Dev1.2.1.9000

.Rbuildignore

@@ -7,4 +7,7 @@
 ^pkgdown$
 ^index\.Rmd$
 ^index\.md$
-^vignettes$
+^vignettes$
+^LICENSE\.md$
+^LICENSE$
+^\.github$

.github/.gitignore

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

.github/workflows/check-standard.yaml

@@ -0,0 +1,84 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on: [push, pull_request]
+
+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: windows-latest, r: 'release'}
+          - {os: windows-latest, r: 'devel'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        # env:
+          # RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          # # # # custom hack to ensure correct version of Matrix for TMB
+          # sudo apt-get install -y --allow-downgrades r-cran-matrix=1.2-18-1focal0
+          # R -e "install.packages('TMB', type = 'source')"
+          # # # # custom hack end
+
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.gitignore

@@ -40,3 +40,4 @@ man/figures/*.png
 rsconnect/
 .Rproj.user
 inst/doc
+debug.log

DESCRIPTION

@@ -1,23 +1,22 @@
 Package: yaps
-Title: Track estimation using YAPS (Yet Another Positioning Solver)
-Version: 1.2.0.9112
+Title: Track Estimation using YAPS (Yet Another Positioning Solver)
+Version: 1.2.2
 Authors@R: c(	person("Henrik", "Baktoft", email = "[email protected]", role = c("cre", "aut")),
 				person("Karl", "Gjelland", role=c("aut")),
 				person("Uffe H.", "Thygesen", role=c("aut")),
 				person("Finn", "Økland", role=c("aut"))
 			)
-Description: Estimate track from acoustic data using YAPS (doi:10.1038/s41598-017-14278-z).
+Description: Estimate track from acoustic data using YAPS.
 Depends: R (>= 3.5.0)
-License: GPL-3 + file LICENSE
+License: GPL-3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.1
 LinkingTo: Rcpp, TMB, RcppEigen
-Imports: circular, data.table (>= 1.12.8), ggplot2, Matrix, nloptr, plyr, Rcpp, RcppEigen, reshape2, splusTimeSeries, stats, tictoc, TMB, viridis, zoo
+Imports: circular, cowplot, data.table, ggplot2, ggrepel, nloptr, plyr, Rcpp, reshape2, splusTimeSeries, stats, tictoc, TMB, viridis, zoo
 Suggests: 
     testthat (>= 2.1.0),
     knitr,
     rmarkdown
 URL: https://github.com/baktoft/yaps
 BugReports: https://github.com/baktoft/yaps/issues
-VignetteBuilder: knitr