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Merge pull request #59 from vwmaus/drop-dependencies
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Drop dependencies
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vwmaus authored Aug 27, 2023
2 parents c7a0273 + 61e5768 commit 1eb27b5
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18 changes: 3 additions & 15 deletions .Rbuildignore
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@@ -1,18 +1,10 @@
^Meta$
^doc$
^.*\.Rproj$
^\.Rproj\.user$
^\vignettes$
^twdtw_results/
^examples/
^.travis.yml$
_config.yml

# Other files
README.md
corinho.R
tardis.f
tardis.o
^\.git/
.gitignore
^README\.Rmd$
Expand All @@ -21,18 +13,14 @@ tardis.o
^.*\.xml$
^README-.*\.png$
^cran-comments\.md$
src/symbols.rds$
jss\.bst$
jss\.cls$
TODO$
tic.R
dtwSat-Ex_i386.Rout
dtwSat-Ex_x64.Rout
examples_i386
examples_x64
vignettes/twdtw03-speed.Rmd

^data/mod13q1/
^data/mod13q1.db
^CRAN-RELEASE$
^CRAN-SUBMISSION$
^LICENSE\.md$
^dtwSat\.Rproj$
^\.github$
1 change: 1 addition & 0 deletions .github/.gitignore
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*.html
49 changes: 49 additions & 0 deletions .github/workflows/R-CMD-check.yaml
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
branches: [main, master]
pull_request:
branches: [main, master]

name: R-CMD-check

jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}

name: ${{ matrix.config.os }} (${{ matrix.config.r }})

strategy:
fail-fast: false
matrix:
config:
- {os: macos-latest, r: 'release'}
- {os: windows-latest, r: 'release'}
- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
- {os: ubuntu-latest, r: 'release'}
- {os: ubuntu-latest, r: 'oldrel-1'}

env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes

steps:
- uses: actions/checkout@v3

- uses: r-lib/actions/setup-pandoc@v2

- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true

- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::rcmdcheck
needs: check

- uses: r-lib/actions/check-r-package@v2
with:
upload-snapshots: true
50 changes: 50 additions & 0 deletions .github/workflows/test-coverage.yaml
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
branches: [main, master]
pull_request:
branches: [main, master]

name: test-coverage

jobs:
test-coverage:
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

steps:
- uses: actions/checkout@v3

- uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true

- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::covr
needs: coverage

- name: Test coverage
run: |
covr::codecov(
quiet = FALSE,
clean = FALSE,
install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
)
shell: Rscript {0}

- name: Show testthat output
if: always()
run: |
## --------------------------------------------------------------------
find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash

- name: Upload test results
if: failure()
uses: actions/upload-artifact@v3
with:
name: coverage-test-failures
path: ${{ runner.temp }}/package
46 changes: 28 additions & 18 deletions .gitignore
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@@ -1,29 +1,39 @@
Meta
doc
# History files
.Rhistory
.Rapp.history
# Session Data files
.RData
# User-specific files
.Ruserdata
# Example code in package build process
*-Ex.R
# R data files from past sessions
.Rdata
# Output files from R CMD build
/*.tar.gz
# Output files from R CMD check
/*.Rcheck/
# RStudio files
.Rproj.user/
# produced vignettes
vignettes/*.html
vignettes/*.pdf
# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
.httr-oauth
# knitr and R markdown default cache directories
*_cache/
/cache/
# Temporary files created by R markdown
*.utf8.md
*.knit.md
# R Environment Variables
.Renviron
.Rproj.user
# Man fileis
#man/
#.Rd
.Rd~
README.md~
.Rdata
.DS_Store
.quarto
revdep/
CRAN-SUBMISSION

# Other files
src/symbols.rds
twdtw_results/
*.xml
corinho.R
tardis.f
*.o
*.so
Makefile
dtw_result_subarea_250m_1_2017-09-01.tif
/doc/
/Meta/
CRAN-SUBMISSION
54 changes: 0 additions & 54 deletions .travis.yml

This file was deleted.

116 changes: 27 additions & 89 deletions DESCRIPTION
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Expand Up @@ -2,7 +2,7 @@ Package: dtwSat
Type: Package
Title: Time-Weighted Dynamic Time Warping for Satellite Image Time Series Analysis
Version: 1.0.0
Date: 2023-06-30
Date: 2023-09-03
Authors@R:
c(person(given = "Victor",
family = "Maus",
Expand All @@ -22,98 +22,36 @@ Authors@R:
role = c("ctb"),
comment = c(ORCID = "0000-0002-6642-2543"))
)
Description: Provides an implementation of the Time-Weighted Dynamic Time
Warping (TWDTW) method for land cover mapping. TWDTW computes the similarity between
satellite image time series with a set of known temporal patterns
(e.g. phenological cycles of the vegetation).
'dtwSat' offers the user methods to create temporal patterns for land cover types,
perform TWDTW analysis for satellite datasets, visualize the results of the analysis,
produce land cover maps, create temporal plots for land cover change, and compute
accuracy metrics.
Description: Provides a robust approach to land use mapping using multi-dimensional
(multi-band) satellite image time series. By leveraging the Time-Weighted Dynamic
Time Warping (TWDTW) distance metric in tandem with a 1-NN classifier, the package
provides functions to produce land use maps based on distinct seasonality patterns,
typically observed in the phenological cycles of vegetation. The TWDTW algorithm is
described in Maus et al. (2016) <doi:10.1109/JSTARS.2016.2517118> and
Maus et al. (2019) <doi:10.18637/jss.v088.i05>. A key strength of TWDTW is its ability
to recognize patterns with only a minimal training set, achieving notable accuracy.
The package features tools for generating temporal patterns for various land cover types,
conducting land use mapping, and visualizing the outcomes.
License: GPL (>= 3)
URL: https://github.com/vwmaus/dtwSat/
BugReports: https://github.com/vwmaus/dtwSat/issues/
Maintainer: Victor Maus <[email protected]>
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Depends:
R (>= 3.5.0),
zoo,
raster,
twdtw,
sf,
stars,
ggplot2
Imports:
methods,
rgdal,
dtw,
proxy,
mgcv,
stats,
scales,
reshape2,
grDevices,
RColorBrewer,
plyr,
stats,
sp,
lubridate,
caret,
mgcv,
xtable,
Rdpack,
data.table,
foreach
rlang
Suggests:
gridExtra,
grid,
png,
Hmisc,
rbenchmark,
doParallel,
knitr,
rmarkdown
License: GPL (>= 3) | file LICENSE
URL: https://www.victor-maus.com/dtwSat/, https://github.com/vwmaus/dtwSat/
BugReports: https://github.com/vwmaus/dtwSat/issues/
Maintainer: Victor Maus <[email protected]>
LazyData: true
VignetteBuilder:
knitr
Encoding: UTF-8
RoxygenNote: 7.2.3
Collate:
'class-crossValidation.R'
'class-twdtwRaster.R'
'class-twdtwAssessment.R'
'class-twdtwTimeSeries.R'
'class-twdtwMatches.R'
'createPatterns.R'
'data.R'
'dtw.R'
'dwtSat.R'
'getInternals.R'
'getMatchingDates.R'
'getTimeSeries.R'
'linearWeight.R'
'logisticWeight.R'
'methods.R'
'miscellaneous.R'
'plot.R'
'plotAccuracy.R'
'plotAdjustedArea.R'
'plotAlignments.R'
'plotArea.R'
'plotChanges.R'
'plotClassification.R'
'plotCostMatrix.R'
'plotDistance.R'
'plotMapSamples.R'
'plotMaps.R'
'plotMatches.R'
'plotPaths.R'
'plotPatterns.R'
'plotTimeSeries.R'
'resampleTimeSeries.R'
'subset.R'
'twdtw.R'
'twdtwApply.R'
'twdtwAssess.R'
'twdtwClassify.R'
'twdtwCrossValidate.R'
'twdtwDist.R'
'twdtwXtable.R'
'twdtw_reduce_time.R'
'utils.R'
'zzz.R'
RdMacros: Rdpack
stringr,
testthat (>= 3.0.0)
Config/testthat/edition: 3
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