Merge pull request #59 from vwmaus/drop-dependencies

Drop dependencies

.Rbuildignore

@@ -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$
@@ -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$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,49 @@
+# 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

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# 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

.gitignore

@@ -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

DESCRIPTION

@@ -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",
@@ -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 <vwmaus1@gmail.com>
+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 <vwmaus1@gmail.com>
-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