Merge pull request #28 from erblast/issue26

Issue26

.Rbuildignore

@@ -19,3 +19,4 @@
 ^tests/figs$
 ^\.github$
 ^README.md$
+^CRAN-SUBMISSION$

.github/workflows/articles.yml

@@ -26,6 +26,9 @@ jobs:
           install.packages(c("remotes", "devtools", "tidyverse", "pkgdown"))
           remotes::install_deps(dependencies = TRUE)
           devtools::install()
+          system("git clone https://github.com/erblast/parcats.git")
+          remotes::install_deps("parcats/", dependencies = TRUE)
+          devtools::install("parcats/")
         shell: Rscript {0}
       - name: Check
         run: |

.github/workflows/pkgdown.yaml

@@ -37,6 +37,9 @@ jobs:
           remotes::install_deps(dependencies = TRUE)
           install.packages("tidyverse")
           install.packages("pkgdown", type = "binary")
+          system("git clone https://github.com/erblast/parcats.git")
+          remotes::install_deps("parcats/", dependencies = TRUE)
+          devtools::install("parcats/")
         shell: Rscript {0}
 
       - name: Install package
@@ -46,4 +49,4 @@ jobs:
         run: |
           git config --local user.email "[email protected]"
           git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, run_dont_run = FALSE)'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: easyalluvial
 Title: Generate Alluvial Plots with a Single Line of Code
-Version: 0.3.0
+Version: 0.3.1
 Authors@R: person( "Bjoern", "Koneswarakantha", role = c("aut","cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-4585-7799") )
 URL: https://github.com/erblast/easyalluvial/
 Description: Alluvial plots are similar to sankey diagrams and visualise categorical data 
@@ -26,7 +26,6 @@ Suggests:
     ISLR,
     nycflights13,
     vdiffr (>= 0.3.1),
-    parcats,
     pkgdown,
     mlbench,
     earth,
@@ -40,7 +39,7 @@ Suggests:
     rpart,
     glmnet,
     xgboost
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.0
 Imports:
   purrr
   , tidyr (>= 1.0.0)

NEWS.md

@@ -1,3 +1,6 @@
+# Version 0.3.1 submitted to CRAN 20220704
+- cleanup package dependencies
+
 # Version 0.3.0 submitted to CRAN 20200111
 - moved modeling packages and vdiffr from imports to suggests
 - added parsnip and workflows wrapper
@@ -33,7 +36,7 @@ Bug Fixes:
 - Compatibility with `recipes 0.1.5`
 - NA values in numerical columns are excepted
 - correct ggplot2 and ggalluvial versions added as dependencies
-- p$data_key does not contain comlumns with empty levels anyomore
+- p$data_key does not contain columns with empty levels anymore
 - better support for numerical variables for alluvial_long()
 
 # Version: 0.1.8, submitted to CRAN 20190115

R/alluvial_long.R

@@ -43,12 +43,11 @@
 #'  ,\code{\link[easyalluvial]{manip_bin_numerics}}
 #' @examples
 #'
-#'
+#' \dontrun{
 #'  data = quarterly_flights
 #'
 #'  alluvial_long( data, key = qu, value = mean_arr_delay, id = tailnum, fill_by = 'last_variable' )
 #'
-#' \dontrun{
 #'  # more flow coloring variants ------------------------------------
 #'
 #'  alluvial_long( data, key = qu, value = mean_arr_delay, id = tailnum, fill_by = 'first_variable' )

R/alluvial_model_response.R

@@ -1,4 +1,4 @@
-
+#' @noRd
 check_degree = function(degree, imp, df){
 
   if( degree > nrow(imp) ){
@@ -11,24 +11,25 @@ check_degree = function(degree, imp, df){
 
 #' @title check if package is installed
 #' @param pkg character, package name
+#' @param raise_error logical
 #' @return logical
 #' @export
+#' @rdname check_pkg_installed 
 #' @examples 
 #' check_pkg_installed("easyalluvial")
-#' 
-check_pkg_installed = function(pkg){
+check_pkg_installed = function(pkg, raise_error = TRUE){
 
   is_installed <- try({
     suppressPackageStartupMessages(requireNamespace(pkg, quietly = TRUE))
   })
 
   msg <- paste("Please install package `", pkg, "`")
 
-  if(! is_installed){
+  if(! is_installed & raise_error){
     stop(msg)
   }
 
-  return(TRUE)
+  return(is_installed)
 }
 
 #' @title pretty numbers
@@ -526,6 +527,7 @@ get_pdp_predictions_seq = function(df, imp, m, degree = 4, bins = 5, .f_predict
 #'@param parallel logical, Default: TRUE
 #'@rdname pdp_predictions
 #'@seealso \code{\link[easyalluvial]{get_pdp_predictions}}
+#' @noRd
 pdp_predictions = function(df, imp, m, degree = 4, bins = 5, .f_predict = predict,
                            parallel = FALSE){
 
@@ -551,6 +553,9 @@ pdp_predictions = function(df, imp, m, degree = 4, bins = 5, .f_predict = predic
     return(pred)
   }
 
+  # we add one call to progress to satisfy R CMD check
+  .f <- progress::progress_bar
+
   progressr::handlers("progress")
   along <- seq(1, nrow(df))
 
@@ -963,7 +968,7 @@ alluvial_model_response = function(pred, dspace, imp, degree = 4
 #'  Analysis and Data Mining 8(4) <doi:10.1002/sam.11271>
 #' @examples
 #' 
-#' if(check_pkg_installed("caret")) {
+#' if(check_pkg_installed("caret", raise_error = FALSE)) {
 #'   df = mtcars2[, ! names(mtcars2) %in% 'ids' ]
 #'
 #'   train = caret::train( disp ~ .,
@@ -1068,7 +1073,7 @@ alluvial_model_response_caret = function(train, data_input, degree = 4, bins = 5
 #'  observation in the training data the displayed variables are set to the
 #'  indicated values. The predict function is called for each modified
 #'  observation and the result is averaged} }. Default: 'median'
-#'@param parallel logical, turn on parallel processing for pdp methof. Default: FALSE
+#'@param parallel logical, turn on parallel processing for pdp method. Default: FALSE
 #'@param params_bin_numeric_pred list, additional parameters passed to
 #'  \code{\link[easyalluvial]{manip_bin_numerics}} which is applied to the pred
 #'  parameter. Default: list(bins = 5, center = T, transform = T, scale = T)
@@ -1090,7 +1095,7 @@ alluvial_model_response_caret = function(train, data_input, degree = 4, bins = 5
 #'@inheritSection get_pdp_predictions Parallel Processing
 #' @examples
 #' 
-#' if(check_pkg_installed("parsnip")) {
+#' if(check_pkg_installed("parsnip", raise_error = FALSE)) {
 #'   df = mtcars2[, ! names(mtcars2) %in% 'ids' ]
 #'
 #'   m = parsnip::rand_forest(mode = "regression") %>%

R/alluvial_wide.R

@@ -52,11 +52,10 @@ if(getRversion() >= "2.15.1"){
 #'  name the order will be the same. If we want to change level order
 #'  independently we have to assign unique level names first.
 #' @examples
-#' alluvial_wide( data = mtcars2, id = ids
-#'                 , max_variables = 5
-#'                 , fill_by = 'first_variable' )
 #'\dontrun{
-#'
+#' alluvial_wide( data = mtcars2, id = ids
+#'                 , max_variables = 3
+#'                 , fill_by = 'first_variable' )#'
 #' # more coloring variants----------------------
 #' alluvial_wide( data = mtcars2, id = ids
 #'                 , max_variables = 5

R/plot_marginal_hist.R

@@ -511,8 +511,10 @@ plot_hist_wide = function( var, p, data_input){
 #'  inferred, Default: NULL } }
 #'@return gtable
 #' @examples
-#' p = alluvial_wide(mtcars2, max_variables = 4)
+#'\dontrun{
+#' p = alluvial_wide(mtcars2, max_variables = 3)
 #' p_grid = add_marginal_histograms(p, mtcars2)
+#'}
 #'@seealso \code{\link[gridExtra]{arrangeGrob}}
 #'@rdname add_marginal_histograms
 #'@export
@@ -574,8 +576,10 @@ add_marginal_histograms = function(p, data_input, top = TRUE, keep_labels = FALS
 #'   can be used to pass training predictions for model response alluvials
 #' @return gtable
 #' @examples
-#' p = alluvial_wide(mtcars2, max_variables = 4)
+#'\dontrun{
+#' p = alluvial_wide(mtcars2, max_variables = 3)
 #' plot_all_hists(p, mtcars2)
+#' }
 #' @seealso \code{\link[gridExtra]{arrangeGrob}}
 #' @seealso \code{\link[easyalluvial]{add_marginal_histograms}}
 #' @rdname plot_all_hists

_pkgdown.yml

@@ -38,6 +38,7 @@ reference:
   contents:
   - starts_with("manip_")
   - tidy_imp
+  - check_pkg_installed
 - title: Helper Functions - Plotting
   desc: ~
   contents:

cran-comments.md

@@ -1,50 +1,25 @@
-# Resubmission 0.3.0 - 3
+# Resubmission after being archived on CRAN
 
-Got one Note from automated CRAN check that tests are too slow.
-Overall checktime 12 min > 10 min
-
-Disabled a few more tests on CRAN
-
-# Resubmission 0.3.0 - 2
-
-Got one Note from automated CRAN check that tests are too slow.
-Disabled some none-essential longer running tests for CRAN
-
-# Resubmission 0.3.0 - 1
-
-For some reasons 'caret' did not install on the Windows Server which ran
-the automated CRAN checks.
-
-Since 'caret' is only in Suggests, the examples will now only execute if 'caret'
-is installed.
-
-# Update 0.3.0
-
-vdiffr and other packages moved to suggests and usage was made conditional
+clean up package dependencies
 
 ## Test Environments
-* local macOS 10.14.6 R 4.0.3
-* Appveyor x86_64-w64-mingw32/x64 (64-bit) R 4.0.3
-* github actions macos-latest R 4.0.3
-* Rhub Fedora Linux, R-devel, clang, gfortran
-* Rhub Ubuntu Linux 16.04 LTS, R-release, GCC --> NOTE
-* Rhub Windows Server 2008 R2 SP1, R-devel, 32/64 bit
-* WinBuilder R 4.0.3
+* local macOS M1 R 4.2.1
+* Appveyor x86_64-w64-mingw32/x64 (64-bit) R 4.2.1
+* github actions macos-latest R 4.2.1
+* WinBuilder R 4.2.1
 * WinBuilder R devel
 
 coverage -> 96 %
 
 
 ## Test Results
 
-No errors or notes except for:
-5 Examples with CPU or elapsed time > 5s
-This server seem to be a bit slower than the others.
-The examples are already pretty minimal and have been around for a while. 
-I would prefer to keep them and not put them into \dontrun{}. 
+Maintainer: ‘Bjoern Koneswarakantha <[email protected]>’
+
+New submission
+
+Package was archived on CRAN
 
 ## Reverse Dependencies
 
-This package has one reverse dependency 'parcats'
-- which is also maintained by me
-- all checks are passing
+no reverse dependencies