            |  10 +-
|  man/duplicate_leaf.Rd                      |  32 +++---
|  man/entanglement.Rd                        |  93 +++++++++--------
|  man/fac2num.Rd                             |  24 ++---
|  man/fix_members_attr.dendrogram.Rd         |  12 +--
|  man/flatten.dendrogram.Rd                  |  19 ++--
|  man/flip_leaves.Rd                         |  19 ++--
|  man/get_branches_attr.Rd                   |  16 ++-
|  man/get_branches_heights.Rd                |  13 ++-
|  man/get_childrens_heights.Rd               |   5 +-
|  man/get_leaves_attr.Rd                     |  23 ++--
|  man/get_nodes_attr.Rd                      |  35 +++----
|  man/hang.dendrogram.Rd                     |  32 +++---
|  man/heights_per_k.dendrogram.Rd            |   9 +-
|  man/intersect_trees.Rd                     |  14 +--
|  man/is.dendrogram.Rd                       |   3 +-
|  man/is.hclust.Rd                           |   3 +-
|  man/is.natural.number.Rd                   |  17 ++-
|  man/is.phylo.Rd                            |   3 +-
|  man/labels-assign.Rd                       |  39 +++----
|  man/labels_colors.Rd                       |  27 +++--
|  man/leaf_Colors.Rd                         |   9 +-
|  man/lowest_common_branch.Rd                |  20 ++--
|  man/match_order_by_labels.Rd               |  25 +++--
|  man/match_order_dendrogram_by_old_order.Rd |  45 ++++----
|  man/nleaves.Rd                             |  33 +++---
|  man/nnodes.Rd                              |  16 ++-
|  man/order.dendrogram-assign.Rd             |  13 +--
|  man/plot_horiz.dendrogram.Rd               |  86 +++++++--------
|  man/prune.Rd                               |  15 ++-
|  man/prune_leaf.Rd                          |   8 +-
|  man/raise.dendrogram.Rd                    |   8 +-
|  man/rank_branches.Rd                       |  29 +++---
|  man/rank_order.dendrogram.Rd               |  11 +-
|  man/remove_branches_edgePar.Rd             |  11 +-
|  man/remove_leaves_nodePar.Rd               |  11 +-
|  man/rllply.Rd                              |  27 +++--
|  man/sample.dendrogram.Rd                   |  62 ++++++-----
|  man/shuffle.Rd                             |  34 +++---
|  man/sort_2_clusters_vectors.Rd             |  31 +++---
|  man/sort_dist_mat.Rd                       |  11 +-
|  man/sort_levels_values.Rd                  |  49 ++++-----
|  man/tanglegram.Rd                          |  23 ++--
|  man/unbranch.Rd                            |  14 ++-
|  man/unclass_dend.Rd                        |   5 +-
|  man/untangle_random_search.Rd              |  75 ++++++--------
|  man/untangle_step_rotate_1side.Rd          |  64 +++++-------
|  man/untangle_step_rotate_2side.Rd          |  57 +++++-----
|  73 files changed, 1170 insertions(+), 1351 deletions(-)

* 2014-07-08(Tal Galili) untangle_DendSer - a new untangle function (this time, only for dendlist), for leverging the serialization package for some more heuristics. |e6c4a48| 
|  ChangeLog                 | 35 ++++++++++++++++--
|  NAMESPACE                 |  7 ++++
|  NEWS                      |  1 +
|  R/untangle.r              | 87 +++++++++++++++++++++++++++++++++++++++++++--
|  man/DendSer.dendrogram.Rd | 38 ++++++++++++++++++++
|  man/as.dendlist.Rd        | 33 +++++++++++++++++
|  man/is.dendlist.Rd        | 23 ++++++++++++
|  man/is_null_list.Rd       | 38 ++++++++++++++++++++
|  man/untangle.Rd           | 84 +++++++++++++++++++++++++++++++++++++++++++
|  man/untangle_DendSer.Rd   | 42 ++++++++++++++++++++++
|  10 files changed, 382 insertions(+), 6 deletions(-)

* 2014-07-08(Tal Galili) Added tests for empty dendlist |d128b2b| 
|  inst/tests/test-dendlist.R | 38 ++++++++++++++++++++++++++++++++++++++
|  1 file changed, 38 insertions(+)

* 2014-07-08(Tal Galili) Added "untangle" - a master function to control all untangle functions (making it much easier to navigate this feature, as well as use it through %>% piping) |f276111| 
|  NEWS                       |   4 ++
|  R/untangle.r               | 100 +++++++++++++++++++++++++++++++++++++++++++
|  inst/tests/test-untangle.r |  35 +++++++++++++++
|  3 files changed, 139 insertions(+)

* 2014-07-08(Tal Galili) Make sure that the main untangle functions will return a dendlist (and also that untangle_step_rotate_2side will be able to work with the new untangle_step_rotate_1side output) |01d5312| 
|  R/untangle.r | 35 ++++++++++++++++++++---------------
|  1 file changed, 20 insertions(+), 15 deletions(-)

* 2014-07-08(Tal Galili) tanglegram - a minor fix to the doc |1470d5a| 
|  R/tanglegram.r | 3 ++-
|  1 file changed, 2 insertions(+), 1 deletion(-)

* 2014-07-08(Tal Galili) added the functions: * is.dendlist - to check that an object is a dendlist * as.dendlist - to turn a list to a dendlist * (hidden) is_null_list |780e851| 
|  NEWS         |   2 ++
|  R/dendlist.R | 103 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 105 insertions(+)

* 2014-07-08(Tal Galili) Added a S3 dendlist method to shuffle |0af1ac2| 
|  NAMESPACE                  |  2 ++
|  R/untangle.r               | 24 ++++++++++++++++++++++++
|  inst/tests/test-untangle.r | 10 ++++++----
|  3 files changed, 32 insertions(+), 4 deletions(-)

* 2014-07-08(Tal Galili) Modify the changelog to a more compact view. |096a505| 
|  ChangeLog | 5373 +++++++++++++++++++++++++++++++++++------------------------
|  R/zzz.r   |    6 +
|  2 files changed, 3231 insertions(+), 2148 deletions(-)

* 2014-07-08(Tal Galili) Start creating "ChangeLog" file, based on my git commits :) |75ab7a8| 
|  ChangeLog | 2148 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  R/zzz.r   |   32 +
|  2 files changed, 2180 insertions(+)

* 2014-07-08(Tal Galili) Added credit to Dylan Beaudette for his dueling.dendrograms function (the origin of the tanglegram plot) |2ff8718| 
|  R/tanglegram.r | 5 +++++
|  1 file changed, 5 insertions(+)

* 2014-07-08(Tal Galili) Add pipes to the untangle docs |6715788| 
|  R/untangle.r | 6 ++----
|  1 file changed, 2 insertions(+), 4 deletions(-)

* 2014-07-08(Tal Galili) Add tests for entenglement on dendlist |39fef73| 
|  inst/tests/test-entanglement.r | 10 ++++++++--
|  1 file changed, 8 insertions(+), 2 deletions(-)

* 2014-07-08(Tal Galili) tanglegram - making its output be a dendlist object |d9db482| 
|  R/tanglegram.r | 16 +++++++++-------
|  1 file changed, 9 insertions(+), 7 deletions(-)

* 2014-07-07(Tal Galili) Added entanglement.dendlist function |f7f8c83| 
|  NEWS             |  2 ++
|  R/entanglement.r | 33 +++++++++++++++++++++++++++------
|  2 files changed, 29 insertions(+), 6 deletions(-)

* 2014-07-07(Tal Galili) tanglegram.dendlist - bug fix for it to work + some minor fixes to the doc |acd20bb| 
|  R/tanglegram.r | 6 +++---
|  1 file changed, 3 insertions(+), 3 deletions(-)

* 2014-07-07(Tal Galili) Move magrittr to Depends, to make it easier to work with examples (this way it will always get the chain %>% operator to be available to all examples) |ec46e29| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 4 ++--
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2014-07-07(Tal Galili) Added horiz and continue paramters to the click_rotate function |e19f738| 
|  R/rotate.r    |  43 ++++++++++++++--------
|  man/rotate.Rd | 110 +++++++++++++++++++++++++-------------------------------
|  2 files changed, 77 insertions(+), 76 deletions(-)

* 2014-07-06(Tal Galili) Check dendlist works (new tests) |c5866a8| 
|  DESCRIPTION                |  1 +
|  NEWS                       |  4 ++++
|  inst/tests/test-dendlist.R | 23 +++++++++++++++++++++++
|  3 files changed, 28 insertions(+)

* 2014-07-06(Tal Galili) Updated DESCRIPTION and NEWS |1ce17d7| 
|  DESCRIPTION |  9 +++++----
|  NEWS        | 29 +++++++++++++++++++++++++++++
|  2 files changed, 34 insertions(+), 4 deletions(-)

* 2014-07-06(Tal Galili) Added the click_rotate function (thanks to Andrej-Nikolai Spiess) |c455d60| 
|  NAMESPACE           |  2 ++
|  R/rotate.r          | 76 +++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/click_rotate.Rd | 47 +++++++++++++++++++++++++++++++
|  3 files changed, 125 insertions(+)

* 2014-07-05(Tal Galili) Added tanglegramm.dendlist S3 method |20e4c79| 
|  NAMESPACE         |   1 +
|  R/attr_access.r   |   2 +-
|  R/tanglegram.r    |  20 +++++-
|  man/tanglegram.Rd | 179 ++++++++++++++++++++++++----------------------------
|  4 files changed, 102 insertions(+), 100 deletions(-)

* 2014-07-05(Tal Galili) Make dendlist handle hclust and phylo |c74f06a| 
|  R/dendlist.R | 21 ++++++++++++++++++---
|  1 file changed, 18 insertions(+), 3 deletions(-)

* 2014-07-04(Tal Galili) dendlist - a function which creates a list of dendrogram of the new "dendlist" class. |2dec5f9| 
|  NAMESPACE       |   3 ++
|  R/dendlist.R    | 104 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/dendlist.Rd |  38 ++++++++++++++++++++
|  3 files changed, 145 insertions(+)

* 2014-04-26(Tal Galili) Version 0.14.3 - minor changes to DESCRIPTION |70b93f9| 
|  DESCRIPTION |  4 ++--
|  NEWS        | 12 ++++++++++++
|  2 files changed, 14 insertions(+), 2 deletions(-)

* 2014-04-26(Tal Galili) minor fixes to examples |d7d3c86| 
|  R/color_branches.r    | 1 +
|  R/cutree.dendrogram.r | 2 +-
|  2 files changed, 2 insertions(+), 1 deletion(-)

* 2014-03-18(Tal Galili) Added dendextendRcpp (>= 0.5.0) to Suggests! |acd6f98| 
|  DESCRIPTION | 16 ++++++++--------
|  1 file changed, 8 insertions(+), 8 deletions(-)

* 2014-03-18(Tal Galili) Fixing spaces |b74e3ba| 
|  README.md | 3 +++
|  1 file changed, 3 insertions(+)

* 2014-03-18(Tal Galili) Fixing "jefferis" to full name |e2f9496| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-03-15(Tal Galili) Added dependency for R (>= 3.0.0) |25e3103| 
|  DESCRIPTION |  6 ++++--
|  NEWS        | 11 +++++++++++
|  2 files changed, 15 insertions(+), 2 deletions(-)

* 2014-03-15(Tal Galili) Note that the package will go on CRAN |8e92afb| 
|  DESCRIPTION | 1 -
|  NEWS        | 8 +++++++-
|  2 files changed, 7 insertions(+), 2 deletions(-)

* 2014-03-15(Tal Galili) Bumped to  0.14.1 |029e5a0| 
|  DESCRIPTION |  3 +--
|  NEWS        | 18 +++++++++++++++---
|  2 files changed, 16 insertions(+), 5 deletions(-)

* 2014-03-15(Tal Galili) Fix Undocumented arguments in documentation object 'dendextend_options'   'option' 'value' |a3d3520| 
|  R/zzz.r                   | 4 ++++
|  man/dendextend_options.Rd | 7 +++++++
|  2 files changed, 11 insertions(+)

* 2014-03-15(Tal Galili) update test_rotate.r so it would make sure ape is loaded BEFORE dendextend. |067afc4| 
|  NEWS                     |  2 +-
|  inst/tests/test-rotate.r | 14 ++++++++++++++
|  2 files changed, 15 insertions(+), 1 deletion(-)

* 2014-03-15(Tal Galili) dendextend_options (actually an enviornment + a function) - added |095861c| 
|  NAMESPACE                 |  1 +
|  NEWS                      |  2 +-
|  R/zzz.r                   | 77 ++++++++++++++++++++++++++++-----------------
|  man/dendextend_options.Rd | 27 ++++++++++++++++
|  4 files changed, 77 insertions(+), 30 deletions(-)

* 2014-03-15(Tal Galili) update tests to the new names in dendextendRcpp (dendextendRcpp_cut_lower_fun, dendextend_options) |d4c03b0| 
|  NEWS                            | 2 ++
|  inst/tests/test-attr_access.r   | 2 +-
|  inst/tests/test-cut_lower_fun.r | 8 ++++----
|  3 files changed, 7 insertions(+), 5 deletions(-)

* 2014-03-15(Tal Galili) assign_dendextend_options - is now exported. |b0f1028| 
|  NAMESPACE                        |  1 +
|  NEWS                             |  5 +++--
|  R/zzz.r                          |  7 +++++++
|  man/assign_dendextend_options.Rd | 10 ++++++++++
|  4 files changed, 21 insertions(+), 2 deletions(-)

* 2014-03-15(Tal Galili) Moved to passing the functions through "dendextend_options" instead of through "options" (Thanks to suggestions by Kurt Hornik and Uwe Ligges). |ce0c91b| 
|  DESCRIPTION           |  9 +++++---
|  NEWS                  | 14 +++++++++++++
|  R/attr_access.r       |  2 +-
|  R/cut_lower_fun.r     |  2 +-
|  R/cutree.dendrogram.r |  2 +-
|  R/zzz.r               | 56 +++++++++++++++++++++++++++++++++++++++++++------
|  6 files changed, 73 insertions(+), 12 deletions(-)

* 2014-03-01(Tal Galili) Bump to version 0.13.0 |7c8c681| 
|  DESCRIPTION |  5 +++--
|  NEWS        | 26 ++++++++++++++++++++++++++
|  README.md   |  6 +++---
|  3 files changed, 32 insertions(+), 5 deletions(-)

* 2014-03-01(Tal Galili) Added a compressed version of the pdf tutorial. |68d7376| 
|  inst/doc/dendextend-tutorial.pdf | Bin 0 -> 569458 bytes
|  1 file changed, 0 insertions(+), 0 deletions(-)

* 2014-03-01(Tal Galili) assign_dendextend_options - we now pass all functions that have a Rcpp equivalent through "options". While this adds a bit of an overhead (sadly), it still gets a much faster speed gain, and without verious warnings that CRAN checks would not like. |4e47c40| 
|  NAMESPACE                       |  3 +++
|  R/attr_access.r                 | 24 +++++++++++++++++++++++-
|  R/cut_lower_fun.r               | 15 ++++++++++++++-
|  R/cutree.dendrogram.r           | 28 +++++++++++++++++++++++++---
|  R/dendextend-package.r          |  2 +-
|  R/zzz.r                         | 21 +++++++++++++++++++--
|  man/cut_lower_fun.Rd            |  1 +
|  man/dendextend-package.Rd       |  4 ++--
|  man/get_branches_heights.Rd     | 14 ++++++++++++++
|  man/heights_per_k.dendrogram.Rd | 15 +++++++++++++++
|  tests/test-all.r                | 10 ++++++++--
|  11 files changed, 125 insertions(+), 12 deletions(-)

* 2014-03-01(Tal Galili) When comparing to dendextendRcpp - added condition to not make the check if the package is not loaded and in the search path (this way I could compare the tests with and without the dendextendRcpp package). |f7bad9b| 
|  inst/tests/test-cut_lower_fun.r     | 148 +++++++++++++++++-----------------
|  inst/tests/test-cutree.dendrogram.r |   6 +-
|  2 files changed, 79 insertions(+), 75 deletions(-)

* 2014-03-01(Tal Galili) added a minor test for dendextend_get_branches_heights - checking the function directly through the options. |523e604| 
|  inst/tests/test-attr_access.r | 4 +++-
|  1 file changed, 3 insertions(+), 1 deletion(-)

* 2014-02-03(Tal Galili) dendextend 0.12.2 is intended to be shipped to CRAN. |d86832f| 
|  NEWS    | 27 ++++++++++++++++++++++++++-
|  R/zzz.r | 29 ++++++++++++++++++++++++++++-
|  2 files changed, 54 insertions(+), 2 deletions(-)

* 2014-02-03(Tal Galili) Hidden "stats" functions have been added to a new file "imports_stats.r"       with a new local copy for                            'stats:::.memberDend' 'stats:::.midDend'                            'stats:::midcache.dendrogram' 'stats:::plotNode'                            'stats:::plotNodeLimit'       with stats::: -> stats_ |62f874e| 
|  R/imports_stats.r     | 285 ++++++++++++++++++++++++++++++++++++++++++++++++
|  R/sample.dendrogram.r |   4 +-
|  R/tanglegram.r        |  16 +--
|  R/trim.r              |   2 +-
|  R/unbranch.r          |   2 +-
|  5 files changed, 297 insertions(+), 12 deletions(-)

* 2014-02-03(Tal Galili) dendextend:::cutree -> dendextend::cutree |c6db8e8| 
|  R/color_branches.r | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2014-02-03(Tal Galili) UPDATED DESCRIPTION:    * Removed VignetteBuilder: knitr (until later)    * Removed Suggests: dendextendRcpp, (until later)    * fixed mis-spelled words: extanding (14:40) |b83bb5a| 
|  DESCRIPTION | 8 +++-----
|  1 file changed, 3 insertions(+), 5 deletions(-)

* 2014-02-03(Tal Galili) stats:::cutree -> stats::cutree |72eee44| 
|  R/cutree.dendrogram.r               | 6 +++---
|  inst/tests/test-cutree.dendrogram.r | 2 +-
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2014-02-02(Tal Galili) Fix "\examples lines wider than 100 characters:" in several places. |18a2420| 
|  NEWS                        |  1 +
|  R/bk_method.r               | 24 ++++++++++++++++--------
|  R/color_branches.r          |  6 ++++--
|  R/cor_bakers_gamma.r        |  3 ++-
|  R/cutree.dendrogram.r       |  7 ++++---
|  R/nleaves.r                 | 15 ++++++++++-----
|  R/trim.r                    | 10 ++++++++--
|  man/Bk_plot.Rd              |  3 ++-
|  man/FM_index.Rd             | 15 ++++++++++-----
|  man/FM_index_profdpm.Rd     |  6 ++++--
|  man/color_branches.Rd       |  6 ++++--
|  man/cor_bakers_gamma.Rd     |  3 ++-
|  man/cutree_1k.dendrogram.Rd |  7 ++++---
|  man/intersect_trees.Rd      | 10 ++++++++--
|  man/unclass_dend.Rd         | 15 ++++++++++-----
|  15 files changed, 89 insertions(+), 42 deletions(-)

* 2014-02-02(Tal Galili) data(iris) -> data(iris, envir = environment()) |c5f56e4| 
|  NEWS                           | 2 ++
|  R/as.dendrogram.randomForest.r | 2 +-
|  R/color_branches.r             | 6 +++---
|  R/zzz.r                        | 8 ++++++++
|  man/color_branches.Rd          | 4 ++--
|  5 files changed, 16 insertions(+), 6 deletions(-)

* 2014-02-02(Tal Galili) Made sure to check dendextendRcpp is available before calling it. |c0b9bc0| 
|  DESCRIPTION                         |  6 ++---
|  NEWS                                |  7 +++--
|  inst/tests/test-bk_method.r         | 32 +++++++++++-----------
|  inst/tests/test-cor_bakers_gamma.r  |  4 +--
|  inst/tests/test-cut_lower_fun.r     | 51 ++++++++++++++++++-----------------
|  inst/tests/test-cutree.dendrogram.r | 20 ++++++++------
|  inst/tests/test-entanglement.r      |  4 +--
|  tests/test-all.r                    |  2 +-
|  8 files changed, 68 insertions(+), 58 deletions(-)

* 2014-02-02(Tal Galili) Commented out manipulations on the search path and of assignInNamespace. (to avoid NOTES/warnings) |d40fc34| 
|  NEWS                            |   9 ++-
|  R/attr_access.r                 |   4 +-
|  R/cut_lower_fun.r               |   6 +-
|  R/cutree.dendrogram.r           |   4 +-
|  R/nleaves.r                     |   3 +-
|  R/zzz.r                         | 160 +++++++++++++++++++-------------------
|  man/cut_lower_fun.Rd            |   1 -
|  man/get_branches_heights.Rd     |   1 -
|  man/heights_per_k.dendrogram.Rd |   1 -
|  9 files changed, 99 insertions(+), 90 deletions(-)

* 2014-02-01(Tal Galili) Vignettes - getting the latest version. |6e073a7| 
|  ...xamples_4afbfd2a825a9cb1746e8a947dcd1ada.RData |  Bin 3520 -> 0 bytes
|  ..._examples_4afbfd2a825a9cb1746e8a947dcd1ada.rdb |  Bin 9497 -> 0 bytes
|  ..._examples_4afbfd2a825a9cb1746e8a947dcd1ada.rdx |  Bin 179 -> 0 bytes
|  ...correct_ba0710e2563b1d13774723d2f4cc3bdc.RData |  Bin 2963 -> 0 bytes
|  ...s_correct_ba0710e2563b1d13774723d2f4cc3bdc.rdb |    0
|  ...s_correct_ba0710e2563b1d13774723d2f4cc3bdc.rdx |  Bin 113 -> 0 bytes
|  ...t_WRONG_e0ef7cc51fd625ff307f2a7a9da2fd5e.RData |  Bin 3004 -> 0 bytes
|  ...ust_WRONG_e0ef7cc51fd625ff307f2a7a9da2fd5e.rdb |    0
|  ...ust_WRONG_e0ef7cc51fd625ff307f2a7a9da2fd5e.rdx |  Bin 113 -> 0 bytes
|  ...mples_1_029622319f287d8b49913a8360888f62.RData |  Bin 3268 -> 0 bytes
|  ...xamples_1_029622319f287d8b49913a8360888f62.rdb |  Bin 4167 -> 0 bytes
|  ...xamples_1_029622319f287d8b49913a8360888f62.rdx |  Bin 153 -> 0 bytes
|  ...ample_1_5611fd32e4958b7af1d3a861c0b0ac03.RData |  Bin 3832 -> 0 bytes
|  ...example_1_5611fd32e4958b7af1d3a861c0b0ac03.rdb |  Bin 20576 -> 0 bytes
|  ...example_1_5611fd32e4958b7af1d3a861c0b0ac03.rdx |  Bin 266 -> 0 bytes
|  ...ample_2_7b84c47fe53f8a70663ff1fa00920e54.RData |  Bin 2924 -> 0 bytes
|  ...example_2_7b84c47fe53f8a70663ff1fa00920e54.rdb |  Bin 27124 -> 0 bytes
|  ...example_2_7b84c47fe53f8a70663ff1fa00920e54.rdx |  Bin 264 -> 0 bytes
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|  vignettes/dendextend-tutorial-concordance.tex     |   14 +-
|  vignettes/dendextend-tutorial.log                 | 1205 +--
|  vignettes/dendextend-tutorial.pdf                 | 8003 ++++++++++---------
|  vignettes/dendextend-tutorial.rnw                 |   21 +-
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|  vignettes/dendextend-tutorial.tex                 |  331 +-
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|  .../untangle_step_rotate_2side_example1.pdf       |  Bin 6158 -> 6158 bytes
|  .../untangle_step_rotate_2side_example2.pdf       |  Bin 6137 -> 6137 bytes
|  .../untangle_step_rotate_2side_example3.pdf       |  Bin 6154 -> 6154 bytes
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|  .../untangle_step_rotate_2side_example6.pdf       |  Bin 6163 -> 6163 bytes
|  231 files changed, 5284 insertions(+), 4290 deletions(-)

* 2014-02-01(Tal Galili) rotate - Remove the "flip" command in the example (after I noticed that "rev" does this just fine...) |4e2b110| 
|  NEWS          | 2 ++
|  R/rotate.r    | 4 ++--
|  man/rotate.Rd | 4 ++--
|  3 files changed, 6 insertions(+), 4 deletions(-)

* 2014-02-01(Tal Galili) Fixed the usage of person() in DESCRIPTION. (props goes to Uwe Ligges for his input) |28d84d8| 
|  DESCRIPTION | 15 ++++++++-------
|  NEWS        |  2 +-
|  2 files changed, 9 insertions(+), 8 deletions(-)

* 2014-02-01(Tal Galili) Fix "Argument items with no description in Rd object": 'plot_horiz.dendrogram', 'untangle_step_rotate_1side'. |6173ec9| 
|  NEWS                              | 2 +-
|  R/tanglegram.r                    | 2 +-
|  R/untangle.r                      | 2 +-
|  man/plot_horiz.dendrogram.Rd      | 3 ++-
|  man/untangle_step_rotate_1side.Rd | 4 +++-
|  5 files changed, 8 insertions(+), 5 deletions(-)

* 2014-02-01(Tal Galili) Fix "Objects in \usage without \alias in documentation object 'shuffle'":   'shuffle.dendrogram' 'shuffle.hclust' 'shuffle.phylo' |87ec513| 
|  NEWS           | 3 +++
|  R/untangle.r   | 4 +++-
|  man/shuffle.Rd | 3 +++
|  3 files changed, 9 insertions(+), 1 deletion(-)

* 2014-02-01(Tal Galili) Fix "Undocumented arguments in documentation object" for:       * 'bakers_gamma_for_2_k_matrix'       * 'cor_bakers_gamma'       * 'cut_lower_fun' |35bf958| 
|  NEWS                               | 4 ++++
|  R/cor_bakers_gamma.r               | 5 +++--
|  R/cut_lower_fun.r                  | 1 +
|  man/bakers_gamma_for_2_k_matrix.Rd | 4 ++--
|  man/cor_bakers_gamma.Rd            | 5 ++++-
|  man/cut_lower_fun.Rd               | 2 ++
|  6 files changed, 16 insertions(+), 5 deletions(-)

* 2014-02-01(Tal Galili) Fix "'library' or 'require' call not declared from: 'ape'" by commenting-off every "require(ape)" command in the code, since it is already mentioned in imports!       (see: http://stackoverflow.com/questions/15648772/how-do-i-prevent-r-library-or-require-calls-not-declared-warnings-when-dev)       The problem still persists because of .onLoad in zzz.r, but we'll look into this later... |651bd98| 
|  NEWS          | 4 +++-
|  R/nleaves.r   | 7 +++----
|  R/rotate.r    | 6 +++---
|  R/trim.r      | 2 +-
|  R/unbranch.r  | 2 +-
|  R/zzz.r       | 7 +++++--
|  man/rotate.Rd | 2 +-
|  7 files changed, 17 insertions(+), 13 deletions(-)

* 2014-02-01(Tal Galili) Fix "Argument names in code not in docs", for: edge.lwd dLeaf_left dLeaf_right main sub rank_branches hang match_order_by_labels cex_main cex_main_left cex_main_right cex_sub |1f58846| 
|  NEWS              |  1 +
|  R/tanglegram.r    | 12 ++++++++++++
|  man/tanglegram.Rd | 12 ++++++++++++
|  3 files changed, 25 insertions(+)

* 2014-02-01(Tal Galili) Fix "Mismatches in argument default values "tanglegram" |a4fe297| 
|  NEWS              | 9 ++++++++-
|  R/tanglegram.r    | 6 +++---
|  man/tanglegram.Rd | 6 +++---
|  3 files changed, 14 insertions(+), 7 deletions(-)

* 2014-02-01(Tal Galili) Fix "Codoc mismatches from documentation object 'rotate':" - by removing k and h (since I never got to implement them...) |12a24bf| 
|  NEWS          |  1 +
|  R/rotate.r    | 15 +++++++++------
|  man/rotate.Rd |  8 --------
|  3 files changed, 10 insertions(+), 14 deletions(-)

* 2014-02-01(Tal Galili) Fix Undocumented code objects: 'old_cut_lower_fun' 'old_get_branches_heights'   'old_heights_per_k.dendrogram'.  By adding them as "#' @aliases" |13c28a1| 
|  NEWS                            | 2 ++
|  R/attr_access.r                 | 2 ++
|  R/cut_lower_fun.r               | 2 ++
|  R/cutree.dendrogram.r           | 2 ++
|  man/cut_lower_fun.Rd            | 1 +
|  man/get_branches_heights.Rd     | 1 +
|  man/heights_per_k.dendrogram.Rd | 1 +
|  7 files changed, 11 insertions(+)

* 2014-02-01(Tal Galili) Fix various "Missing link or links in documentation object" |cb607c6| 
|  NEWS                                       | 8 +++++---
|  NEWS.md                                    | 2 +-
|  R/color_branches.r                         | 2 +-
|  R/cutree.dendrogram.r                      | 1 -
|  R/entanglement.r                           | 8 ++++----
|  R/tanglegram.r                             | 2 +-
|  R/unbranch.r                               | 2 +-
|  man/all_couple_rotations_at_k.Rd           | 5 ++---
|  man/cutree-methods.Rd                      | 1 -
|  man/entanglement.Rd                        | 5 ++---
|  man/flip_leaves.Rd                         | 4 ++--
|  man/leaf_Colors.Rd                         | 2 +-
|  man/match_order_by_labels.Rd               | 2 +-
|  man/match_order_dendrogram_by_old_order.Rd | 2 +-
|  man/plot_horiz.dendrogram.Rd               | 2 +-
|  man/unbranch.Rd                            | 2 +-
|  man/untangle_random_search.Rd              | 4 ++--
|  man/untangle_step_rotate_1side.Rd          | 6 +++---
|  man/untangle_step_rotate_2side.Rd          | 6 +++---
|  19 files changed, 32 insertions(+), 34 deletions(-)

* 2014-02-01(Tal Galili) remove \link{untangle} from various .Rd (I never created this function...) |0d9c368| 
|  NEWS         |  6 ++++--
|  R/untangle.r | 10 +++++-----
|  2 files changed, 9 insertions(+), 7 deletions(-)

* 2014-02-01(Tal Galili) fix "Unknown package 'dendroextra' in Rd xrefs" in color_branches docs. |52b0ff4| 
|  NEWS                  | 4 ++++
|  R/color_branches.r    | 6 +++---
|  R/tanglegram.r        | 2 +-
|  R/unbranch.r          | 2 +-
|  man/color_branches.Rd | 8 ++++----
|  5 files changed, 13 insertions(+), 9 deletions(-)

* 2014-02-01(Tal Galili) Add DESCRIPTION and NEWS to git. |e80c96f| 
|  DESCRIPTION | 40 ++++++++--------------------
|  NEWS        | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++---
|  NEWS.md     |  6 ++---
|  R/zzz.r     | 10 ++++---
|  4 files changed, 100 insertions(+), 39 deletions(-)

* 2014-02-01(Tal Galili) Return "as.phylo.dendrogram" by adding "ape" to "Imports" in DESCRIPTION and "import" to NAMESPACE. Also fixing consistancy (using x instead of object). |6706c68| 
|  NAMESPACE   |  2 ++
|  R/nleaves.r | 17 +++++++++++------
|  2 files changed, 13 insertions(+), 6 deletions(-)

* 2014-02-01(Tal Galili) Remove "as.phylo.dendrogram" so to not force the package to depend on "ape" |52f4780| 
|  NAMESPACE      |  2 --
|  R/dendextend.r | 15 +++++++++++++++
|  R/nleaves.r    | 18 +++++++++++-------
|  3 files changed, 26 insertions(+), 9 deletions(-)

* 2014-02-01(Tal Galili) Moved from ::: to :: (where possible with dendextendRcpp). |519cad5| 
|  NAMESPACE                           | 1 +
|  R/cut_lower_fun.r                   | 2 +-
|  R/cutree.dendrogram.r               | 3 +--
|  inst/tests/test-cut_lower_fun.r     | 3 ++-
|  inst/tests/test-cutree.dendrogram.r | 4 +++-
|  man/cut_lower_fun.Rd                | 2 +-
|  vignettes/dendextend-tutorial.rnw   | 8 ++++----
|  7 files changed, 13 insertions(+), 10 deletions(-)

* 2014-02-01(Tal Galili) Using 'talgalili/dendextend', in install_github |ec75abf| 
|  README.md | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2014-02-01(Tal Galili) Moved from ::: to :: (where possible). |f4cff30| 
|  R/rotate.r                        |  5 ++++-
|  R/trim.r                          | 13 +++++++++----
|  R/unbranch.r                      |  2 +-
|  R/zzz.r                           | 12 +++++++++++-
|  vignettes/dendextend-tutorial.rnw |  2 +-
|  vignettes/dendextend-tutorial.tex |  2 +-
|  6 files changed, 27 insertions(+), 9 deletions(-)

* 2014-02-01(Tal Galili) cutree.dendrogram - turned into S3 (no longer exported) |20e1dae| 
|  man/cutree.dendrogram.Rd | 118 ---------------------------------------------
|  1 file changed, 118 deletions(-)

* 2014-02-01(Tal Galili) changed functions names:       * trim -> prune       * unroot -> unbranch |9ca729c| 
|  man/prune.Rd     |  2 +-
|  man/trim.Rd      | 48 ------------------------------------------------
|  man/trim_leaf.Rd | 32 --------------------------------
|  man/unroot.Rd    | 50 --------------------------------------------------
|  4 files changed, 1 insertion(+), 131 deletions(-)

* 2014-02-01(Tal Galili) cut_lower_fun acts diffirently on dendextendRcpp vs old dendextend, so I updated the tests to reflect that. |b520e84| 
|  inst/tests/test-cut_lower_fun.r | 25 ++++++++++++++++++-------
|  1 file changed, 18 insertions(+), 7 deletions(-)

* 2014-02-01(Tal Galili) S3methods no longer seem to be exported (due to something in roxygen2), I chose to update the tests accordingly.       * cutree.hclust -> dendextend:::cutree.hclust       * cutree.dendrogram -> dendextend:::cutree.dendrogram |e8ac80b| 
|  R/nleaves.r                         |  4 ++++
|  inst/tests/test-cutree.dendrogram.r | 12 ++++++------
|  2 files changed, 10 insertions(+), 6 deletions(-)

* 2014-01-31(Tal Galili) Added to .Rbuildignore "vignettes/" (we'll deal with this later...) |4ea429e| 
|  .Rbuildignore | 3 ++-
|  1 file changed, 2 insertions(+), 1 deletion(-)

* 2014-01-31(Tal Galili) leaf_Colors - fix example (added "dend"). |0594889| 
|  R/color_branches.r | 1 +
|  man/leaf_Colors.Rd | 1 +
|  2 files changed, 2 insertions(+)

* 2014-01-31(Tal Galili) exported prune_leaf |c572359| 
|  NAMESPACE         | 1 +
|  R/trim.r          | 3 ++-
|  man/prune_leaf.Rd | 2 +-
|  man/trim_leaf.Rd  | 2 +-
|  4 files changed, 5 insertions(+), 3 deletions(-)

* 2014-01-31(Tal Galili) README.md - invitation to get credit for using dendextend. |dcc55c3| 
|  README.md | 17 +++++++++++++++++
|  1 file changed, 17 insertions(+)

* 2014-01-31(Tal Galili) Added to .Rbuildignore: (large files which are not essential)       * inst/doc/2013-09-05_Boston-useR       * vignettes/figure |a2a4684| 
|  .Rbuildignore | 4 +++-
|  1 file changed, 3 insertions(+), 1 deletion(-)

* 2014-01-31(Tal Galili) Added "ape::" to as.phylo |e7cbf41| 
|  R/nleaves.r  | 6 ++++--
|  R/unbranch.r | 3 ++-
|  2 files changed, 6 insertions(+), 3 deletions(-)

* 2014-01-31(Tal Galili) Fix S3method in NAMESPACE |738d0ed| 
|  NAMESPACE | 29 +++++++++++------------------
|  1 file changed, 11 insertions(+), 18 deletions(-)

* 2014-01-31(Tal Galili) Fixing .Rd indentation. |8c68f20| 
|  man/Bk.Rd                                  |  42 +++++-----
|  man/Bk_permutations.Rd                     |  57 +++++++-------
|  man/Bk_plot.Rd                             |  79 +++++++++----------
|  man/FM_index.Rd                            |  56 +++++++-------
|  man/FM_index_R.Rd                          |  54 +++++++------
|  man/FM_index_permutation.Rd                |  26 +++----
|  man/FM_index_profdpm.Rd                    |  70 +++++++++--------
|  man/all_couple_rotations_at_k.Rd           |  23 +++---
|  man/as_hclust_fixed.Rd                     |  14 ++--
|  man/assign_values_to_branches_edgePar.Rd   |  13 ++--
|  man/assign_values_to_leaves_nodePar.Rd     |  13 ++--
|  man/bakers_gamma_for_2_k_matrix.Rd         |   9 +--
|  man/color_branches.Rd                      |  85 ++++++++++-----------
|  man/color_labels.Rd                        |  35 +++++----
|  man/cor_bakers_gamma.Rd                    |  82 ++++++++++----------
|  man/cor_cophenetic.Rd                      |  63 ++++++++-------
|  man/count_terminal_nodes.Rd                |  29 ++++---
|  man/cut_lower_fun.Rd                       |  28 +++----
|  man/cutree-methods.Rd                      | 100 ++++++++++++------------
|  man/cutree_1h.dendrogram.Rd                |  17 ++---
|  man/cutree_1k.dendrogram.Rd                |  33 ++++----
|  man/dendextend-package.Rd                  |   6 +-
|  man/duplicate_leaf.Rd                      |  16 ++--
|  man/entanglement.Rd                        |  53 +++++++------
|  man/fac2num.Rd                             |  16 ++--
|  man/fix_members_attr.dendrogram.Rd         |  10 +--
|  man/flatten.dendrogram.Rd                  |  12 +--
|  man/flip_leaves.Rd                         |  18 ++---
|  man/get_branches_attr.Rd                   |  10 +--
|  man/get_branches_heights.Rd                |   9 +--
|  man/get_childrens_heights.Rd               |  10 +--
|  man/get_leaves_attr.Rd                     |  17 ++---
|  man/get_nodes_attr.Rd                      |  24 +++---
|  man/hang.dendrogram.Rd                     |  22 +++---
|  man/heights_per_k.dendrogram.Rd            |   9 +--
|  man/intersect_trees.Rd                     |  10 +--
|  man/is.dendrogram.Rd                       |   6 +-
|  man/is.hclust.Rd                           |   6 +-
|  man/is.natural.number.Rd                   |  20 ++---
|  man/is.phylo.Rd                            |   6 +-
|  man/labels-assign.Rd                       |  36 +++++----
|  man/labels_colors.Rd                       |  22 +++---
|  man/leaf_Colors.Rd                         |  15 ++--
|  man/lowest_common_branch.Rd                |  18 ++---
|  man/match_order_by_labels.Rd               |  22 +++---
|  man/match_order_dendrogram_by_old_order.Rd |  37 +++++----
|  man/nleaves.Rd                             |  33 ++++----
|  man/nnodes.Rd                              |  26 +++----
|  man/order.dendrogram-assign.Rd             |  12 +--
|  man/plot_horiz.dendrogram.Rd               |  39 +++++-----
|  man/prune.Rd                               |  22 +++---
|  man/prune_leaf.Rd                          |   8 +-
|  man/raise.dendrogram.Rd                    |   6 +-
|  man/rank_branches.Rd                       |  31 ++++----
|  man/rank_order.dendrogram.Rd               |  14 ++--
|  man/remove_branches_edgePar.Rd             |  13 ++--
|  man/remove_leaves_nodePar.Rd               |  12 +--
|  man/rllply.Rd                              |  20 ++---
|  man/rotate.Rd                              | 110 +++++++++++++--------------
|  man/sample.dendrogram.Rd                   |  27 +++----
|  man/shuffle.Rd                             |  37 +++++----
|  man/sort_2_clusters_vectors.Rd             |  12 +--
|  man/sort_dist_mat.Rd                       |   9 +--
|  man/sort_levels_values.Rd                  |  32 ++++----
|  man/tanglegram.Rd                          |  77 ++++++++++---------
|  man/unbranch.Rd                            |  16 ++--
|  man/unclass_dend.Rd                        |   8 +-
|  man/untangle_random_search.Rd              |  26 +++----
|  man/untangle_step_rotate_1side.Rd          |  38 ++++-----
|  man/untangle_step_rotate_2side.Rd          |  31 ++++----
|  70 files changed, 987 insertions(+), 1030 deletions(-)

* 2014-01-31(Tal Galili) Added a placeholder for "as.dendrogram.randomForest" |2172548| 
|  R/as.dendrogram.randomForest.r | 54 ++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 54 insertions(+)

* 2013-12-10(Tal Galili) heirarchical -> Hierarchical |ee796c1| 
|  vignettes/dendextend-tutorial.rnw | 14 +++++++-------
|  1 file changed, 7 insertions(+), 7 deletions(-)

* 2013-09-05(Tal Galili) Added a fix to declare the UTF-8 encoding (for non-Windows users trying to install from github) |9bd9615| 
|  vignettes/dendextend-tutorial.rnw | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2013-09-01(Tal Galili) NEWS.md file added. |73e0f18| 
|  .Rbuildignore |   2 +-
|  NEWS.md       | 383 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  R/zzz.r       |   1 +
|  README.md     |   6 +
|  4 files changed, 391 insertions(+), 1 deletion(-)

* 2013-08-31(Tal Galili) Added R code for the presentations. |e4a1fc2| 
|  .../2013-09-05_Boston-useR_01_intro.R             |   8 +-
|  .../2013-09-05_Boston-useR_01_intro.Rpres         |   2 +-
|  .../2013-09-05_Boston-useR_02_dendextend.R        |   4 +-
|  .../2013-09-05_Boston-useR_03_untangle_iris.R     | 179 ++++++++++++++++++++
|  .../2013-09-05_Boston-useR_04_tree_inference.R    | 125 ++++++++++++++
|  5 files changed, 314 insertions(+), 4 deletions(-)

* 2013-08-31(Tal Galili) Updated presentations links |3197196| 
|  README.md | 6 +++++-
|  1 file changed, 5 insertions(+), 1 deletion(-)

* 2013-08-31(Tal Galili) Finished tanglegram and untangle.  Finished statistical measures of similarity between trees. |0f265bf| 
|  DESCRIPTION                                       |    2 +-
|  NEWS                                              |    8 +-
|  inst/doc/2013-09-05_Boston-useR/.gitignore        |    3 +-
|  ...chunk-1_58a12d7b33c21c7d7cf3b61809b68f49.RData |  Bin 3018 -> 0 bytes
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|  ...d-chunk-1_58a12d7b33c21c7d7cf3b61809b68f49.rdx |  Bin 175 -> 0 bytes
|  .../dend1_plot_1.png                              |  Bin 0 -> 3877 bytes
|  .../precip_dend5_plot_2.png                       |  Bin 0 -> 3334 bytes
|  .../tanglegram_dend12_1.png                       |  Bin 0 -> 4528 bytes
|  .../unnamed-chunk-10.png                          |  Bin 0 -> 7186 bytes
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|  .../unnamed-chunk-7.png                           |  Bin 0 -> 6419 bytes
|  .../unnamed-chunk-9.png                           |  Bin 0 -> 2000 bytes
|  ...2013-09-05_Boston-useR_04_tree_inference.Rpres |  182 ++-
|  .../2013-09-05_Boston-useR_04_tree_inference.html | 1100 +++++++++++++++++++
|  .../2013-09-05_Boston-useR_04_tree_inference.md   |  229 +++-
|  19 files changed, 1466 insertions(+), 58 deletions(-)

* 2013-08-31(Tal Galili) Vignettes tweaks |c992a7b| 
|  .gitignore                                        |    1 +
|  vignettes/.gitignore                              |    1 +
|  ...hunk-28_a920283370fb5e377c9ab52b0e8e6f00.RData |  Bin 3490 -> 0 bytes
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|  ...-chunk-29_12f892b1ead1d73ff2f1d0c38721055f.rdx |  Bin 206 -> 0 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    2 +-
|  vignettes/dendextend-tutorial.log                 |   22 +-
|  vignettes/dendextend-tutorial.pdf                 | 1569 ++++++++++---------
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 240665 -> 240890 bytes
|  vignettes/dendextend-tutorial.tex                 |   18 +-
|  vignettes/figure/unnamed-chunk-28.pdf             |  Bin 4694 -> 4694 bytes
|  vignettes/figure/unnamed-chunk-29.pdf             |  Bin 5655 -> 5655 bytes
|  15 files changed, 814 insertions(+), 799 deletions(-)

* 2013-08-30(Tal Galili) "trim" is now called "prune"! |e783d26| 
|  DESCRIPTION                                       |   7 +-
|  NAMESPACE                                         |  10 +-
|  NEWS                                              |   9 +-
|  R/attr_access.r                                   |  14 +-
|  R/cutree.dendrogram.r                             |   4 +-
|  R/sample.dendrogram.r                             |   6 +-
|  R/tanglegram.r                                    |   6 +-
|  R/trim.r                                          |  96 +++---
|  README.md                                         |   2 +-
|  demo/dendextend.r                                 |   2 +-
|  .../2013-09-05_Boston-useR_02_dendextend.R        |   8 +-
|  .../2013-09-05_Boston-useR_02_dendextend.Rpres    |   6 +-
|  .../2013-09-05_Boston-useR_02_dendextend.html     |   8 +-
|  .../2013-09-05_Boston-useR_02_dendextend.md       |   8 +-
|  inst/tests/test-trim.r                            |  34 +-
|  man/fix_members_attr.dendrogram.Rd                |  10 +-
|  man/intersect_trees.Rd                            |  14 +-
|  man/prune.Rd                                      |  48 +++
|  man/prune_leaf.Rd                                 |  32 ++
|  man/rank_order.dendrogram.Rd                      |   4 +-
|  man/sample.dendrogram.Rd                          |   2 +-
|  man/tanglegram.Rd                                 |   4 +-
|  man/trim.Rd                                       |  30 +-
|  man/trim_leaf.Rd                                  |  14 +-
|  vignettes/dendextend-tutorial.bib                 |   2 +-
|  vignettes/dendextend-tutorial.log                 |   4 +-
|  vignettes/dendextend-tutorial.pdf                 | 328 ++++++++++----------
|  vignettes/dendextend-tutorial.rnw                 |  18 +-
|  vignettes/dendextend-tutorial.tex                 |  22 +-
|  29 files changed, 416 insertions(+), 336 deletions(-)

* 2013-08-30(Tal Galili) Finished tanglegram and untangle. We are left with |3689f21| 
|  NEWS                                              |    3 +
|  inst/doc/2013-09-05_Boston-useR/.gitignore        |    3 +-
|  .../2013-09-05_Boston-useR_01_intro.Rpres         |    8 +-
|  .../dend_hang_tree_1.png                          |  Bin 0 -> 4731 bytes
|  .../dend_rotating_example_1.png                   |  Bin 0 -> 4759 bytes
|  .../dend_trimming_example_1.png                   |  Bin 0 -> 4139 bytes
|  .../dend_unbranching_example_1.png                |  Bin 0 -> 4748 bytes
|  .../first_tanglegram_with_code.png                |  Bin 0 -> 40772 bytes
|  .../simple_tanglegram_1.png                       |  Bin 2846 -> 3256 bytes
|  .../simple_tanglegram_1_worst_case.png            |  Bin 4124 -> 4577 bytes
|  .../simple_tanglegram_one_shuffle_1.png           |  Bin 2932 -> 3621 bytes
|  .../simple_tanglegram_random_search_1.png         |  Bin 2296 -> 2846 bytes
|  ...ple_tanglegram_step_rotate_1side_example_1.png |  Bin 0 -> 2822 bytes
|  .../tanglegram_iris_untangle_random.png           |  Bin 0 -> 42100 bytes
|  .../unnamed-chunk-15.png                          |  Bin 4731 -> 4755 bytes
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|  .../unnamed-chunk-24.png                          |  Bin 0 -> 22344 bytes
|  .../2013-09-05_Boston-useR_02_dendextend.R        |  122 +-
|  .../2013-09-05_Boston-useR_02_dendextend.Rpres    |  103 +-
|  .../2013-09-05_Boston-useR_02_dendextend.html     | 1666 +++++++++++++++++++
|  .../2013-09-05_Boston-useR_02_dendextend.md       |   95 +-
|  .../first_tanglegram_with_2side_untangle.png      |  Bin 0 -> 18166 bytes
|  .../first_tanglegram_with_2side_untangle_hang.png |  Bin 0 -> 26292 bytes
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|  .../2013-09-05_Boston-useR_03_untangle_iris.Rpres |  184 ++
|  .../2013-09-05_Boston-useR_03_untangle_iris.html  | 1058 ++++++++++++
|  .../2013-09-05_Boston-useR_03_untangle_iris.md    |  200 +++
|  .../__packages                                    |    8 +
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|  ...2013-09-05_Boston-useR_04_tree_inference.Rpres |   80 +
|  .../2013-09-05_Boston-useR_04_tree_inference.md   |   62 +
|  46 files changed, 3471 insertions(+), 121 deletions(-)

* 2013-08-30(Tal Galili)  untangle_step_rotate_2side added k_seq parameter. |b3aab6a| 
|  R/untangle.r                      | 13 ++++++++-----
|  man/untangle_step_rotate_2side.Rd |  7 ++++++-
|  2 files changed, 14 insertions(+), 6 deletions(-)

* 2013-08-30(Tal Galili) tanglegram now has "sub" and "cex_sub" parameters. |eecbd30| 
|  NEWS              | 7 +++++++
|  R/tanglegram.r    | 7 ++++++-
|  man/tanglegram.Rd | 6 +++++-
|  3 files changed, 18 insertions(+), 2 deletions(-)

* 2013-08-30(Tal Galili) Seperated 2013-09-05_Boston-useR.Rpres into two files (since RStudio is not able to handle them) |73d9714| 
|  NAMESPACE                                         |   90 +-
|  NEWS                                              |    2 +
|  R/tanglegram.r                                    |    2 +-
|  inst/doc/2013-09-05_Boston-useR/.gitignore        |    3 +-
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|  .../2013-09-05_Boston-useR.md                     | 1161 -------------------
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|  .../2013-09-05_Boston-useR_01_intro.R             |  192 +++
|  .../2013-09-05_Boston-useR_01_intro.Rpres         |  448 +++++++
|  ....html => 2013-09-05_Boston-useR_01_intro.html} |  340 +-----
|  .../2013-09-05_Boston-useR_01_intro.md            |  659 +++++++++++
|  .../first_tanglegram.png                          |  Bin
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|  ...R.R => 2013-09-05_Boston-useR_02_dendextend.R} |  289 ++---
|  ...=> 2013-09-05_Boston-useR_02_dendextend.Rpres} |  589 ++++------
|  .../2013-09-05_Boston-useR_02_dendextend.md       |  853 ++++++++++++++
|  man/leaf_Colors.Rd                                |    2 +-
|  vignettes/dendextend-tutorial.log                 |    2 +-
|  vignettes/dendextend-tutorial.pdf                 |   13 +-
|  vignettes/dendextend-tutorial.tex                 |    4 +-
|  66 files changed, 2519 insertions(+), 2130 deletions(-)

* 2013-08-29(Tal Galili) untangle_random_search - made sure the function will return the original trees if no better tree was found. |1d6d9fb| 
|  NEWS         | 2 ++
|  R/untangle.r | 2 ++
|  2 files changed, 4 insertions(+)

* 2013-08-29(Tal Galili) tanglegram now returns an invisible list with the two dendrograms (after they have been modified within the function). |d3b0f07| 
|  NEWS              | 1 +
|  R/tanglegram.r    | 5 +++--
|  man/tanglegram.Rd | 3 ++-
|  3 files changed, 6 insertions(+), 3 deletions(-)

* 2013-08-29(Tal Galili) Added "warn" parameter to: assign_values_to_leaves_nodePar, And set it to FALSE when used inside "tanglegram". |5e1abf1| 
|  NEWS                                   |  1 +
|  R/attr_access.r                        |  9 +++++++--
|  R/tanglegram.r                         | 12 ++++++------
|  man/assign_values_to_leaves_nodePar.Rd |  7 ++++++-
|  4 files changed, 20 insertions(+), 9 deletions(-)

* 2013-08-29(Tal Galili) color_labels - added a "warn" parameter. And also set the default (in case no k/h is supplied) - to just color all of the labels. |2fc659e| 
|  NEWS                |  7 +++++++
|  R/color_branches.r  | 16 ++++++++++++----
|  man/color_labels.Rd |  7 ++++++-
|  man/tanglegram.Rd   |  8 ++++++++
|  4 files changed, 33 insertions(+), 5 deletions(-)

* 2013-08-29(Tal Galili) Version bump to 0.11.0 |10d8cc3| 
|  DESCRIPTION | 14 ++++++++------
|  NEWS        | 12 ++++++++++++
|  2 files changed, 20 insertions(+), 6 deletions(-)

* 2013-08-29(Tal Galili) tangelgram - added cex_main parameter. |79ab582| 
|  R/tanglegram.r | 11 ++++++++++-
|  1 file changed, 10 insertions(+), 1 deletion(-)

* 2013-08-26(Tal Galili) Adding links to the documents, and a better "install" code sequence. |2c9b5b4| 
|  README.md | 10 ++++++++--
|  1 file changed, 8 insertions(+), 2 deletions(-)

* 2013-08-26(Tal Galili) Added auto purl for extracting the R code. |d86616c| 
|  .../2013-09-05_Boston-useR.R                      | 459 ++++++++++++++++++++
|  .../2013-09-05_Boston-useR.Rpres                  |   5 +-
|  2 files changed, 462 insertions(+), 2 deletions(-)

* 2013-08-26(Tal Galili) Boston-useR presentation |d1f14cf| 
|  inst/doc/2013-09-05_Boston-useR/.gitignore        |    1 +
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|  .../2013-09-05_Boston-useR.Rpres                  |  863 +++++++++
|  .../2013-09-05_Boston-useR.html                   | 1803 +++++++++++++++++++
|  .../2013-09-05_Boston-useR.md                     | 1161 ++++++++++++
|  48 files changed, 3828 insertions(+)

* 2013-08-24(Tal Galili) vignette - minor fixes |a286c6e| 
|  vignettes/dendextend-tutorial.bib        |   11 -
|  vignettes/dendextend-tutorial.blg        |    6 +-
|  vignettes/dendextend-tutorial.log        |  116 +-
|  vignettes/dendextend-tutorial.pdf        | 2559 ++++++++++++++--------------
|  vignettes/dendextend-tutorial.rnw        |    2 +-
|  vignettes/dendextend-tutorial.synctex.gz |  Bin 240127 -> 240665 bytes
|  vignettes/dendextend-tutorial.tex        |    6 +-
|  7 files changed, 1316 insertions(+), 1384 deletions(-)

* 2013-08-22(Tal Galili) Updated the list of contributors to the package. |325c8df| 
|  DESCRIPTION | 7 ++++++-
|  1 file changed, 6 insertions(+), 1 deletion(-)

* 2013-08-21(Tal Galili) VIGNETTES: Added FM-index and Bk plot sections. |fba17c3| 
|  NEWS                                              |    2 +-
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|  vignettes/dendextend-tutorial-concordance.tex     |    6 +-
|  vignettes/dendextend-tutorial.log                 |  270 +-
|  vignettes/dendextend-tutorial.pdf                 | 4212 ++++++++++++-------
|  vignettes/dendextend-tutorial.rnw                 |  232 +-
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|  vignettes/dendextend-tutorial.tex                 |  322 +-
|  vignettes/figure/Bk_examples.pdf                  |  Bin 0 -> 20539 bytes
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|  vignettes/figure/FM_permutation_example_1.pdf     |  Bin 0 -> 10674 bytes
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|  41 files changed, 3391 insertions(+), 1653 deletions(-)

* 2013-08-21(Tal Galili) New tests for Bk methods and some minor doc changes. |35df06c| 
|  NEWS                        |  4 ++++
|  R/bk_method.r               |  5 +++-
|  inst/tests/test-bk_method.r | 56 +++++++++++++++++++++++++++++++++++++++++++
|  man/FM_index_permutation.Rd |  1 +
|  4 files changed, 65 insertions(+), 1 deletion(-)

* 2013-08-20(Tal Galili) Version bump - 0.10.0 |0079a2c| 
|  DESCRIPTION | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2013-08-20(Tal Galili) Vignette - cut_lower_fun PDF and extra files are updated. |c08cec1| 
|  ...wer_fun_11e6d15e4d39a2eca09990d42c1235c0.RData |  Bin 0 -> 3255 bytes
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|  vignettes/dendextend-tutorial-concordance.tex     |    4 +-
|  vignettes/dendextend-tutorial.log                 |   62 +-
|  vignettes/dendextend-tutorial.pdf                 | 1653 +++++++++----------
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 223843 -> 223345 bytes
|  vignettes/dendextend-tutorial.tex                 |   70 +-
|  8 files changed, 880 insertions(+), 909 deletions(-)

* 2013-08-20(Tal Galili) cut_lower_fun function added - it wraps the "cut" function, and is built to be masked by the function in dendextendRcpp in order to gain 4-14 speed gain. |987af61| 
|  DESCRIPTION                       |  1 +
|  NAMESPACE                         |  1 +
|  NEWS                              | 13 ++++++
|  R/cut_lower_fun.r                 | 86 +++++++++++++++++++++++++++++++++++++
|  R/cutree.dendrogram.r             |  3 +-
|  R/zzz.r                           | 15 +++++--
|  inst/tests/test-cut_lower_fun.r   | 78 +++++++++++++++++++++++++++++++++
|  man/cut_lower_fun.Rd              | 59 +++++++++++++++++++++++++
|  vignettes/dendextend-tutorial.rnw | 12 ++++++
|  9 files changed, 263 insertions(+), 5 deletions(-)

* 2013-08-20(Tal Galili) cor_bakers_gamma.hclust function added. |9bd41bf| 
|  NAMESPACE             |  1 +
|  NEWS                  | 10 ++++++++++
|  R/cor_bakers_gamma.r  | 16 +++++++++++++++-
|  R/cutree.dendrogram.r |  2 ++
|  man/cutree-methods.Rd |  4 ++--
|  5 files changed, 30 insertions(+), 3 deletions(-)

* 2013-08-20(Tal Galili) Vignettes - some Bk thoery, and Rcpp section. |c534cc0| 
|  NEWS                                              |    3 +
|  ...heights_849ab68f2f2a2097dd7a0ed7aff83b86.RData |  Bin 0 -> 3252 bytes
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|  vignettes/cache/__packages                        |    4 +
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|  vignettes/dendextend-tutorial-concordance.tex     |    6 +-
|  vignettes/dendextend-tutorial.bib                 |  110 +-
|  vignettes/dendextend-tutorial.blg                 |    2 +-
|  vignettes/dendextend-tutorial.log                 |  129 +-
|  vignettes/dendextend-tutorial.pdf                 | 3607 ++++++++++---------
|  vignettes/dendextend-tutorial.rnw                 |   69 +-
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|  vignettes/dendextend-tutorial.tex                 |  153 +-
|  25 files changed, 2376 insertions(+), 1707 deletions(-)

* 2013-08-19(Tal Galili) Create hidden backups of the R functions which are replaced by the Rcpp function so that we will be able to benchmark them. |a8b17c0| 
|  DESCRIPTION | 4 ++--
|  R/zzz.r     | 8 ++++++++
|  2 files changed, 10 insertions(+), 2 deletions(-)

* 2013-08-19(Tal Galili) UPDATED FUNCTIONS:  * Bk_plot - now adds dots for the asymptotic lines in case of NA's    * Bk - now calculates cutree once for all relevant k's - and only then goes forth with FM_index. |0d4d3dd| 
|  NEWS              | 20 +++++++++++--
|  R/bk_method.r     | 85 +++++++++++++++++++++++++++++++++++++++++++++--------
|  man/Bk.Rd         | 15 ++++++++--
|  man/Bk_plot.Rd    |  1 +
|  man/FM_index_R.Rd |  5 ++++
|  5 files changed, 108 insertions(+), 18 deletions(-)

* 2013-08-19(Tal Galili) Rename the package RcppDend-> dendextendRcpp |8903084| 
|  DESCRIPTION                         |  2 +-
|  NEWS                                |  3 ++-
|  R/color_branches.r                  |  2 +-
|  R/zzz.r                             | 22 +++++++++++-----------
|  inst/tests/test-cutree.dendrogram.r |  2 +-
|  tests/test-all.r                    |  2 +-
|  6 files changed, 17 insertions(+), 16 deletions(-)

* 2013-08-19(Tal Galili) note on labels.dendrogram. |740aaf7| 
|  R/zzz.r | 12 ++++++++++++
|  1 file changed, 12 insertions(+)

* 2013-08-19(Tal Galili) color_labels - added "labels" parameter for selective coloring of labels by name. |730cf25| 
|  NEWS                |  1 +
|  R/color_branches.r  | 20 +++++++++++++++++---
|  man/color_labels.Rd |  9 ++++++++-
|  3 files changed, 26 insertions(+), 4 deletions(-)

* 2013-08-19(Tal Galili) Make RcppDend loads and override core functions in dendextend in order to make it MUCH faster :) |ffb7187| 
|  R/zzz.r          | 70 ++++++++++++++++++++++++++++++++++++++++++++----------
|  tests/test-all.r |  1 +
|  2 files changed, 59 insertions(+), 12 deletions(-)

* 2013-08-19(Tal Galili) add more explenation in the tests for how labels.dendrogram acts when there are missing labels. (in stats vs RcppDend package) |979beed| 
|  inst/tests/test-cutree.dendrogram.r | 9 ++++++++-
|  1 file changed, 8 insertions(+), 1 deletion(-)

* 2013-08-19(Tal Galili) T -> TRUE |fc3ea18| 
|  R/trim.r | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2013-08-19(Tal Galili) being explisit about "sort" in get_branches_heights |f532205| 
|  R/cutree.dendrogram.r | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2013-08-18(Tal Galili) Bk_plot function added! |814a668| 
|  NAMESPACE             |   1 +
|  NEWS                  |   3 +-
|  R/bk_method.r         | 382 ++++++++++++++++++++----------------------------
|  R/cutree.dendrogram.r |   2 +-
|  R/sample.dendrogram.r |   2 +-
|  man/Bk.Rd             |  83 -----------
|  man/Bk_plot.Rd        | 180 +++++++++++++++++++++++
|  man/cutree-methods.Rd |   4 +-
|  8 files changed, 343 insertions(+), 314 deletions(-)

* 2013-08-18(Tal Galili) Bk_permutations function added. |d5a24cd| 
|  NAMESPACE              |   1 +
|  NEWS                   |   1 +
|  R/bk_method.r          | 232 +++++++++++++++++++++++++++++++++++++++++++++++
|  man/Bk.Rd              |  83 +++++++++++++++++
|  man/Bk_permutations.Rd |  93 +++++++++++++++++++
|  5 files changed, 410 insertions(+)

* 2013-08-18(Tal Galili) Bk Function added! |bf73478| 
|  NAMESPACE     |   1 +
|  NEWS          |   1 +
|  R/bk_method.r | 207 +++++++++++++++++++++++++++++---------------------------
|  man/Bk.Rd     |  93 +++++++++++++++++++++++++
|  4 files changed, 202 insertions(+), 100 deletions(-)

* 2013-08-18(Tal Galili) Exaplin what happens to FM distribution for different values of k. |feb6432| 
|  R/bk_method.r               | 7 ++++++-
|  man/FM_index_permutation.Rd | 7 ++++++-
|  2 files changed, 12 insertions(+), 2 deletions(-)

* 2013-08-18(Tal Galili) FM_index_permutation function added |4cc208d| 
|  DESCRIPTION                 |   6 ++-
|  NAMESPACE                   |   1 +
|  NEWS                        |  25 ++++++++++-
|  R/bk_method.r               | 102 ++++++++++++++++++++++++++++++++++++++++++
|  inst/tests/test-bk_method.r |  34 ++++++++++++++
|  man/FM_index_permutation.Rd |  85 +++++++++++++++++++++++++++++++++++
|  6 files changed, 250 insertions(+), 3 deletions(-)

* 2013-08-18(Tal Galili) tests for FM_index_R and FM_index |ee50173| 
|  inst/tests/test-bk_method.r | 112 ++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 112 insertions(+)

* 2013-08-18(Tal Galili) FM_index_R and FM_index functions added. |e7a250b| 
|  NAMESPACE               |   2 +
|  R/bk_method.r           | 244 +++++++++++++++++++++++++++++++++++++++-------
|  man/FM_index.Rd         | 113 +++++++++++++++++++++
|  man/FM_index_R.Rd       |  94 ++++++++++++++++++
|  man/FM_index_profdpm.Rd |  13 ++-
|  5 files changed, 427 insertions(+), 39 deletions(-)

* 2013-08-18(Tal Galili) sort_2_clusters_vectors function added. |e4913b5| 
|  NAMESPACE                      |  1 +
|  R/bk_method.r                  | 99 +++++++++++++++++++++++++++++++---------
|  inst/tests/test-bk_method.r    | 52 +++++++++++++++------
|  man/sort_2_clusters_vectors.Rd | 59 ++++++++++++++++++++++++
|  4 files changed, 177 insertions(+), 34 deletions(-)

* 2013-08-18(Tal Galili) export lowest_common_branch. |f2dc78b| 
|  NAMESPACE            | 1 +
|  R/cor_bakers_gamma.r | 1 +
|  2 files changed, 2 insertions(+)

* 2013-08-18(Tal Galili) FM_index_profdpm function added. |35cf12d| 
|  NAMESPACE                   |   1 +
|  R/bk_method.r               | 338 +++++++++++++++++++++++++++++++++++-------
|  inst/tests/test-bk_method.r |  58 ++++++++
|  man/FM_index_profdpm.Rd     |  96 ++++++++++++
|  man/color_labels.Rd         |   3 +-
|  5 files changed, 437 insertions(+), 59 deletions(-)

* 2013-08-18(Tal Galili) Change variable names from "." to "_" |858167f| 
|  R/bk_method.r | 98 ++++++++++++++++++++++++++++++++++-----------------------
|  1 file changed, 59 insertions(+), 39 deletions(-)

* 2013-08-17(Tal Galili) Added a commented-out section which could (in the future) be the basis of an Rcpp cutree (actually cutree_1h.dendrogram) function! |cde09ff| 
|  R/cutree.dendrogram.r | 46 ++++++++++++++++++++++++++++++++++++++++++++--
|  1 file changed, 44 insertions(+), 2 deletions(-)

* 2013-08-16(Tal Galili) color_labels_by_labels - code added (now need to document, and add to color_labels). |88c8685| 
|  R/color_branches.r | 64 ++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 64 insertions(+)

* 2013-08-16(Tal Galili) color_labels - removed unused 'groupLabels' parameter. |4680820| 
|  R/color_branches.r | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2013-08-16(Tal Galili) copyright notice. |02c1f28| 
|  R/bk_method.r | 19 +++++++++++++++++++
|  1 file changed, 19 insertions(+)

* 2013-08-16(Tal Galili) Bk-method.r file added |5db46e6| 
|  R/bk_method.r | 260 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 260 insertions(+)

* 2013-08-15(Tal Galili) Added some ref for tanglegram problem |f5fbc66| 
|  vignettes/dendextend-tutorial.bib | 12 +++++-------
|  1 file changed, 5 insertions(+), 7 deletions(-)

* 2013-08-14(Tal Galili) Vignettes - Cophenetic correlation |8d83bee| 
|  NEWS                                              |    1 +
|  ...ample_1_49438132f802c72c76330a0c6277e5c9.RData |  Bin 0 -> 3844 bytes
|  ...example_1_49438132f802c72c76330a0c6277e5c9.rdb |  Bin 0 -> 1636 bytes
|  ...example_1_49438132f802c72c76330a0c6277e5c9.rdx |  Bin 0 -> 174 bytes
|  ...ation_2_f52d3297030e8ccb9446f2dc58662c66.RData |  Bin 0 -> 3525 bytes
|  ...ulation_2_f52d3297030e8ccb9446f2dc58662c66.rdb |  Bin 0 -> 9947 bytes
|  ...ulation_2_f52d3297030e8ccb9446f2dc58662c66.rdx |  Bin 0 -> 264 bytes
|  ...on_CI_3_3243f384d2df989a75438b63f85f44f5.RData |  Bin 0 -> 3884 bytes
|  ...tion_CI_3_3243f384d2df989a75438b63f85f44f5.rdb |  Bin 0 -> 9380 bytes
|  ...tion_CI_3_3243f384d2df989a75438b63f85f44f5.rdx |  Bin 0 -> 308 bytes
|  ...on_CI_4_dd6497988cbed58310cbeaaabb6163b2.RData |  Bin 0 -> 3904 bytes
|  ...tion_CI_4_dd6497988cbed58310cbeaaabb6163b2.rdb |  Bin 0 -> 8389 bytes
|  ...tion_CI_4_dd6497988cbed58310cbeaaabb6163b2.rdx |  Bin 0 -> 308 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    3 +-
|  vignettes/dendextend-tutorial.bib                 |   16 +
|  vignettes/dendextend-tutorial.blg                 |    6 +-
|  vignettes/dendextend-tutorial.log                 |  152 +-
|  vignettes/dendextend-tutorial.pdf                 | 2769 +++++++++++--------
|  vignettes/dendextend-tutorial.rnw                 |  213 ++
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 182727 -> 203406 bytes
|  vignettes/dendextend-tutorial.tex                 |  299 ++
|  vignettes/figure/cor_cophenetic_simulation_2.pdf  |  Bin 0 -> 7663 bytes
|  .../figure/cor_cophenetic_simulation_CI_3.pdf     |  Bin 0 -> 7152 bytes
|  .../figure/cor_cophenetic_simulation_CI_4.pdf     |  Bin 0 -> 7524 bytes
|  24 files changed, 2315 insertions(+), 1144 deletions(-)

* 2013-08-14(Tal Galili) cor_cophenetic function added (also sort_dist_mat) |cecaa2a| 
|  DESCRIPTION             |   1 +
|  NAMESPACE               |   3 +
|  NEWS                    |   6 +-
|  R/cor_bakers_gamma.r    |   4 +-
|  R/cor_cophenetic.r      | 187 ++++++++++++++++++++++++++++++++++++++++++++++
|  man/cor_bakers_gamma.Rd |   7 +-
|  man/cor_cophenetic.Rd   | 112 +++++++++++++++++++++++++++
|  man/sort_dist_mat.Rd    |  28 +++++++
|  8 files changed, 341 insertions(+), 7 deletions(-)

* 2013-08-14(Tal Galili) Adding copyright notice |87bce54| 
|  R/sample.dendrogram.r | 20 ++++++++++++++++++++
|  1 file changed, 20 insertions(+)

* 2013-08-14(Tal Galili) VIGNETTES: Added a bootstrap and permutation examples for inference on Baker's Gamma. |08fb0c3| 
|  NEWS                                              |    1 +
|  R/sample.dendrogram.r                             |    2 +-
|  ...ation_1_80285bbfbf4a8a4612444b6a03b5bfa2.RData |  Bin 3496 -> 0 bytes
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|  ...ulation_1_dd930ca5c4802d808d8e1ff37bc0edef.rdx |  Bin 0 -> 257 bytes
|  ...ation_2_a386542ebf46e61430ae6d546755ef8a.RData |  Bin 0 -> 3513 bytes
|  ...lation_2_a386542ebf46e61430ae6d546755ef8a.rdb} |  Bin 8761 -> 8768 bytes
|  ...ulation_2_a386542ebf46e61430ae6d546755ef8a.rdx |  Bin 0 -> 259 bytes
|  ...ation_2_faf7c50fae3d6d1cf2dedf6718056d8a.RData |  Bin 3503 -> 0 bytes
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|  ...ulation_3_a2067a06e2dadc01a424503feeb67ad9.rdx |  Bin 0 -> 269 bytes
|  ...on_CI_4_a4452373b91f83c32fa8ad187e0fa475.RData |  Bin 0 -> 3914 bytes
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|  ...tion_CI_4_a4452373b91f83c32fa8ad187e0fa475.rdx |  Bin 0 -> 310 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    4 +-
|  vignettes/dendextend-tutorial.log                 |  110 +-
|  vignettes/dendextend-tutorial.pdf                 | 1667 ++++++++++++-------
|  vignettes/dendextend-tutorial.rnw                 |   71 +-
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 175961 -> 182727 bytes
|  vignettes/dendextend-tutorial.tex                 |  107 +-
|  .../figure/cor_bakers_gamma_simulation_1.pdf      |  Bin 7148 -> 7148 bytes
|  .../figure/cor_bakers_gamma_simulation_2.pdf      |  Bin 7609 -> 7609 bytes
|  .../figure/cor_bakers_gamma_simulation_3.pdf      |  Bin 7596 -> 7596 bytes
|  .../figure/cor_bakers_gamma_simulation_CI_41.pdf  |  Bin 0 -> 5047 bytes
|  .../figure/cor_bakers_gamma_simulation_CI_42.pdf  |  Bin 0 -> 4848 bytes
|  .../figure/cor_bakers_gamma_simulation_CI_43.pdf  |  Bin 0 -> 7496 bytes
|  32 files changed, 1307 insertions(+), 655 deletions(-)

* 2013-08-14(Tal Galili) Added a "warn" parameter to cor_bakers_gamma |f6f62b2| 
|  R/cor_bakers_gamma.r    | 8 +++++---
|  man/cor_bakers_gamma.Rd | 4 ++++
|  2 files changed, 9 insertions(+), 3 deletions(-)

* 2013-08-14(Tal Galili) sample.dendrogram function added - it allows for permutation and bootstrap tests for comparing two trees. |e02436f| 
|  NAMESPACE                |   1 +
|  NEWS                     |   7 +-
|  R/sample.dendrogram.r    | 229 +++++++++++++++++++++++++++++++++++++++++++--
|  man/duplicate_leaf.Rd    |  53 +++++++++++
|  man/sample.dendrogram.Rd |  77 +++++++++++++++
|  5 files changed, 355 insertions(+), 12 deletions(-)

* 2013-08-14(Tal Galili) Fix cor_bakers_gamma to work in case if trees with only leaves. |e264773| 
|  R/cor_bakers_gamma.r | 6 +++++-
|  1 file changed, 5 insertions(+), 1 deletion(-)

* 2013-08-14(Tal Galili) nleaves - fix doc. |8735d55| 
|  R/nleaves.r    | 2 +-
|  man/nleaves.Rd | 4 ++--
|  2 files changed, 3 insertions(+), 3 deletions(-)

* 2013-08-14(Tal Galili) More protection for cutree by forcing nleaves to use method order. |aa129cd| 
|  R/cutree.dendrogram.r | 7 ++++---
|  1 file changed, 4 insertions(+), 3 deletions(-)

* 2013-08-14(Tal Galili) fix_members_attr.dendrogram - fixed a bug introduced by the new "members" method in nleaves. (test added) |6ba6295| 
|  DESCRIPTION                   |  2 +-
|  NEWS                          |  2 ++
|  R/attr_access.r               |  2 +-
|  inst/tests/test-attr_access.r | 15 +++++++++++++++
|  4 files changed, 19 insertions(+), 2 deletions(-)

* 2013-08-14(Tal Galili) sample.dendrogram function added. Only works for replace = FALSE |c213ffc| 
|  DESCRIPTION           |  5 +++--
|  NAMESPACE             |  1 +
|  NEWS                  |  5 +++++
|  R/sample.dendrogram.r | 38 ++++++++++++++++++++++++++++++++++++++
|  4 files changed, 47 insertions(+), 2 deletions(-)

* 2013-08-14(Tal Galili) rank_order.dendrogram function added. |39a5237| 
|  NAMESPACE                    |  2 +
|  R/attr_access.r              | 95 ++++++++++++++++++++++++++++++++++++++++++
|  R/trim.r                     | 49 ----------------------
|  man/rank_order.dendrogram.Rd | 33 +++++++++++++++
|  4 files changed, 130 insertions(+), 49 deletions(-)

* 2013-08-14(Tal Galili) added ref to Baker 1974 |33390db| 
|  man/cor_bakers_gamma.Rd | 6 ++++++
|  1 file changed, 6 insertions(+)

* 2013-08-14(Tal Galili) Vignettes: adding a third simulation |bfef209| 
|  ...ation_3_1728f5856aa0b70528c40164da84c605.RData |  Bin 0 -> 3522 bytes
|  ...ulation_3_1728f5856aa0b70528c40164da84c605.rdb |  Bin 0 -> 9119 bytes
|  ...ulation_3_1728f5856aa0b70528c40164da84c605.rdx |  Bin 0 -> 268 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    4 +-
|  vignettes/dendextend-tutorial.log                 |   67 +-
|  vignettes/dendextend-tutorial.pdf                 | 1024 +++++++++++--------
|  vignettes/dendextend-tutorial.rnw                 |   34 +
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 172701 -> 175961 bytes
|  vignettes/dendextend-tutorial.tex                 |   58 +-
|  .../figure/cor_bakers_gamma_simulation_3.pdf      |  Bin 0 -> 7596 bytes
|  10 files changed, 730 insertions(+), 457 deletions(-)

* 2013-08-14(Tal Galili) VIGNETTES - Added the Baker's Gamma Index section. |9dd5cdd| 
|  NEWS                                              |    3 +
|  ...ample_1_a6f852561e8ce9d553b9d2b27b424b22.RData |  Bin 0 -> 3823 bytes
|  ...example_1_a6f852561e8ce9d553b9d2b27b424b22.rdb |  Bin 0 -> 2409 bytes
|  ...example_1_a6f852561e8ce9d553b9d2b27b424b22.rdx |  Bin 0 -> 204 bytes
|  ...ation_1_80285bbfbf4a8a4612444b6a03b5bfa2.RData |  Bin 0 -> 3496 bytes
|  ...ulation_1_80285bbfbf4a8a4612444b6a03b5bfa2.rdb |  Bin 0 -> 7993 bytes
|  ...ulation_1_80285bbfbf4a8a4612444b6a03b5bfa2.rdx |  Bin 0 -> 257 bytes
|  ...ation_2_faf7c50fae3d6d1cf2dedf6718056d8a.RData |  Bin 0 -> 3503 bytes
|  ...ulation_2_faf7c50fae3d6d1cf2dedf6718056d8a.rdb |  Bin 0 -> 8761 bytes
|  ...ulation_2_faf7c50fae3d6d1cf2dedf6718056d8a.rdx |  Bin 0 -> 259 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    3 +-
|  vignettes/dendextend-tutorial.log                 |  175 +-
|  vignettes/dendextend-tutorial.pdf                 | 3073 ++++++++++++-------
|  vignettes/dendextend-tutorial.rnw                 |  153 +-
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 154731 -> 172701 bytes
|  vignettes/dendextend-tutorial.tex                 |  283 +-
|  vignettes/figure/cor_bakers_gamma_example_11.pdf  |  Bin 0 -> 5053 bytes
|  vignettes/figure/cor_bakers_gamma_example_12.pdf  |  Bin 0 -> 5082 bytes
|  vignettes/figure/cor_bakers_gamma_example_13.pdf  |  Bin 0 -> 5053 bytes
|  vignettes/figure/cor_bakers_gamma_example_14.pdf  |  Bin 0 -> 5056 bytes
|  .../figure/cor_bakers_gamma_simulation_1.pdf      |  Bin 0 -> 7148 bytes
|  .../figure/cor_bakers_gamma_simulation_2.pdf      |  Bin 0 -> 7609 bytes
|  22 files changed, 2500 insertions(+), 1190 deletions(-)

* 2013-08-14(Tal Galili) Adding reference to Baker's paper from 1974. |5a0209d| 
|  R/cor_bakers_gamma.r              |  7 +++++++
|  vignettes/dendextend-tutorial.bib | 36 ++++++++++++++++++++++++++++++++++++
|  2 files changed, 43 insertions(+)

* 2013-08-14(Tal Galili) cor_bakers_gamma function added. |8857952| 
|  DESCRIPTION                        |   2 +-
|  NAMESPACE                          |   3 +
|  NEWS                               |   9 ++
|  R/cor_bakers_gamma.r               | 210 +++++++++++++++++++++++++++++++++++
|  inst/tests/test-cor_bakers_gamma.r |  48 ++++++++
|  man/bakers_gamma_for_2_k_matrix.Rd |  31 ++++++
|  man/cor_bakers_gamma.Rd            |  99 +++++++++++++++++
|  man/lowest_common_branch.Rd        |  35 ++++++
|  8 files changed, 436 insertions(+), 1 deletion(-)

* 2013-08-14(Tal Galili) Added {} |da980a9| 
|  R/trim.r | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2013-08-14(Tal Galili) tanglegram - added the match_order_by_labels parameter. |646329a| 
|  R/tanglegram.r    | 9 ++++++++-
|  man/tanglegram.Rd | 7 +++++++
|  2 files changed, 15 insertions(+), 1 deletion(-)

* 2013-08-14(Tal Galili) Added test for cutree's use_labels_not_values parameter. |733f127| 
|  inst/tests/test-cutree.dendrogram.r | 11 +++++++++++
|  1 file changed, 11 insertions(+)

* 2013-08-14(Tal Galili) tanglegram - added the hang parameter. |82b3bd2| 
|  NEWS                                              |    1 +
|  R/tanglegram.r                                    |   11 +-
|  man/tanglegram.Rd                                 |    6 +-
|  ...example_802a64d3a4c0dd3e9bb0e2a4dee353da.RData |  Bin 0 -> 3699 bytes
|  ..._example_802a64d3a4c0dd3e9bb0e2a4dee353da.rdb} |  Bin
|  ..._example_802a64d3a4c0dd3e9bb0e2a4dee353da.rdx} |  Bin
|  ...example_bb4ceb1d930b3bb07d6747839ba48794.RData |  Bin 3657 -> 0 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    2 +-
|  vignettes/dendextend-tutorial.log                 |   59 +-
|  vignettes/dendextend-tutorial.pdf                 | 1103 +++++++++++--------
|  vignettes/dendextend-tutorial.rnw                 |   11 +
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 153993 -> 154731 bytes
|  vignettes/dendextend-tutorial.tex                 |   14 +
|  .../untangle_step_rotate_2side_example1.pdf       |  Bin 6158 -> 6158 bytes
|  .../untangle_step_rotate_2side_example2.pdf       |  Bin 6137 -> 6137 bytes
|  .../untangle_step_rotate_2side_example3.pdf       |  Bin 6154 -> 6154 bytes
|  .../untangle_step_rotate_2side_example4.pdf       |  Bin 6141 -> 6141 bytes
|  .../untangle_step_rotate_2side_example5.pdf       |  Bin 5714 -> 5714 bytes
|  .../untangle_step_rotate_2side_example6.pdf       |  Bin 0 -> 6163 bytes
|  19 files changed, 694 insertions(+), 513 deletions(-)

* 2013-08-14(Tal Galili) Version bump 0.7.3 |2bb5655| 
|  DESCRIPTION                                       |    4 +-
|  NEWS                                              |   41 +-
|  ...hunk-40_9f83c05b11ed630ecb319c8a28110b35.RData |  Bin 3466 -> 0 bytes
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|  ...chunk-40_b48b442cc366777991b02835121a00b7.rdb} |  Bin
|  ...chunk-40_b48b442cc366777991b02835121a00b7.rdx} |  Bin
|  ...example_bb4ceb1d930b3bb07d6747839ba48794.RData |  Bin 0 -> 3657 bytes
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|  ...e_example_bb4ceb1d930b3bb07d6747839ba48794.rdx |  Bin 0 -> 205 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    2 +-
|  vignettes/dendextend-tutorial.log                 |  259 +--
|  vignettes/dendextend-tutorial.pdf                 | 2039 +++++++------------
|  vignettes/dendextend-tutorial.rnw                 |   11 +-
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 153579 -> 153993 bytes
|  vignettes/dendextend-tutorial.tex                 |   36 +-
|  vignettes/figure/unnamed-chunk-34.pdf             |  Bin 6773 -> 0 bytes
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|  .../untangle_step_rotate_2side_example1.pdf       |  Bin 0 -> 6158 bytes
|  ...df => untangle_step_rotate_2side_example2.pdf} |  Bin 6027 -> 6137 bytes
|  ...df => untangle_step_rotate_2side_example3.pdf} |  Bin 6036 -> 6154 bytes
|  ...df => untangle_step_rotate_2side_example4.pdf} |  Bin 6078 -> 6141 bytes
|  ...df => untangle_step_rotate_2side_example5.pdf} |  Bin 6016 -> 5714 bytes
|  26 files changed, 946 insertions(+), 1446 deletions(-)

* 2013-08-14(Tal Galili) tanglegram - fixed the right tree's labels position relative to the leaves tips. (they were too far away because of a combination of text_adj with dLeaf) |5c0f75e| 
|  R/tanglegram.r               | 15 +++++++++++----
|  man/plot_horiz.dendrogram.Rd |  6 ++----
|  man/tanglegram.Rd            |  4 ++++
|  3 files changed, 17 insertions(+), 8 deletions(-)

* 2013-08-14(Tal Galili) rank_branches function added. |f56a9d8| 
|  NAMESPACE                     |   2 +
|  R/attr_access.r               | 104 ++++++++++++++++++++++++++++++++++++++--
|  R/tanglegram.r                |  12 +++--
|  inst/tests/test-attr_access.r |  11 +++++
|  man/get_childrens_heights.Rd  |  27 +++++++++++
|  man/rank_branches.Rd          |  48 +++++++++++++++++++
|  man/tanglegram.Rd             |   8 +++-
|  7 files changed, 204 insertions(+), 8 deletions(-)

* 2013-08-14(Tal Galili) sort_levels_values now deals with vectors haing NA values (just returning the vector as is) |62631fa| 
|  R/cutree.dendrogram.r         | 17 ++++++++++++-----
|  man/get_heights.dendrogram.Rd | 26 --------------------------
|  man/sort_levels_values.Rd     | 13 ++++++++-----
|  3 files changed, 20 insertions(+), 36 deletions(-)

* 2013-08-13(Tal Galili) Version bump to 0.7.2 |7d8ae64| 
|  DESCRIPTION |  5 +++--
|  NEWS        | 17 ++++++++++++++++-
|  2 files changed, 19 insertions(+), 3 deletions(-)

* 2013-08-13(Tal Galili) tanglegram - labels are now alligned to the leaves tips in the right dendrogram. |e153fd2| 
|  R/tanglegram.r               | 384 +++++++++++++++++++++++++++++++++++------
|  man/cutree-methods.Rd        |  10 +-
|  man/plot_horiz.dendrogram.Rd |  53 ++++--
|  man/tanglegram.Rd            |  27 ++-
|  4 files changed, 406 insertions(+), 68 deletions(-)

* 2013-08-13(Tal Galili) Set sort_cluster_numbers = TRUE for cutree, in order to make it compatible with stats:::cutree |e7a0dcb| 
|  NEWS                                |  3 +-
|  R/cutree.dendrogram.r               | 60 +++++++++++++++++++++++++++++++----
|  inst/tests/test-cutree.dendrogram.r | 13 ++++++--
|  3 files changed, 66 insertions(+), 10 deletions(-)

* 2013-08-13(Tal Galili) Fix untangle_step_rotate_1side to work with non-missing dend_heights_per_k |3ed6210| 
|  NEWS         | 8 ++++++++
|  R/untangle.r | 8 +++-----
|  2 files changed, 11 insertions(+), 5 deletions(-)

* 2013-08-13(Tal Galili) Fix some names in untangle_step_rotate_2side test |889c0e8| 
|  inst/tests/test-untangle.r | 9 ++++++---
|  1 file changed, 6 insertions(+), 3 deletions(-)

* 2013-08-13(Tal Galili) Make a quicker test for untangle_step_rotate_2side |0d4b138| 
|  inst/tests/test-untangle.r | 69 ++++++++++++++++++++++++++++----------------
|  1 file changed, 44 insertions(+), 25 deletions(-)

* 2013-08-12(Tal Galili) Set print_times=FALSE for tests. |b36c95d| 
|  inst/tests/test-untangle.r | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2013-08-12(Tal Galili) Version bump to 0.7.1 |3109111| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 2 ++
|  2 files changed, 4 insertions(+), 2 deletions(-)

* 2013-08-12(Tal Galili) Vignettes - untangle_step_rotate_2side |1026419| 
|  vignettes/cache/__packages                        |    1 +
|  ...hunk-34_4cad004366f0784e24de81f2f1e1a5b1.RData |  Bin 0 -> 3372 bytes
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|  vignettes/dendextend-tutorial-concordance.tex     |    7 +-
|  vignettes/dendextend-tutorial.log                 |  673 ++-
|  vignettes/dendextend-tutorial.pdf                 | 5274 ++++++++++++-------
|  vignettes/dendextend-tutorial.rnw                 |   65 +-
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 133707 -> 153579 bytes
|  vignettes/dendextend-tutorial.tex                 |  357 +-
|  vignettes/figure/unnamed-chunk-34.pdf             |  Bin 0 -> 6773 bytes
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|  39 files changed, 4214 insertions(+), 2163 deletions(-)

* 2013-08-12(Tal Galili) untangle_step_rotate_2side - added tests |af6c7bf| 
|  inst/tests/test-untangle.r | 35 ++++++++++++++++++++++++++++++++++-
|  1 file changed, 34 insertions(+), 1 deletion(-)

* 2013-08-12(Tal Galili) Moving old code done (maybe I will document it in the future, and maybe not...) |08ba75f| 
|  R/untangle.r | 169 +++++++++++++++++++++++++++++++--------------------------
|  1 file changed, 92 insertions(+), 77 deletions(-)

* 2013-08-12(Tal Galili) untangle_step_rotate_2side function added. |07e1fb0| 
|  NAMESPACE                         |   1 +
|  NEWS                              |   9 +++
|  R/untangle.r                      | 123 ++++++++++++++++++++++++++++++------
|  man/untangle_step_rotate_1side.Rd |   7 +-
|  man/untangle_step_rotate_2side.Rd |  85 +++++++++++++++++++++++++
|  5 files changed, 203 insertions(+), 22 deletions(-)

* 2013-08-12(Tal Galili) Version bump to 0.7 |ddd2552| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 3 +++
|  2 files changed, 5 insertions(+), 2 deletions(-)

* 2013-08-12(Tal Galili) Vignettes doc for untangaling trees. |e208ba3| 
|  vignettes/dendextend-tutorial.rnw | 103 ++++++++++++++++++++++++++++++++++++
|  1 file changed, 103 insertions(+)

* 2013-08-12(Tal Galili) Added k_seq and dend_heights_per_k to untangle_step_rotate_1side. |581245c| 
|  R/untangle.r                      | 26 ++++++++++++++++++--------
|  man/untangle_step_rotate_1side.Rd | 13 +++++++++++--
|  2 files changed, 29 insertions(+), 10 deletions(-)

* 2013-08-12(Tal Galili) Rename: untangle_forward_rotate_1side -> untangle_step_rotate_1side |43178f5| 
|  NAMESPACE                                         |  2 +-
|  R/untangle.r                                      | 68 ++++++++++-----------
|  inst/tests/test-untangle.r                        |  7 ++-
|  ...ate_1side.Rd => untangle_step_rotate_1side.Rd} | 16 +++--
|  4 files changed, 49 insertions(+), 44 deletions(-)

* 2013-08-11(Tal Galili) untangle_forward_rotate_1side function added! |f721906| 
|  NAMESPACE                            |  1 +
|  NEWS                                 |  1 +
|  R/untangle.r                         | 84 +++++++++++++++++++++++++---------
|  inst/tests/test-untangle.r           | 18 ++++++++
|  man/all_couple_rotations_at_k.Rd     |  2 +-
|  man/untangle_forward_rotate_1side.Rd | 59 ++++++++++++++++++++++++
|  6 files changed, 142 insertions(+), 23 deletions(-)

* 2013-08-11(Tal Galili) There is some problem with match_order_dendrogram_by_old_order - might need to revisit this in the future... |88175b6| 
|  R/entanglement.r               |  2 ++
|  inst/tests/test-entanglement.r | 31 ++++++++++++++++++++++++++++---
|  2 files changed, 30 insertions(+), 3 deletions(-)

* 2013-08-11(Tal Galili) Added shuffle to the namespace. |a85ad68| 
|  NAMESPACE                        |  3 ++
|  R/untangle.r                     | 66 ++++++++++++++++----------------------
|  man/all_couple_rotations_at_k.Rd |  8 +++++
|  man/shuffle.Rd                   |  6 ++++
|  4 files changed, 45 insertions(+), 38 deletions(-)

* 2013-08-11(Tal Galili) all_couple_rotations_at_k function added. |6acc7e7| 
|  NAMESPACE                        |   1 +
|  NEWS                             |   1 +
|  R/untangle.r                     | 105 +++++++++++++++++++++----------------
|  inst/tests/test-attr_access.r    |   2 +-
|  inst/tests/test-untangle.r       |  13 ++++-
|  man/all_couple_rotations_at_k.Rd |  47 +++++++++++++++++
|  6 files changed, 123 insertions(+), 46 deletions(-)

* 2013-08-11(Tal Galili) scaler -> scalar |01b489e| 
|  R/attr_access.r        | 4 ++--
|  man/get_leaves_attr.Rd | 2 +-
|  man/get_nodes_attr.Rd  | 2 +-
|  3 files changed, 4 insertions(+), 4 deletions(-)

* 2013-08-11(Tal Galili) donotrun  -> dontrun |2b65ab3| 
|  R/cutree.dendrogram.r           | 2 +-
|  man/heights_per_k.dendrogram.Rd | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2013-08-11(Tal Galili) flip_leaves function added |3d9fda5| 
|  NAMESPACE                  |   1 +
|  NEWS                       |   1 +
|  R/untangle.r               | 111 ++++++++++++++++++++++++-------------------
|  inst/tests/test-untangle.r |  19 ++++++--
|  man/flip_leaves.Rd         |  42 ++++++++++++++++
|  5 files changed, 121 insertions(+), 53 deletions(-)

* 2013-08-11(Tal Galili) move some code down the file. |7e840b5| 
|  R/untangle.r | 126 ++++++++++++++++++++++++++++++---------------------------
|  1 file changed, 66 insertions(+), 60 deletions(-)

* 2013-08-11(Tal Galili) untangle_random_search function added - random search for two trees with low entanglement. |4fe24f9| 
|  NAMESPACE                     |   1 +
|  NEWS                          |   2 +-
|  R/untangle.r                  |  92 +++++++++++++++++++++++----
|  man/shuffle.Rd                | 137 +++++++---------------------------------
|  man/untangle_random_search.Rd |  84 ++++++++++++++++++++++++
|  5 files changed, 190 insertions(+), 126 deletions(-)

* 2013-08-11(Tal Galili) shuffle function added. |79ec35e| 
|  NAMESPACE                      |   1 +
|  NEWS                           |   4 ++
|  R/untangle.r                   |  71 +++++++++++++++-----
|  inst/tests/test-entanglement.r |   2 +-
|  inst/tests/test-untangle.r     |  23 +++++++
|  man/shuffle.Rd                 | 137 +++++++++++++++++++++++++++++++++++++++
|  6 files changed, 222 insertions(+), 16 deletions(-)

* 2013-08-11(Tal Galili) rotate - minor code and doc improvements. |270ae47| 
|  NAMESPACE     |  1 -
|  NEWS          |  8 ++++++++
|  R/rotate.r    | 18 ++++++++++--------
|  man/rotate.Rd |  6 ++++--
|  4 files changed, 22 insertions(+), 11 deletions(-)

* 2013-08-11(Tal Galili) Bump version to 0.6 |b483d57| 
|  DESCRIPTION | 2 +-
|  NEWS        | 7 ++++++-
|  2 files changed, 7 insertions(+), 2 deletions(-)

* 2013-08-11(Tal Galili) Vignettes - added tanglegram and entanglement. |4e258d0| 
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|  176 files changed, 3207 insertions(+), 2367 deletions(-)

* 2013-08-11(Tal Galili) entanglement - added .Rd example |1cf03a8| 
|  R/entanglement.r    |  3 ++-
|  man/entanglement.Rd | 43 +++++++++++++++++++++++++++++++++++++++----
|  2 files changed, 41 insertions(+), 5 deletions(-)

* 2013-08-11(Tal Galili) tanglegram  - added a "main" parameter. |af21484| 
|  R/tanglegram.r    | 4 +++-
|  man/tanglegram.Rd | 2 ++
|  2 files changed, 5 insertions(+), 1 deletion(-)

* 2013-08-10(Tal Galili) entanglement function added! |df51acb| 
|  DESCRIPTION                    |   1 -
|  NAMESPACE                      |   4 +
|  NEWS                           |   1 +
|  R/entanglement.r               | 238 +++++++++++++++++++++++++++++----------
|  R/nleaves.r                    |   6 +-
|  inst/tests/test-entanglement.r |  44 ++++++++
|  man/entanglement.Rd            |  83 ++++++++++++++
|  man/nleaves.Rd                 |   2 +-
|  8 files changed, 313 insertions(+), 66 deletions(-)

* 2013-08-10(Tal Galili) moved code from entanglement.r. -> to -> untangle.r |a10f2bd| 
|  DESCRIPTION      |   1 +
|  R/entanglement.r | 760 ----------------------------------------------------
|  R/untangle.r     | 772 +++++++++++++++++++++++++++++++++++++++++++++++++++++
|  3 files changed, 773 insertions(+), 760 deletions(-)

* 2013-08-10(Tal Galili) Rename: 'untangle.r' -> 'entanglement.r' |83e7293| 
|  DESCRIPTION                                         | 3 ++-
|  R/{untangle.r => entanglement.r}                    | 2 --
|  inst/tests/{test-untangle.r => test-entanglement.r} | 0
|  3 files changed, 2 insertions(+), 3 deletions(-)

* 2013-08-10(Tal Galili) match_order_dendrogram_by_old_order function added. |3a1c4e2| 
|  NAMESPACE                                  |   1 +
|  NEWS                                       |   1 +
|  R/tanglegram.r                             |   4 +
|  R/untangle.r                               | 158 +++++++++++++++++----------
|  inst/tests/test-untangle.r                 |  34 ++++++
|  man/match_order_by_labels.Rd               |   6 +-
|  man/match_order_dendrogram_by_old_order.Rd |  76 +++++++++++++
|  7 files changed, 219 insertions(+), 61 deletions(-)

* 2013-08-10(Tal Galili) nleaves - now allow the use of the "members" attr of a dendrogram for telling us the size of the tree. |52e15fe| 
|  NEWS                      |  1 +
|  R/nleaves.r               | 42 ++++++++++++++++++++++++++++++++----------
|  inst/tests/test-nleaves.r |  6 ++++++
|  man/nleaves.Rd            | 10 +++++++++-
|  4 files changed, 48 insertions(+), 11 deletions(-)

* 2013-08-10(Tal Galili) length(order.dendrogram(object)) -> nleaves(object) |9c65dd8| 
|  R/untangle.r | 6 +++---
|  1 file changed, 3 insertions(+), 3 deletions(-)

* 2013-08-10(Tal Galili) abels_order_labels -> labels |d8932be| 
|  R/untangle.r               | 15 +++++++--------
|  inst/tests/test-untangle.r |  3 +++
|  2 files changed, 10 insertions(+), 8 deletions(-)

* 2013-08-10(Tal Galili) match_order_by_labels function added. |c11b0ee| 
|  NAMESPACE                    |   1 +
|  NEWS                         |   2 +
|  R/untangle.r                 | 243 +++++++++++++++++++++++------------------
|  inst/tests/test-untangle.r   |  34 ++++--
|  man/match_order_by_labels.Rd |  51 +++++++++
|  5 files changed, 215 insertions(+), 116 deletions(-)

* 2013-08-10(Tal Galili) dendo -> dend |4080be6| 
|  R/untangle.r | 625 +++++++++++++++++++++++++++++----------------------------
|  1 file changed, 322 insertions(+), 303 deletions(-)

* 2013-08-10(Tal Galili) leaves.values -> order.dendrogram |38073ca| 
|  R/untangle.r | 80 ++++++++++++++++++++++++++++++----------------------------
|  1 file changed, 42 insertions(+), 38 deletions(-)

* 2013-08-10(Tal Galili) Old code added (it now requires modifications) |022419b| 
|  R/untangle.r | 955 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 955 insertions(+)

* 2013-08-10(Tal Galili) untangle.r file added |1f6319a| 
|  DESCRIPTION                |  1 +
|  NEWS                       |  3 +++
|  R/untangle.r               | 28 ++++++++++++++++++++++++++++
|  inst/tests/test-rotate.r   |  2 +-
|  inst/tests/test-untangle.r | 17 +++++++++++++++++
|  5 files changed, 50 insertions(+), 1 deletion(-)

* 2013-08-10(Tal Galili) vignettes - added an example of the tanglegram. |13b84b9| 
|  vignettes/dendextend-tutorial.rnw | 27 +++++++++++++++++++++++++++
|  1 file changed, 27 insertions(+)

* 2013-08-10(Tal Galili) tanglegram function officially added! |48ea0d0| 
|  NAMESPACE         |   9 +-
|  NEWS              |   1 +
|  R/tanglegram.r    | 312 +++++++++++++++++++++++++++-------------------------
|  man/tanglegram.Rd | 152 +++++++++++++++++++++++++
|  4 files changed, 324 insertions(+), 150 deletions(-)

* 2013-08-10(Tal Galili) nleaves - changed some export rules. |90c8b95| 
|  R/nleaves.r | 3 +--
|  1 file changed, 1 insertion(+), 2 deletions(-)

* 2013-08-10(Tal Galili) fix tests for the automatic addition of pch=NA. |da98bde| 
|  inst/tests/test-attr_access.r | 7 ++++---
|  1 file changed, 4 insertions(+), 3 deletions(-)

* 2013-08-10(Tal Galili) Makes sure pch==NA if we are modifying a nodePar value which is other than pch (and pch did not exist before) - in assign_values_to_leaves_nodePar |307f0b0| 
|  NEWS                                   |  3 +++
|  R/attr_access.r                        | 18 +++++++++++++++++-
|  man/assign_values_to_leaves_nodePar.Rd |  4 ++++
|  3 files changed, 24 insertions(+), 1 deletion(-)

* 2013-08-10(Tal Galili) assign_values_to_branches_edgePar function added |d11873b| 
|  NEWS                                     |  2 +
|  R/attr_access.r                          | 80 ++++++++++++++++++++++++++++++
|  man/assign_values_to_branches_edgePar.Rd | 43 ++++++++++++++++
|  man/remove_branches_edgePar.Rd           | 35 +++++++++++++
|  4 files changed, 160 insertions(+)

* 2013-08-10(Tal Galili) remove_leaves_nodePar function added. |d15f8d6| 
|  NEWS                          |  2 +-
|  R/attr_access.r               | 48 +++++++++++++++++++++++++++++++++++++++++
|  inst/tests/test-attr_access.r | 15 +++++++++++++
|  man/get_leaves_attr.Rd        |  2 ++
|  man/remove_leaves_nodePar.Rd  | 40 ++++++++++++++++++++++++++++++++++
|  5 files changed, 106 insertions(+), 1 deletion(-)

* 2013-08-10(Tal Galili) plot_horiz.dendrogram function added |0badd90| 
|  DESCRIPTION                  |   4 +-
|  NAMESPACE                    |   1 +
|  NEWS                         |   6 +
|  R/tanglegram.r               | 321 +++++++++++++++++++++++++++++++++++++----
|  man/plot_horiz.dendrogram.Rd |  84 +++++++++++
|  5 files changed, 389 insertions(+), 27 deletions(-)

* 2013-08-10(Tal Galili) fix donotrun ->dontrun |8ad570c| 
|  R/attr_access.r                        | 4 ++--
|  man/assign_values_to_leaves_nodePar.Rd | 2 +-
|  man/get_nodes_attr.Rd                  | 2 +-
|  3 files changed, 4 insertions(+), 4 deletions(-)

* 2013-08-05(Tal Galili) intersect_trees - added the "warn" parameter. |fed9f78| 
|  NEWS                   |  1 +
|  R/trim.r               | 16 +++++++++++-----
|  man/intersect_trees.Rd |  5 ++++-
|  3 files changed, 16 insertions(+), 6 deletions(-)

* 2013-08-05(Tal Galili) Changed "dend1" -> "tree1", and added methods for hclust/phylo (by simply turning them into dendrograms) |055fad9| 
|  R/tanglegram.r | 42 ++++++++++++++++++++++++------------------
|  1 file changed, 24 insertions(+), 18 deletions(-)

* 2013-08-05(Tal Galili) fac2num - updated doc |980e0c5| 
|  R/rotate.r     | 24 ++++++++++++++++++++++++
|  man/fac2num.Rd |  9 ++++++---
|  man/rotate.Rd  |  8 ++++++++
|  3 files changed, 38 insertions(+), 3 deletions(-)

* 2013-08-05(Tal Galili) tanglegram- remove un-needed comments |11ffb1f| 
|  R/tanglegram.r | 69 +++++++++++---------------------------------------------
|  1 file changed, 13 insertions(+), 56 deletions(-)

* 2013-08-05(Tal Galili) tanglegram - more parameters. Made it so that the labels will be handled by plot.dendrogram (instead of by me) |4edbc4d| 
|  R/tanglegram.r | 107 +++++++++++++++++++++++++++++++++++--------------------
|  1 file changed, 69 insertions(+), 38 deletions(-)

* 2013-08-05(Tal Galili) tanglegram file/function added! |61b7f11| 
|  DESCRIPTION    |   1 +
|  NEWS           |   2 +
|  R/tanglegram.r | 162 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  3 files changed, 165 insertions(+)

* 2013-08-05(Tal Galili) order.dendrogram - added tests and made the function a bit more optimized. |3468f62| 
|  R/labels.r                      | 22 +++++++++++++++-------
|  inst/tests/test-labels-assign.r | 25 +++++++++++++++++++++++++
|  2 files changed, 40 insertions(+), 7 deletions(-)

* 2013-08-05(Tal Galili) fac2num - added tests and a keep_names parameter |cdde4d4| 
|  NEWS                                |  4 ++++
|  R/cutree.dendrogram.r               |  8 +++++---
|  inst/tests/test-cutree.dendrogram.r | 13 ++++++++++++-
|  3 files changed, 21 insertions(+), 4 deletions(-)

* 2013-08-05(Tal Galili) rotate - fixes calling the same functions more than once (minor improvements) |28e6de1| 
|  NEWS                     |  9 +++++++++
|  R/labels.r               |  4 ++--
|  R/rotate.r               | 19 +++++++++++++------
|  inst/tests/test-rotate.r |  3 +++
|  4 files changed, 27 insertions(+), 8 deletions(-)

* 2013-08-04(Tal Galili) Change title |b9a64d9| 
|  vignettes/dendextend-tutorial.rnw | 6 +++---
|  1 file changed, 3 insertions(+), 3 deletions(-)

* 2013-08-02(Tal Galili) bump date, and added a link to where I'll publish posts about the package. |f7e66bc| 
|  DESCRIPTION | 5 +++--
|  1 file changed, 3 insertions(+), 2 deletions(-)

* 2013-08-02(Tal Galili) Vignettes - added Coloring branches example! |89e6431| 
|  NEWS                                              |    5 +-
|  man/leaf_Colors.Rd                                |   35 +
|  vignettes/cache/__packages                        |    1 +
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|  vignettes/dendextend-tutorial-concordance.tex     |   12 +-
|  vignettes/dendextend-tutorial.log                 |  463 +--
|  vignettes/dendextend-tutorial.pdf                 | 3359 +++++++++++--------
|  vignettes/dendextend-tutorial.rnw                 |  105 +-
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|  126 files changed, 2543 insertions(+), 1715 deletions(-)

* 2013-08-02(Tal Galili) Added an example to color_branches |b34b15b| 
|  R/color_branches.r            | 39 ++++++++++++++++++++++++++++++++++++---
|  inst/tests/test-attr_access.r | 25 +++++++++++++++++++++++++
|  man/color_branches.Rd         | 38 +++++++++++++++++++++++++++++++++++---
|  3 files changed, 96 insertions(+), 6 deletions(-)

* 2013-08-02(Tal Galili) "labels_colors<-" - fix the classes of the tree's branches. |7e97f68| 
|  R/labels_colors.r | 11 +++++++++--
|  1 file changed, 9 insertions(+), 2 deletions(-)

* 2013-08-02(Tal Galili) Function added: assign_values_to_leaves_nodePar - allows for complex manipulation of dendrogram's leaves parameters. |b9c5d91| 
|  NAMESPACE                              |  1 +
|  NEWS                                   |  4 +-
|  R/attr_access.r                        | 88 ++++++++++++++++++++++++++++++--
|  man/assign_values_to_leaves_nodePar.Rd | 55 ++++++++++++++++++++
|  man/get_leaves_attr.Rd                 | 14 +++--
|  5 files changed, 154 insertions(+), 8 deletions(-)

* 2013-08-02(Tal Galili) test to show that labels with integer values are VERY possible. |94f1aa7| 
|  inst/tests/test-labels-assign.r | 10 ++++++++++
|  1 file changed, 10 insertions(+)

* 2013-08-02(Tal Galili) test-unroot.r -> test-unbranch.r |cefa337| 
|  inst/tests/{test-unroot.r => test-unbranch.r} | 0
|  1 file changed, 0 insertions(+), 0 deletions(-)

* 2013-08-02(Tal Galili) as.phylo.dendrogram function added |ff0b4bc| 
|  NAMESPACE   | 1 +
|  NEWS        | 3 ++-
|  R/nleaves.r | 4 +++-
|  3 files changed, 6 insertions(+), 2 deletions(-)

* 2013-08-02(Tal Galili) Renaming the file: unroot.r -> unbranch.r |d467113| 
|  DESCRIPTION                |  2 +-
|  R/{unroot.r => unbranch.r} | 10 +++++++++-
|  2 files changed, 10 insertions(+), 2 deletions(-)

* 2013-08-02(Tal Galili) unroot -> unbranch: modify .Rd files |a05d617| 
|  NAMESPACE                       | 10 ++++----
|  NEWS                            |  2 +-
|  man/color_branches.Rd           |  2 +-
|  man/cutree-methods.Rd           | 22 ++++++++---------
|  man/heights_per_k.dendrogram.Rd |  6 ++---
|  man/unbranch.Rd                 | 50 +++++++++++++++++++++++++++++++++++++++
|  6 files changed, 71 insertions(+), 21 deletions(-)

* 2013-08-02(Tal Galili) Renaming the unroot function -> to -> unbranch |938a300| 
|  R/color_branches.r                  |  2 +-
|  R/cutree.dendrogram.r               | 28 ++++++++++----------
|  R/unroot.r                          | 50 +++++++++++++++++------------------
|  R/zzz.r                             |  2 +-
|  inst/tests/test-attr_access.r       | 16 +++++------
|  inst/tests/test-cutree.dendrogram.r | 46 ++++++++++++++++----------------
|  inst/tests/test-trim.r              | 22 +++++++--------
|  inst/tests/test-unroot.r            | 20 +++++++-------
|  8 files changed, 93 insertions(+), 93 deletions(-)

* 2013-08-02(Tal Galili) cutree.dendogram - Prevent R from crashing when using cutree on a subset tree (e.g: dend[[1]]) |1cd0014| 
|  NEWS                                |  5 ++
|  R/cutree.dendrogram.r               | 36 ++++++++++++-
|  inst/tests/test-cutree.dendrogram.r | 96 ++++++++++++++++++++++++-----------
|  man/cutree-methods.Rd               |  2 +-
|  4 files changed, 106 insertions(+), 33 deletions(-)

* 2013-08-02(Tal Galili) "order.dendrogram<-" - now returns an integer (instead of numeric) |cc0d038| 
|  R/labels.r                      | 33 +++++++++++++++++++++++++++++++--
|  inst/tests/test-labels-assign.r | 22 ++++++++++++++++++++++
|  man/order.dendrogram-assign.Rd  | 13 +++++++++++++
|  3 files changed, 66 insertions(+), 2 deletions(-)

* 2013-08-02(Tal Galili) making sure labels.hclust is exported! |af9751e| 
|  NAMESPACE  |  5 +++++
|  R/labels.r | 12 ++++++------
|  2 files changed, 11 insertions(+), 6 deletions(-)

* 2013-08-02(Tal Galili) Fixed a bug in color_branches when the tree's labels are integers! |32e2a42| 
|  NEWS                                |  4 +--
|  R/color_branches.r                  | 51 ++++++++++++++++++++++++++++++++---
|  inst/tests/test-cutree.dendrogram.r | 41 ++++++++++++++++++++++++++++
|  man/color_branches.Rd               | 46 ++++++++++++++++++++++++++++++-
|  4 files changed, 136 insertions(+), 6 deletions(-)

* 2013-08-02(Tal Galili) Extend color_branches to allow REPEATED cluster color assignments to branches on to the same tree. Something which the original function was not able to handle. |479ca6f| 
|  NEWS                  |  4 ++--
|  R/color_branches.r    | 53 ++++++++++++++++++++++++++++++++++++++++---------
|  man/color_branches.Rd | 24 +++++++++++++++++++++-
|  man/color_labels.Rd   |  3 +++
|  4 files changed, 72 insertions(+), 12 deletions(-)

* 2013-08-01(Tal Galili) "labels_colors<-" - fixed it so that by default it would not add phc=1 to the leaves. |7d8d9d0| 
|  NEWS              |  2 +-
|  R/labels_colors.r | 20 +++++++++++++++++++-
|  2 files changed, 20 insertions(+), 2 deletions(-)

* 2013-08-01(Tal Galili) color_labels function added. |c17a1d1| 
|  NAMESPACE             |   1 +
|  NEWS                  |   2 +
|  R/color_branches.r    | 111 +++++++++++++++++++++++++++++++++++++++++++++---
|  man/color_branches.Rd |   5 ++-
|  man/color_labels.Rd   |  70 ++++++++++++++++++++++++++++++
|  5 files changed, 182 insertions(+), 7 deletions(-)

* 2013-08-01(Tal Galili) Fix cutree.dendrogram for the case of using hclust - so it will respect sort_cluster_numbers! |f4bd3ce| 
|  R/cutree.dendrogram.r | 4 +++-
|  1 file changed, 3 insertions(+), 1 deletion(-)

* 2013-08-01(Tal Galili) fix missed \code{ and added "..." |21b2009| 
|  man/color_branches.Rd | 8 +++++---
|  1 file changed, 5 insertions(+), 3 deletions(-)

* 2013-08-01(Tal Galili) Another test for intersect_trees |c5b15e4| 
|  inst/tests/test-trim.r | 13 +++++++++++++
|  1 file changed, 13 insertions(+)

* 2013-08-01(Tal Galili) color_branches function added. |243a91b| 
|  NAMESPACE             |   4 ++
|  NEWS                  |   1 +
|  R/color_branches.r    | 125 ++++++++++++++++++++++++++++++++----------------
|  man/color_branches.Rd |  77 +++++++++++++++++++++++++++++
|  4 files changed, 167 insertions(+), 40 deletions(-)

* 2013-08-01(Tal Galili) Fixed typo |af1128d| 
|  R/labels_colors.r | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2013-08-01(Tal Galili) Updated the is.X functions docs |606044e| 
|  NEWS                 | 10 +++++++++-
|  man/is.dendrogram.Rd |  6 ++++++
|  man/is.hclust.Rd     |  6 ++++++
|  man/is.phylo.Rd      |  6 ++++++
|  4 files changed, 27 insertions(+), 1 deletion(-)

* 2013-08-01(Tal Galili) sort_levels_values function added. |d591a2d| 
|  R/cutree.dendrogram.r               | 126 ++++++++++++++++++++++++++++++++++
|  inst/tests/test-cutree.dendrogram.r |  96 ++++++++++++++++++++++++++
|  man/cutree-methods.Rd               |  20 +++++-
|  man/fac2num.Rd                      |  31 +++++++++
|  man/sort_levels_values.Rd           |  67 ++++++++++++++++++
|  5 files changed, 337 insertions(+), 3 deletions(-)

* 2013-08-01(Tal Galili) color_branches.r file added - it includes the original "colour_clusters" and "leaf_colours" from the {dendroextras} package. |a0d3281| 
|  DESCRIPTION        |   1 +
|  R/color_branches.r | 133 +++++++++++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 134 insertions(+)

* 2013-08-01(Tal Galili) Fix license reference (now pointing to http://www.r-project.org/Licenses/) |5330e51| 
|  DESCRIPTION            |  2 +-
|  R/attr_access.r        | 20 +++++++++++++++++---
|  R/cutree.dendrogram.r  | 19 +++++++++++++++++++
|  R/dendextend-package.r |  5 +++--
|  R/dendextend.r         |  5 +++--
|  R/labels.r             |  5 +++--
|  R/labels_colors.r      |  5 +++--
|  R/nleaves.r            |  5 +++--
|  R/rotate.r             |  5 +++--
|  R/trim.r               |  5 +++--
|  R/unroot.r             |  5 +++--
|  R/zzz.r                |  5 +++--
|  12 files changed, 64 insertions(+), 22 deletions(-)

* 2013-07-31(Tal Galili) vignettes - adding examples for cutree.dendrogram and hang.dendrogram. |1d9844d| 
|  vignettes/cache/__packages                        |    8 +-
|  ...hunk-30_cc171774502992645f046bd982a86244.RData |  Bin 0 -> 4206 bytes
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|  ...-chunk-31_79bbada7960ab7612f76987dabda2a1b.rdx |  Bin 0 -> 156 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    4 +-
|  vignettes/dendextend-tutorial.log                 |  265 ++-
|  vignettes/dendextend-tutorial.pdf                 | 2322 ++++++++++---------
|  vignettes/dendextend-tutorial.rnw                 |   85 +
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 92717 -> 110745 bytes
|  vignettes/dendextend-tutorial.tex                 |  234 +-
|  vignettes/figure/unnamed-chunk-19.pdf             |  Bin 4578 -> 4578 bytes
|  vignettes/figure/unnamed-chunk-23.pdf             |  Bin 4921 -> 4921 bytes
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|  vignettes/figure/unnamed-chunk-30.pdf             |  Bin 0 -> 6361 bytes
|  vignettes/figure/unnamed-chunk-4.pdf              |  Bin 4198 -> 4198 bytes
|  23 files changed, 1769 insertions(+), 1149 deletions(-)

* 2013-07-31(Tal Galili) cutree.dendrogram function added. With many docs and tests! |715711a| 
|  NAMESPACE                           |   6 +
|  NEWS                                |   8 +
|  R/cutree.dendrogram.r               | 305 +++++++++++++++++++++++++++++-----
|  inst/tests/test-attr_access.r       |   2 +-
|  inst/tests/test-cutree.dendrogram.r | 114 ++++++++++++-
|  man/cutree-methods.Rd               | 167 +++++++++++++++++++
|  man/cutree.dendrogram.Rd            | 118 +++++++++++++
|  man/cutree_1h.dendrogram.Rd         |   5 +-
|  man/cutree_1k.dendrogram.Rd         |   6 +-
|  man/is.dendrogram.Rd                |  10 ++
|  man/is.hclust.Rd                    |  10 ++
|  man/is.phylo.Rd                     |  10 ++
|  12 files changed, 714 insertions(+), 47 deletions(-)

* 2013-07-31(Tal Galili) cutree_1k.dendrogram - added tests |e58929f| 
|  R/cutree.dendrogram.r               | 33 +++++++++++++++++++-----
|  inst/tests/test-cutree.dendrogram.r | 48 +++++++++++++++++++++++++++++++++++
|  2 files changed, 75 insertions(+), 6 deletions(-)

* 2013-07-31(Tal Galili) dendrogram_heights_per_k -> dend_heights_per_k |2e971e2| 
|  R/cutree.dendrogram.r               | 36 +++++++++++++++++++----------------
|  inst/tests/test-cutree.dendrogram.r |  9 ++-------
|  man/cutree_1k.dendrogram.Rd         | 28 +++++++++++++++------------
|  3 files changed, 38 insertions(+), 35 deletions(-)

* 2013-07-31(Tal Galili) cutree_1k.dendrogram function added. |7c5fff9| 
|  NAMESPACE                   |   1 +
|  NEWS                        |   4 +-
|  R/cutree.dendrogram.r       | 126 ++++++++++++++++++++++++++++++------------
|  man/cutree_1h.dendrogram.Rd |  21 ++++---
|  man/cutree_1k.dendrogram.Rd |  88 +++++++++++++++++++++++++++++
|  man/is.natural.number.Rd    |   2 +-
|  6 files changed, 197 insertions(+), 45 deletions(-)

* 2013-07-31(Tal Galili) Moving hang.dendrogram from cutree.dendrogram.r to attr_access.r |4dc03d9| 
|  R/attr_access.r                     | 97 +++++++++++++++++++++++++++++++++++
|  R/cutree.dendrogram.r               | 89 --------------------------------
|  inst/tests/test-attr_access.r       | 31 +++++++++++
|  inst/tests/test-cutree.dendrogram.r | 32 ------------
|  4 files changed, 128 insertions(+), 121 deletions(-)

* 2013-07-31(Tal Galili) Make cutree_1h.dendrogram identical to cutree when height is above ALL clusters |0395b13| 
|  R/cutree.dendrogram.r               | 10 ++++++++--
|  inst/tests/test-cutree.dendrogram.r | 12 ++++++------
|  2 files changed, 14 insertions(+), 8 deletions(-)

* 2013-07-31(Tal Galili) Fix a major bug in cutree_1h.dendrogram due to some line getting erased at some point (not clear when that bug was introduced). |981a6a3| 
|  NEWS                                |  2 ++
|  R/cutree.dendrogram.r               | 16 ++++++++++++----
|  inst/tests/test-cutree.dendrogram.r | 30 ++++++++++++++++++++++++++++++
|  man/heights_per_k.dendrogram.Rd     |  7 +++++++
|  4 files changed, 51 insertions(+), 4 deletions(-)

* 2013-07-31(Tal Galili) vignettes - added some attr extraction examples. |6779acf| 
|  vignettes/dendextend-tutorial-concordance.tex |    8 +-
|  vignettes/dendextend-tutorial.log             |  509 +++--
|  vignettes/dendextend-tutorial.pdf             | 2724 ++++++++++++-----------
|  vignettes/dendextend-tutorial.rnw             |   81 +-
|  vignettes/dendextend-tutorial.synctex.gz      |  Bin 82110 -> 92717 bytes
|  vignettes/dendextend-tutorial.tex             |  243 +-
|  vignettes/figure/unnamed-chunk-19.pdf         |  Bin 4578 -> 4578 bytes
|  vignettes/figure/unnamed-chunk-22.pdf         |  Bin 4925 -> 4921 bytes
|  vignettes/figure/unnamed-chunk-23.pdf         |  Bin 4897 -> 4921 bytes
|  vignettes/figure/unnamed-chunk-24.pdf         |  Bin 5132 -> 4576 bytes
|  vignettes/figure/unnamed-chunk-25.pdf         |  Bin 6930 -> 4925 bytes
|  vignettes/figure/unnamed-chunk-26.pdf         |  Bin 6361 -> 4897 bytes
|  vignettes/figure/unnamed-chunk-27.pdf         |  Bin 0 -> 5132 bytes
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|  vignettes/figure/unnamed-chunk-29.pdf         |  Bin 0 -> 6361 bytes
|  vignettes/figure/unnamed-chunk-4.pdf          |  Bin 4198 -> 4198 bytes
|  16 files changed, 2013 insertions(+), 1552 deletions(-)

* 2013-07-31(Tal Galili) test when get_nodes_attr doesn't get an attribute |b333ba4| 
|  inst/tests/test-attr_access.r | 3 +++
|  1 file changed, 3 insertions(+)

* 2013-07-31(Tal Galili) hang.dendrogram - added a test, and source ref for the function |7fa3d0e| 
|  inst/tests/test-cutree.dendrogram.r | 22 +++++++++++++++++++---
|  man/hang.dendrogram.Rd              |  5 +++++
|  2 files changed, 24 insertions(+), 3 deletions(-)

* 2013-07-31(Tal Galili) fix_members_attr.dendrogram function added. |b471984| 
|  NEWS       |  1 +
|  R/labels.r |  1 +
|  R/trim.r   | 56 +++++++++++++++++++++++++++++++++++++++++++++++++++++---
|  3 files changed, 55 insertions(+), 3 deletions(-)

* 2013-07-31(Tal Galili) bumping version to 0.4 (we'll stay here for a while...) |8a55104| 
|  DESCRIPTION | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2013-07-31(Tal Galili) fix .bib (commas were missing) |fb394a7| 
|  vignettes/dendextend-tutorial.bib | 8 ++++----
|  1 file changed, 4 insertions(+), 4 deletions(-)

* 2013-07-31(Tal Galili) get_nodes_attr function added |01613a2| 
|  NAMESPACE                     |   3 +-
|  NEWS                          |   4 +-
|  R/attr_access.r               | 218 +++++++++++++++++++++++++++++++++++++++-
|  R/cutree.dendrogram.r         |  92 +++--------------
|  inst/tests/test-attr_access.r |  78 ++++++++++++++
|  man/get_branches_heights.Rd   |  30 ++++++
|  man/get_leaves_attr.Rd        |  12 ++-
|  man/get_nodes_attr.Rd         |  84 ++++++++++++++++
|  8 files changed, 436 insertions(+), 85 deletions(-)

* 2013-07-31(Tal Galili) nnodes function added - count the number of nodes in a tree |1187719| 
|  NAMESPACE                 |  8 ++++
|  NEWS                      |  6 +++
|  R/nleaves.r               | 89 ++++++++++++++++++++++++++++++++++++++++++++-
|  inst/tests/test-nleaves.r | 16 +++++++-
|  man/nleaves.Rd            |  7 ++++
|  man/nnodes.Rd             | 47 ++++++++++++++++++++++++
|  6 files changed, 170 insertions(+), 3 deletions(-)

* 2013-07-30(Tal Galili) vignettes - expended the abstract a bit. |f8491a5| 
|  vignettes/dendextend-tutorial.bib | 69 +++++++++++++++++++++++++++++++++++++
|  vignettes/dendextend-tutorial.rnw | 13 ++++---
|  2 files changed, 77 insertions(+), 5 deletions(-)

* 2013-07-30(Tal Galili) hang.dendrogram function added, including tests and doc. |82846ea| 
|  NAMESPACE                           |   8 ++
|  NEWS                                |   5 +-
|  R/cutree.dendrogram.r               | 262 +++++++++++++++++++++++++++++-----
|  inst/tests/test-cutree.dendrogram.r |  17 +++
|  man/fix_members_attr.dendrogram.Rd  |  38 +++++
|  man/get_heights.dendrogram.Rd       |  26 ++++
|  man/hang.dendrogram.Rd              |  53 +++++++
|  man/heights_per_k.dendrogram.Rd     |  31 ++++
|  man/rllply.Rd                       |  50 +++++++
|  9 files changed, 452 insertions(+), 38 deletions(-)

* 2013-07-28(Tal Galili) cutree_1h.dendrogram function added (with doc and tests) - like cutree, but only for 1 height |4754ba0| 
|  NAMESPACE                           |   3 +
|  NEWS                                |   6 +-
|  R/cutree.dendrogram.r               | 119 +++++++++++++++++++++++-----------
|  inst/tests/test-cutree.dendrogram.r |  39 +++++++++--
|  man/cutree_1h.dendrogram.Rd         |  63 ++++++++++++++++++
|  man/get_leaves_attr.Rd              |  10 +--
|  man/is.natural.number.Rd            |  40 ++++++++++++
|  7 files changed, 225 insertions(+), 55 deletions(-)

* 2013-07-28(Tal Galili) Changed functions names to be more S3 like. |2d125d0| 
|  R/cutree.dendrogram.r | 99 +++++++++++++++++--------------------------------
|  1 file changed, 33 insertions(+), 66 deletions(-)

* 2013-07-28(Tal Galili) is.natural.number function added (with tests and documentation) |58922db| 
|  NEWS                                |  3 +++
|  R/cutree.dendrogram.r               | 43 ++++++++++++++++++++++++-----------
|  inst/tests/test-cutree.dendrogram.r | 22 ++++++++++++++----
|  3 files changed, 51 insertions(+), 17 deletions(-)

* 2013-07-28(Tal Galili) cutree.dendrogram.r - added first version of the file (with the old functions which will now be revised to newer naming conventions and documentation) |55598e4| 
|  DESCRIPTION                         |   1 +
|  NEWS                                |  12 +-
|  R/attr_access.r                     |  12 +-
|  R/cutree.dendrogram.r               | 265 ++++++++++++++++++++++++++++++++++
|  inst/tests/test-cutree.dendrogram.r |  14 ++
|  vignettes/dendextend-tutorial.rnw   |   2 +-
|  6 files changed, 295 insertions(+), 11 deletions(-)

* 2013-07-27(Tal Galili) Vignettes - updated noisense files. |6793d20| 
|  vignettes/dendextend-tutorial-concordance.tex |   5 +-
|  vignettes/dendextend-tutorial.blg             |   2 +
|  vignettes/dendextend-tutorial.log             | 356 ++++++++++++------------
|  vignettes/dendextend-tutorial.synctex.gz      | Bin 65670 -> 82110 bytes
|  vignettes/dendextend-tutorial.tex             | 102 ++++++-
|  vignettes/figure/unnamed-chunk-19.pdf         | Bin 4578 -> 4578 bytes
|  vignettes/figure/unnamed-chunk-20.pdf         | Bin 4921 -> 4921 bytes
|  vignettes/figure/unnamed-chunk-21.pdf         | Bin 4576 -> 4576 bytes
|  vignettes/figure/unnamed-chunk-22.pdf         | Bin 4925 -> 4925 bytes
|  vignettes/figure/unnamed-chunk-23.pdf         | Bin 4897 -> 4897 bytes
|  vignettes/figure/unnamed-chunk-24.pdf         | Bin 5126 -> 5132 bytes
|  vignettes/figure/unnamed-chunk-25.pdf         | Bin 6930 -> 6930 bytes
|  vignettes/figure/unnamed-chunk-26.pdf         | Bin 0 -> 6361 bytes
|  vignettes/figure/unnamed-chunk-4.pdf          | Bin 4198 -> 4198 bytes
|  14 files changed, 274 insertions(+), 191 deletions(-)

* 2013-07-27(Tal Galili) Various changes to rotate - adding documentation and testing! |74ece8d| 
|  NAMESPACE                         |    3 +-
|  NEWS                              |    7 +-
|  R/rotate.r                        |   52 +-
|  inst/tests/test-rotate.r          |   74 ++
|  man/as_hclust_fixed.Rd            |    3 +-
|  man/get_leaves_attr.Rd            |   42 +
|  man/rotate.Rd                     |   40 +-
|  vignettes/dendextend-tutorial.pdf | 1754 +++++++++++++++++++----------------
|  vignettes/dendextend-tutorial.rnw |   53 +-
|  9 files changed, 1198 insertions(+), 830 deletions(-)

* 2013-07-27(Tal Galili) Some work on attr_access.r (not sure if this would be used later or not...). |5d6414e| 
|  DESCRIPTION     |  1 +
|  R/attr_access.r | 43 +++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 44 insertions(+)

* 2013-07-27(Tal Galili) as_hclust_fixed - now works just as as.hclust when hc is missing. |a613071| 
|  R/dendextend.r | 22 ++++++++++++++--------
|  1 file changed, 14 insertions(+), 8 deletions(-)

* 2013-07-27(Tal Galili) Bump release date for DESCRIPTION (although it will keep moving until a specific stage is released...) |a74140f| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 4 ++--
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2013-07-27(Tal Galili) Move from length(order.dendrogram(x)) to nleaves(x) |1e0501a| 
|  R/labels.r | 8 ++++----
|  1 file changed, 4 insertions(+), 4 deletions(-)

* 2013-07-27(Tal Galili) Vignettes - adding references to other packages. |8b105cd| 
|  vignettes/dendextend-tutorial-concordance.tex |    6 +-
|  vignettes/dendextend-tutorial.bib             |   78 +
|  vignettes/dendextend-tutorial.pdf             | 2740 +++++++++++++----------
|  vignettes/dendextend-tutorial.rnw             |   20 +-
|  vignettes/dendextend.bib                      |  636 ------
|  5 files changed, 1633 insertions(+), 1847 deletions(-)

* 2013-07-27(Tal Galili) Forcing {ape} to load before {dendextend}, thus allowing for both rotate and unroot to work for BOTH packages. It does add extra noise when loading the package, but it is the best solution I can think of at this point. |ae741d8| 
|  R/zzz.r | 22 ++++++++++++++++++++--
|  1 file changed, 20 insertions(+), 2 deletions(-)

* 2013-07-27(Tal Galili) labels_colors - added checks for "dendrogram" class |fb6dad9| 
|  R/labels_colors.r                 |  4 ++++
|  inst/tests/test-labels_colors.r   |  9 +++++++++
|  vignettes/dendextend-tutorial.rnw | 27 +++++++++++++++++++--------
|  3 files changed, 32 insertions(+), 8 deletions(-)

* 2013-07-27(Tal Galili) Fix a wrong variable name. |1c96d06| 
|  inst/tests/test-trim.r | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2013-07-27(Tal Galili) Testing for partial assignment. |197370e| 
|  inst/tests/test-labels-assign.r | 11 +++++++++++
|  1 file changed, 11 insertions(+)

* 2013-07-27(Tal Galili) Adding credit. |634a7a7| 
|  R/labels.r | 6 +++++-
|  1 file changed, 5 insertions(+), 1 deletion(-)

* 2013-07-27(Tal Galili) labels_colors - adding leaves labels as names to the color vector. Giving credit to Gregory Jefferis. |0d61899| 
|  R/labels_colors.r               | 19 ++++++++++----
|  inst/tests/test-labels_colors.r | 53 ++++++++++++++++++++++++++++++++++++---
|  man/labels-assign.Rd            |  2 ++
|  man/labels_colors.Rd            | 16 +++++++++---
|  4 files changed, 78 insertions(+), 12 deletions(-)

* 2013-07-26(Tal Galili) Vignettes PDF - updated |e74fe57| 
|  vignettes/dendextend-tutorial-concordance.tex |    6 +-
|  vignettes/dendextend-tutorial.log             |  607 +++++-
|  vignettes/dendextend-tutorial.pdf             | 2378 ++++++++++++++++-------
|  vignettes/dendextend-tutorial.synctex.gz      |  Bin 44992 -> 65670 bytes
|  vignettes/dendextend-tutorial.tex             |  400 +++-
|  vignettes/dendextend-tutorial.toc             |    0
|  vignettes/figure/unnamed-chunk-19.pdf         |  Bin 4626 -> 4578 bytes
|  vignettes/figure/unnamed-chunk-20.pdf         |  Bin 0 -> 4921 bytes
|  vignettes/figure/unnamed-chunk-21.pdf         |  Bin 0 -> 4576 bytes
|  vignettes/figure/unnamed-chunk-22.pdf         |  Bin 0 -> 4925 bytes
|  vignettes/figure/unnamed-chunk-23.pdf         |  Bin 0 -> 4897 bytes
|  vignettes/figure/unnamed-chunk-24.pdf         |  Bin 0 -> 5126 bytes
|  vignettes/figure/unnamed-chunk-25.pdf         |  Bin 0 -> 6930 bytes
|  vignettes/figure/unnamed-chunk-4.pdf          |  Bin 4198 -> 4198 bytes
|  14 files changed, 2570 insertions(+), 821 deletions(-)

* 2013-07-26(Tal Galili) Updated NEWS/DESCRIPTION (still not done with V0.3) |e389f99| 
|  DESCRIPTION                       |  2 ++
|  NEWS                              | 13 +++++++++----
|  vignettes/dendextend-tutorial.rnw |  6 +++---
|  3 files changed, 14 insertions(+), 7 deletions(-)

* 2013-07-26(Tal Galili) Vignettes - added a section on labels_colors |9a558ea| 
|  vignettes/dendextend-tutorial.rnw | 62 ++++++++++++++++++++++++++++---------
|  1 file changed, 47 insertions(+), 15 deletions(-)

* 2013-07-26(Tal Galili) labels_colors - moved to their own file, Also added new tests. |68eba04| 
|  R/dendextend.r                  |  84 ------------------------------
|  R/labels_colors.r               | 105 ++++++++++++++++++++++++++++++++++++++
|  inst/tests/test-labels_colors.r |  25 +++++++++
|  man/labels_colors.Rd            |   4 ++
|  4 files changed, 134 insertions(+), 84 deletions(-)

* 2013-07-26(Tal Galili) Trimming by labels. |2ea1933| 
|  R/trim.r                          | 10 +++--
|  inst/tests/test-trim.r            | 68 +++++++++++++++++++++++++++++++++
|  vignettes/dendextend-tutorial.rnw | 75 ++++++++++++++++++++++++++++++++++++-
|  3 files changed, 148 insertions(+), 5 deletions(-)

* 2013-07-26(Tal Galili) Vignettes - unroot, raise.dendrogram |d7402e7| 
|  vignettes/dendextend-tutorial.rnw | 89 +++++++++++++++++++++++++++++++++++++
|  1 file changed, 89 insertions(+)

* 2013-07-26(Tal Galili) Fixes and extensions to unroot |9085f8d| 
|  R/unroot.r                  | 117 +++++++++++++++++++++++++-----------------
|  inst/tests/test-unroot.r    |  45 ++++++++++++++++
|  man/count_terminal_nodes.Rd |   8 ++-
|  man/flatten.dendrogram.Rd   |   4 +-
|  man/get_branches_attr.Rd    |   9 +++-
|  man/unclass_dend.Rd         |   4 +-
|  man/unroot.Rd               |   3 +-
|  7 files changed, 134 insertions(+), 56 deletions(-)

* 2013-07-25(Tal Galili) vignettes - spell checked. |7d6cb65| 
|  vignettes/dendextend-tutorial.rnw | 28 ++++++++++++++--------------
|  1 file changed, 14 insertions(+), 14 deletions(-)

* 2013-07-25(Tal Galili) Added tests for tree size :) |f95c928| 
|  DESCRIPTION               |  7 ++++---
|  NEWS                      |  4 +++-
|  inst/tests/test-nleaves.r | 50 +++++++++++++++++++++++++++++++++++++++++++++
|  3 files changed, 57 insertions(+), 4 deletions(-)

* 2013-07-25(Tal Galili) Vignettes - assignment recycling and tree sizes |da05752| 
|  vignettes/cache/__packages                        |   10 +
|  ...hunk-18_d9d3a2e4138d97442a69288b169de349.RData |  Bin 0 -> 3121 bytes
|  ...-chunk-18_d9d3a2e4138d97442a69288b169de349.rdb |    0
|  ...-chunk-18_d9d3a2e4138d97442a69288b169de349.rdx |  Bin 0 -> 113 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    7 +-
|  vignettes/dendextend-tutorial.log                 |  297 +++-
|  vignettes/dendextend-tutorial.pdf                 | 1743 +++++++++++--------
|  vignettes/dendextend-tutorial.rnw                 |  102 +-
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 30645 -> 44992 bytes
|  vignettes/dendextend-tutorial.tex                 |  357 +++-
|  vignettes/figure/unnamed-chunk-19.pdf             |  Bin 0 -> 4626 bytes
|  vignettes/figure/unnamed-chunk-4.pdf              |  Bin 4198 -> 4198 bytes
|  12 files changed, 1582 insertions(+), 934 deletions(-)

* 2013-07-25(Tal Galili) fix labeels-assign.Rd |14a1e5e| 
|  R/labels.r           | 2 +-
|  man/labels-assign.Rd | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2013-07-25(Tal Galili) unclass_dend now uses dendrapply |6e287f4| 
|  R/nleaves.r | 29 ++++++++++++++++++-----------
|  1 file changed, 18 insertions(+), 11 deletions(-)

* 2013-07-25(Tal Galili) Vignettes: a section on dendrapply |cea57f9| 
|  vignettes/dendextend-tutorial-concordance.tex |    6 +-
|  vignettes/dendextend-tutorial.log             |  421 +++---
|  vignettes/dendextend-tutorial.pdf             | 1379 ++++++++++---------
|  vignettes/dendextend-tutorial.rnw             |   59 +-
|  vignettes/dendextend-tutorial.synctex.gz      |  Bin 27918 -> 30645 bytes
|  vignettes/dendextend-tutorial.tex             |  109 +-
|  vignettes/dendextend.bib                      |  636 +++++++++
|  vignettes/figure/unnamed-chunk-4.pdf          |  Bin 4198 -> 4198 bytes
|  vignettes/jss.bst                             | 1631 +++++++++++++++++++++++
|  vignettes/jss.cls                             |  487 +++++++
|  vignettes/jsslogo.jpg                         |  Bin 0 -> 22731 bytes
|  11 files changed, 3907 insertions(+), 821 deletions(-)

* 2013-07-25(Tal Galili) Fix assignment recycling And also class of nodes are no longer "dendrogram" after label assignment |fec015c| 
|  NEWS                            |  1 +
|  R/labels.r                      | 40 ++++++++++++++++++++---
|  inst/tests/test-labels-assign.r | 68 +++++++++++++++++++++++++++++++++------
|  3 files changed, 95 insertions(+), 14 deletions(-)

* 2013-07-25(Tal Galili) Vignettes: switched from markdown to LaTeX (to make it easier to submit to a journal later on) |15d1492| 
|  .Rbuildignore                                 |    8 +-
|  NEWS                                          |    4 +-
|  dendextend.Rproj                              |    2 +-
|  vignettes/dendextend-tutorial-concordance.tex |    4 +
|  vignettes/dendextend-tutorial.Rmd             |  169 ---
|  vignettes/dendextend-tutorial.bib             |  636 +++++++++
|  vignettes/dendextend-tutorial.blg             |    3 +
|  vignettes/dendextend-tutorial.html            |  482 -------
|  vignettes/dendextend-tutorial.log             |  896 +++++++++++++
|  vignettes/dendextend-tutorial.md              |  382 ------
|  vignettes/dendextend-tutorial.pdf             | 1576 +++++++++++++++++++++++
|  vignettes/dendextend-tutorial.rnw             |  400 ++++++
|  vignettes/dendextend-tutorial.synctex.gz      |  Bin 0 -> 27918 bytes
|  vignettes/dendextend-tutorial.tex             |  664 ++++++++++
|  vignettes/figure/unnamed-chunk-11.png         |  Bin 9139 -> 0 bytes
|  vignettes/figure/unnamed-chunk-3.png          |  Bin 2766 -> 0 bytes
|  vignettes/figure/unnamed-chunk-4.pdf          |  Bin 0 -> 4198 bytes
|  vignettes/figure/unnamed-chunk-8.png          |  Bin 9139 -> 0 bytes
|  vignettes/figure/unnamed-chunk-9.png          |  Bin 9139 -> 0 bytes
|  19 files changed, 4189 insertions(+), 1037 deletions(-)

* 2013-07-25(Tal Galili) Added a clear GPL-2 copyright notice on each r file. |aebbbc0| 
|  NEWS                   |  6 ++++--
|  R/dendextend-package.r | 21 +++++++++++++++++++++
|  R/dendextend.r         | 23 +++++++++++++++++++++++
|  R/labels.r             | 26 ++++++++++++++++++++++++++
|  R/nleaves.r            | 24 ++++++++++++++++++++++++
|  R/rotate.r             | 16 ++++++++++++++++
|  R/trim.r               | 24 ++++++++++++++++++++++++
|  R/unroot.r             | 20 ++++++++++++++++++++
|  R/zzz.r                | 18 ++++++++++++++++++
|  9 files changed, 176 insertions(+), 2 deletions(-)

* 2013-07-24(Tal Galili) Updated NEWS and DESCRIPTION |35db6ed| 
|  DESCRIPTION | 17 ++++++++++++-----
|  NEWS        | 31 +++++++++++++++++++++++++++++++
|  2 files changed, 43 insertions(+), 5 deletions(-)

* 2013-07-24(Tal Galili) vingettes - labels assignment for vectors. |5a20227| 
|  inst/tests/test-labels-assign.r    |   2 +-
|  vignettes/dendextend-tutorial.Rmd  |  49 +++++++++++++++--
|  vignettes/dendextend-tutorial.html |  73 ++++++++++++++++++++++++-
|  vignettes/dendextend-tutorial.md   | 100 +++++++++++++++++++++++++++++++++--
|  4 files changed, 215 insertions(+), 9 deletions(-)

* 2013-07-24(Tal Galili) "labels.hclust" and "labels.hclust<-" - now both use order=TRUE as default. this makes them consistent with labels.dendrogram. Proper tests have been implemented. |34151cb| 
|  R/labels.r                      |  4 ++--
|  inst/tests/test-labels-assign.r | 28 ++++++++++++++++++++++++----
|  2 files changed, 26 insertions(+), 6 deletions(-)

* 2013-07-24(Tal Galili) tests - changed names, and added quick way for checking the code while developing the package. |7b1d8f9| 
|  inst/tests/test-labels-assign.r | 2 +-
|  tests/test-all.r                | 2 ++
|  2 files changed, 3 insertions(+), 1 deletion(-)

* 2013-07-24(Tal Galili) vignettes - first part of the introduction written (it is a very rough draft, but readable). |6304231| 
|  .Rbuildignore                         |   4 +-
|  vignettes/dendextend-tutorial.Rmd     | 123 ++++++++-------
|  vignettes/dendextend-tutorial.html    | 223 ++++++++++++++++++++-------
|  vignettes/dendextend-tutorial.md      | 257 +++++++++++++++++++++++++-------
|  vignettes/figure/unnamed-chunk-11.png | Bin 0 -> 9139 bytes
|  vignettes/figure/unnamed-chunk-3.png  | Bin 9139 -> 2766 bytes
|  vignettes/figure/unnamed-chunk-8.png  | Bin 0 -> 9139 bytes
|  vignettes/figure/unnamed-chunk-9.png  | Bin 0 -> 9139 bytes
|  8 files changed, 441 insertions(+), 166 deletions(-)

* 2013-07-24(Tal Galili) Added tests for labels assignment |10e9885| 
|  inst/tests/test-labels-assign.r | 55 +++++++++++++++++++++++++++++++++++++++
|  1 file changed, 55 insertions(+)

* 2013-07-24(Tal Galili) Fixes for CMD CHECK |5ee9655| 
|  R/labels.r                                                  | 7 ++++---
|  demo/00Index                                                | 2 +-
|  man/{labels-set.Rd => labels-assign.Rd}                     | 2 +-
|  man/{order.dendrogram-set.Rd => order.dendrogram-assign.Rd} | 0
|  tests/test-all.r                                            | 2 +-
|  5 files changed, 7 insertions(+), 6 deletions(-)

* 2013-07-24(Tal Galili) New: demo, vignettes (knitr), tests (testthat) - |857e081| 
|  .Rbuildignore                        |   3 +
|  demo/00Index                         |   1 +
|  demo/dendextend.r                    |  23 +++
|  dendextend.Rproj                     |   2 +-
|  tests/test-all.r                     |   4 +
|  vignettes/dendextend-tutorial.Rmd    | 109 ++++++++++++
|  vignettes/dendextend-tutorial.html   | 298 +++++++++++++++++++++++++++++++++
|  vignettes/dendextend-tutorial.md     | 147 ++++++++++++++++
|  vignettes/figure/unnamed-chunk-3.png | Bin 0 -> 9139 bytes
|  9 files changed, 586 insertions(+), 1 deletion(-)

* 2013-07-24(Tal Galili) labels.hclust - added the 'order' parameter |3f515a1| 
|  R/labels.r | 41 ++++++++++++++++++++++++++++++++++++-----
|  1 file changed, 36 insertions(+), 5 deletions(-)

* 2013-07-24(Tal Galili) Updated doc - |b3eed86| 
|  R/dendextend-package.r    |  8 ++++++
|  R/rotate.r                | 65 +++++++++++++++++++++++++++++++++++---------
|  R/unroot.r                |  1 +
|  R/zzz.r                   | 66 +++++++++++++++++++++++++++++++++++++++++++++
|  man/dendextend-package.Rd | 15 +++++++++++
|  man/get_branches_attr.Rd  |  1 +
|  man/intersect_trees.Rd    |  6 ++---
|  man/labels-set.Rd         | 15 +++++++++--
|  man/rotate.Rd             | 25 ++++++++++-------
|  9 files changed, 176 insertions(+), 26 deletions(-)

* 2013-04-10(Tal Galili) intersect_trees function added |988374d| 
|  NAMESPACE              |  1 +
|  NEWS                   |  3 ++-
|  R/trim.r               | 50 +++++++++++++++++++++++++++++++++++++++++++++++-
|  README.md              |  3 ++-
|  man/intersect_trees.Rd | 37 +++++++++++++++++++++++++++++++++++
|  5 files changed, 91 insertions(+), 3 deletions(-)

* 2013-04-06(Tal Galili) order.dendrogram<- function added. |cf1c863| 
|  NAMESPACE                   |  1 +
|  NEWS                        |  1 +
|  R/labels.r                  | 55 +++++++++++++++++++++++++++++++++++++++++++
|  README.md                   |  1 +
|  man/order.dendrogram-set.Rd | 39 ++++++++++++++++++++++++++++++
|  5 files changed, 97 insertions(+)

* 2013-04-06(Tal Galili) Notes on rotate and {ape} masking it. |ca4edad| 
|  NEWS          | 3 ++-
|  R/rotate.r    | 1 +
|  README.md     | 4 ++--
|  man/rotate.Rd | 6 ++++++
|  4 files changed, 11 insertions(+), 3 deletions(-)

* 2013-04-06(Tal Galili) updated README |0549266| 
|  README.md | 23 +++++++----------------
|  1 file changed, 7 insertions(+), 16 deletions(-)

* 2013-04-06(Tal Galili) unroot (S3'd), raise.dendrogram, flatten.dendrogram |a765a29| 
|  DESCRIPTION               |   1 +
|  NAMESPACE                 |   8 ++
|  NEWS                      |   5 +-
|  R/nleaves.r               |   3 -
|  R/rotate.r                |   6 +-
|  R/trim.r                  |   4 +-
|  R/unroot.r                | 194 ++++++++++++++++++++++++++++++++++++++++++++
|  man/flatten.dendrogram.Rd |  36 ++++++++
|  man/get_branches_attr.Rd  |  31 +++++++
|  man/raise.dendrogram.Rd   |  29 +++++++
|  man/rotate.Rd             |   6 +-
|  man/unroot.Rd             |  49 +++++++++++
|  12 files changed, 365 insertions(+), 7 deletions(-)

* 2013-04-06(Tal Galili) as_hclust_fixed function added (and implemented in trim and rotate) |67b220e| 
|  NAMESPACE              |  1 +
|  NEWS                   |  2 ++
|  R/dendextend.r         | 25 ++++++++++++++++++++++++-
|  R/rotate.r             |  7 +------
|  R/trim.r               | 16 +++++++++-------
|  man/as_hclust_fixed.Rd | 34 ++++++++++++++++++++++++++++++++++
|  man/trim.Rd            |  2 +-
|  man/trim_leaf.Rd       |  2 +-
|  8 files changed, 73 insertions(+), 16 deletions(-)

* 2013-04-06(Tal Galili) trim (leaves by labels) function added :) |0fcde8e| 
|  DESCRIPTION      |   1 +
|  NAMESPACE        |   5 ++
|  NEWS             |   1 +
|  R/nleaves.r      |   9 +++-
|  R/trim.r         | 148 +++++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/rotate.Rd    |   9 +++-
|  man/trim.Rd      |  48 +++++++++++++++++
|  man/trim_leaf.Rd |  32 ++++++++++++
|  8 files changed, 250 insertions(+), 3 deletions(-)

* 2013-04-06(Tal Galili) rotate.phylo S3 method (and doc) added. |7228393| 
|  DESCRIPTION   |  2 ++
|  NAMESPACE     |  1 +
|  NEWS          |  2 +-
|  R/rotate.r    | 12 ++++++++++--
|  README.md     |  2 +-
|  man/rotate.Rd | 13 +++++++++++--
|  6 files changed, 26 insertions(+), 6 deletions(-)

* 2013-04-06(Tal Galili) rotate, sort, flip, nleaves functions were added! |84ccfd6| 
|  DESCRIPTION                 |   2 +
|  NAMESPACE                   |  11 ++++
|  NEWS                        |   7 +-
|  R/dendextend.r              | 102 -----------------------------
|  R/nleaves.r                 | 148 ++++++++++++++++++++++++++++++++++++++++++
|  R/rotate.r                  | 113 ++++++++++++++++++++++++++++++++
|  README.md                   |   5 ++
|  man/count_terminal_nodes.Rd |  14 ++--
|  man/nleaves.Rd              |  44 +++++++++++++
|  man/rotate.Rd               |  86 ++++++++++++++++++++++++
|  man/unclass_dend.Rd         |   3 +
|  11 files changed, 426 insertions(+), 109 deletions(-)

* 2013-04-06(Tal Galili) head.dendrogram S3 method to head |fe4dbbb| 
|  DESCRIPTION    |  2 ++
|  NAMESPACE      |  2 ++
|  NEWS           |  1 +
|  R/dendextend.r | 13 +++++++++++++
|  4 files changed, 18 insertions(+)

* 2013-04-06(Tal Galili) unclass_dend function added |b37a26b| 
|  NAMESPACE           |  1 +
|  NEWS                |  1 +
|  R/dendextend.r      | 36 ++++++++++++++++++++++++++++++++++++
|  README.md           |  5 +++--
|  man/unclass_dend.Rd | 29 +++++++++++++++++++++++++++++
|  5 files changed, 70 insertions(+), 2 deletions(-)

* 2013-04-06(Tal Galili) labels_colors function added |718899f| 
|  NAMESPACE                                         |   4 +-
|  NEWS                                              |   5 +-
|  R/dendextend.r                                    | 102 ++++++++++++++++++--
|  ....terminal.nodes.Rd => count_terminal_nodes.Rd} |  12 +--
|  man/labels_colors.Rd                              |  49 ++++++++++
|  5 files changed, 158 insertions(+), 14 deletions(-)

* 2013-04-06(Tal Galili) "labels<-.dendrogram" updated - to allow duplicate labels, and shorter labels than the size of the tree. |f82ed9b| 
|  NEWS              |  2 ++
|  R/dendextend.r    |  2 +-
|  R/labels.r        | 47 +++++++++++++++++++----------------------------
|  man/labels-set.Rd |  4 ++++
|  4 files changed, 26 insertions(+), 29 deletions(-)

* 2013-04-06(Tal Galili) count.terminal.nodes function added |cbcab99| 
|  DESCRIPTION                 |  8 +++----
|  NAMESPACE                   |  1 +
|  NEWS                        |  6 ++++++
|  R/dendextend.r              | 50 +++++++++++++++++++++++++++++++++++++++++--
|  R/labels.r                  | 36 -------------------------------
|  README.md                   |  5 +++--
|  man/count.terminal.nodes.Rd | 48 +++++++++++++++++++++++++++++++++++++++++
|  7 files changed, 110 insertions(+), 44 deletions(-)

* 2013-04-06(Tal Galili) Merged "labels<-" help files |8a55439| 
|  DESCRIPTION          |   2 +-
|  NAMESPACE            |  10 ++--
|  NEWS                 |   3 +-
|  R/labels.r           | 126 +++++++++++++++++++++++++++----------------------
|  man/labels-set.Rd    |  48 ++++++++++++++++---
|  man/labels.matrix.Rd |  47 ------------------
|  6 files changed, 119 insertions(+), 117 deletions(-)

* 2013-04-05(Tal Galili) NEWS and README.md files added |0a117ae| 
|  NAMESPACE  |  8 +++++++-
|  NEWS       | 18 ++++++++++++++++++
|  R/labels.r |  4 ++--
|  README.md  | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  4 files changed, 86 insertions(+), 3 deletions(-)

* 2013-04-05(Tal Galili) labels assignment operators for matrix added |25d9c1c| 
|  DESCRIPTION          |  8 +++--
|  R/dendextend.r       |  3 ++
|  R/labels.r           | 96 +++++++++++++++++++++++++++++++++++++++++++++++++-
|  dendextend.Rproj     |  1 +
|  man/labels-set.Rd    | 57 ++++++++++++++++++++++++++++++
|  man/labels.matrix.Rd | 47 ++++++++++++++++++++++++
|  6 files changed, 209 insertions(+), 3 deletions(-)

* 2013-04-05(Tal Galili) labels.r added |2e4a497| 
|  R/labels.r | 120 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 120 insertions(+)

* 2013-04-05(Tal Galili) minor edit to DESCRIPTION |8479c64| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2013-04-05(Tal Galili) Package shell |05eb3f9  
   .Rbuildignore    |  2 ++
   .gitignore       |  3 +++
   DESCRIPTION      |  9 +++++++++
   NAMESPACE        |  1 +
   R/dendextend.r   |  0
   dendextend.Rproj | 16 ++++++++++++++++
   6 files changed, 31 insertions(+)