Merge branch 'release/1.0.0'

.Rbuildignore

@@ -10,3 +10,11 @@
 ^vignettes/.RData$
 ^output
 ^oddities
+^CHANGES\.md$
+^CONTRIBUTING\.md$
+^CNAME$
+^index\.md$
+^[^/]+\.[Rr]$
+^information$
+^example_external_data_adjustments\.Rmd$
+^data/example_[^/]+/?.*$

.github/workflows/build.yml

@@ -28,6 +28,9 @@ jobs:
         with:
           use-public-rspm: true
 
+      ## qpdf is needed for size checks on outputs, otherwise we get spurious warnings
+      - run: sudo apt-get install -y libqpdf-dev
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
@@ -36,6 +39,10 @@ jobs:
           needs: |
             check
 
+      - name: Reinstall Matrix
+        run: install.packages("Matrix")
+        shell: Rscript {0}
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           args: 'c("--no-manual")'

.github/workflows/pkgdown-dev.yaml

@@ -0,0 +1,113 @@
+# 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
+#
+# This is a secondary pkgdown action, linked only to pushes to develop, i.e., 
+# when a develop pull request is merged. This will update the web site when
+# a develop PR is merged. It is a transitional flow.
+#
+# TODO: Remove this action when we want to link documentation only to the 
+# main branch and public releases.
+
+on:
+  push:
+    branches: [develop]
+  workflow_dispatch:
+
+name: pkgdown-dev
+
+jobs:
+  pkgdown-dev:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-dev-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+    - uses: actions/checkout@v3
+
+    - uses: r-lib/actions/setup-pandoc@v2
+
+    - uses: r-lib/actions/setup-r@v2
+      with:
+        use-public-rspm: true
+
+    ## qpdf is needed for size checks on outputs, otherwise we get spurious warnings
+    - run: sudo apt-get install -y libqpdf-dev
+
+    - uses: r-lib/actions/setup-r-dependencies@v2
+      with:
+        extra-packages: |
+            any::pkgdown
+            any::rcmdcheck
+            local::.
+        needs: |
+            website
+            check
+
+    - name: Build site
+      run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+      shell: Rscript {0}
+
+    ## Note that by using renames and recursive copies, dates are preserved, so
+    ## the zip files will be identical. This minimizes the changes to gh-pages.
+    ## At least, that's the general idea. 
+    ##
+    ## It may seem complex, but it's pretty quick.
+    - name: Create a working directory for archive creation
+      run: |
+        echo "TEMP_DIR=$(mktemp -d)" >> $GITHUB_ENV
+        echo "WORK_DIR=$(pwd)" >> $GITHUB_ENV
+
+    - name: Build data and configuration archive for AMAP/external
+      run: |
+        set +f
+        mkdir -p $TEMP_DIR/external
+        cp -R data/example_external_data $TEMP_DIR/external/
+        mv $TEMP_DIR/external/example_external_data $TEMP_DIR/external/data
+        cp -R information/AMAP $TEMP_DIR/external/
+        mv $TEMP_DIR/external/AMAP $TEMP_DIR/external/information
+        mv $TEMP_DIR/external/data/README*.* $TEMP_DIR/external/
+        cd $TEMP_DIR
+        zip -r $WORK_DIR/docs/external.zip external
+        cd $WORK_DIR
+      continue-on-error: true
+
+    - name: Build data and configuration archive for OSPAR 2022
+      run: |
+        set +f
+        mkdir -p $TEMP_DIR/ospar
+        cp -R data/example_OSPAR $TEMP_DIR/ospar/
+        mv $TEMP_DIR/ospar/example_OSPAR $TEMP_DIR/ospar/data
+        cp -R information/OSPAR_2022 $TEMP_DIR/ospar/
+        mv $TEMP_DIR/ospar/OSPAR_2022 $TEMP_DIR/ospar/information
+        mv $TEMP_DIR/ospar/data/README*.* $TEMP_DIR/ospar/
+        cd $TEMP_DIR
+        zip -r $WORK_DIR/docs/ospar.zip ospar
+        cd $WORK_DIR
+      continue-on-error: true
+
+    - name: Build data and configuration archive for HELCOM 2023
+      run: |
+        set +f
+        mkdir -p $TEMP_DIR/helcom
+        cp -R data/example_HELCOM $TEMP_DIR/helcom/
+        mv $TEMP_DIR/helcom/example_HELCOM $TEMP_DIR/helcom/data
+        cp -R information/HELCOM_2023 $TEMP_DIR/helcom/
+        mv $TEMP_DIR/helcom/HELCOM_2023 $TEMP_DIR/helcom/information
+        mv $TEMP_DIR/helcom/data/README*.* $TEMP_DIR/helcom/
+        cd $TEMP_DIR
+        zip -r $WORK_DIR/docs/helcom.zip helcom
+        cd $WORK_DIR
+      continue-on-error: true
+
+    ## Deploys everything in the docs/ folder to gh-pages. This means
+    ## additional files can be deployed here.
+    - name: Deploy to GitHub pages 🚀
+      uses: JamesIves/github-pages-deploy-action@v4.4.1
+      with:
+        clean: false
+        branch: gh-pages
+        folder: docs

.github/workflows/pkgdown.yaml

@@ -28,6 +28,9 @@ jobs:
         with:
           use-public-rspm: true
 
+      ## qpdf is needed for size checks on outputs, otherwise we get spurious warnings
+      - run: sudo apt-get install -y libqpdf-dev
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
@@ -52,38 +55,41 @@ jobs:
 
       - name: Build data and configuration archive for AMAP/external
         run: |
+          set +f
           mkdir -p $TEMP_DIR/external
           cp -R data/example_external_data $TEMP_DIR/external/
           mv $TEMP_DIR/external/example_external_data $TEMP_DIR/external/data
           cp -R information/AMAP $TEMP_DIR/external/
           mv $TEMP_DIR/external/AMAP $TEMP_DIR/external/information
-          mv $TEMP_DIR/external/information/README*.* $TEMP_DIR/external/
+          mv $TEMP_DIR/external/data/README*.* $TEMP_DIR/external/
           cd $TEMP_DIR
           zip -r $WORK_DIR/docs/external.zip external
           cd $WORK_DIR
         continue-on-error: true
 
       - name: Build data and configuration archive for OSPAR 2022
         run: |
+          set +f
           mkdir -p $TEMP_DIR/ospar
           cp -R data/example_OSPAR $TEMP_DIR/ospar/
           mv $TEMP_DIR/ospar/example_OSPAR $TEMP_DIR/ospar/data
           cp -R information/OSPAR_2022 $TEMP_DIR/ospar/
           mv $TEMP_DIR/ospar/OSPAR_2022 $TEMP_DIR/ospar/information
-          mv $TEMP_DIR/ospar/information/README*.* $TEMP_DIR/ospar/
+          mv $TEMP_DIR/ospar/data/README*.* $TEMP_DIR/ospar/
           cd $TEMP_DIR
           zip -r $WORK_DIR/docs/ospar.zip ospar
           cd $WORK_DIR
         continue-on-error: true
 
       - name: Build data and configuration archive for HELCOM 2023
         run: |
+          set +f
           mkdir -p $TEMP_DIR/helcom
           cp -R data/example_HELCOM $TEMP_DIR/helcom/
           mv $TEMP_DIR/helcom/example_HELCOM $TEMP_DIR/helcom/data
           cp -R information/HELCOM_2023 $TEMP_DIR/helcom/
           mv $TEMP_DIR/helcom/HELCOM_2023 $TEMP_DIR/helcom/information
-          mv $TEMP_DIR/helcom/information/README*.* $TEMP_DIR/helcom/
+          mv $TEMP_DIR/helcom/data/README*.* $TEMP_DIR/helcom/
           cd $TEMP_DIR
           zip -r $WORK_DIR/docs/helcom.zip helcom
           cd $WORK_DIR

.gitignore

@@ -4,7 +4,7 @@
 .Ruserdata
 .build.timestamp
 HARSAT.RProj
-HARSAT.Rcheck
+harsat.Rcheck
 harsat_*.tar.gz
 oddities/
 output/

CHANGES.md

@@ -1,5 +1,13 @@
 ## Change log
 
+### Version 1.0.0
+
+- Initial public release
+
+### Version 0.1.3
+
+- Various fixes
+
 ### Version 0.1.2
 
 - Fixed issues when packaged; see #326, #328
@@ -13,4 +21,4 @@
 
 ### Version 0.1.0
 
-- Initial release
+- Initial release

CONTRIBUTING.md

@@ -100,7 +100,8 @@ Let's assume the current version is `x.y.z`
 ```
 git checkout develop
 git flow release start x.y.z+1
-emacs DESCRIPTION ## Update version x.y.z-9000 -> x.y.z+1
+emacs DESCRIPTION     ## Update version x.y.z-9000 -> x.y.z+1
+emacs CHANGES.md      ## Update the change log, as appropriate
 R --quiet --vanilla < vignettes/precompile.R
 R CMD build .
 R CMD check --no-manual harsat_x.y.z+1.tar.gz
@@ -113,7 +114,7 @@ git push --tags
 git push upstream
 git push --tags upstream
 git checkout develop
-emacs DESCRIPTION ## Bump version to x.y.(z+1)-9000
+emacs DESCRIPTION      ## Bump version to x.y.(z+1)-9000
 git commit -am "Bump develop version [ci skip]"
 git push
 git push upstream

DESCRIPTION

@@ -1,12 +1,13 @@
 Package: harsat
 Title: Harmonized Regional Seas Assessment Tool
-Version: 0.1.3.1003
+Version: 1.0.0
 Authors@R: c(
     person(given = "Arctic Monitoring and Assessment Programme (AMAP)", email = "amap@amap.no", role = c("cph", "fnd", "aut")),
     person(given = "Helsinki Commission (HELCOM)", email = "secretariat@helcom.fi", role = c("cph", "fnd", "aut")),
     person(given = "OSPAR Commission (OSPAR)", email = "data@ospar.org", role = c("cph", "fnd", "cre", "aut")),
     person(given = "International Council for the Exploration of the Sea (ICES)", email = "info@ices.dk", role = c("cph", "aut")),
-    person(given = "AmbieSense Ltd", email = "info@ambiesense.com", role = c("cph", "aut"))
+    person(given = "AmbieSense Ltd", email = "info@ambiesense.com", role = c("cph", "aut")),
+    person(given = "HARSAT User Group", email = "harsat@ospar.org", role = c("ctb"))
   )
 Description: Tools for the assessment of data concerning contaminants (hazardous
   substances) and their effects in the marine environment. The code includes
@@ -19,7 +20,7 @@ BugReports: https://github.com/osparcomm/HARSAT/issues
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 VignetteBuilder: knitr, rmarkdown
-Depends: R (>= 4.2.1)
+Depends: R (>= 4.2.1.0)
 Imports:
   flexsurv,
   lme4,
@@ -31,6 +32,8 @@ Imports:
   MASS,
   mvtnorm, 
   dplyr,
+  magrittr,
+  lattice,
   lubridate,
   readr,
   stringr,
@@ -42,5 +45,6 @@ Imports:
 Suggests: 
   knitr,
   rmarkdown,
+  rprojroot,
   testthat (>= 3.0.0)
 Config/testthat/edition: 3

NAMESPACE

@@ -21,7 +21,6 @@ export(ctsm_get_info)
 export(ctsm_read_determinand)
 export(ctsm_read_species)
 export(ctsm_read_thresholds)
-export(ctsm_subset_assessment)
 export(ctsm_summary_overview)
 export(ctsm_symbology_OSPAR)
 export(ctsm_uncrt_estimate)
@@ -35,13 +34,87 @@ export(get_basis_default)
 export(get_basis_most_common)
 export(get_station_code)
 export(get_timeseries)
+export(info_TEF)
 export(normalise_biota_HELCOM)
 export(normalise_sediment_HELCOM)
 export(normalise_sediment_OSPAR)
 export(plot_assessment)
 export(read_contaminants)
 export(read_data)
+export(report_assessment)
 export(run_assessment)
+export(subset_assessment)
 export(tidy_data)
 export(update_assessment)
 export(write_summary_table)
+importFrom(grDevices,dev.off)
+importFrom(grDevices,extendrange)
+importFrom(grDevices,grey)
+importFrom(grDevices,pdf)
+importFrom(grDevices,png)
+importFrom(graphics,par)
+importFrom(grid,arrow)
+importFrom(grid,convertY)
+importFrom(grid,gpar)
+importFrom(grid,grid.layout)
+importFrom(grid,grid.lines)
+importFrom(grid,grid.newpage)
+importFrom(grid,grid.rect)
+importFrom(grid,grid.text)
+importFrom(grid,pushViewport)
+importFrom(grid,unit)
+importFrom(grid,unit.c)
+importFrom(grid,upViewport)
+importFrom(grid,viewport)
+importFrom(lattice,current.panel.limits)
+importFrom(lattice,current.row)
+importFrom(lattice,llines)
+importFrom(lattice,lpoints)
+importFrom(lattice,lpolygon)
+importFrom(lattice,panel.abline)
+importFrom(lattice,panel.axis)
+importFrom(lattice,panel.rug)
+importFrom(lattice,panel.superpose)
+importFrom(lattice,splom)
+importFrom(lattice,trellis.par.get)
+importFrom(lattice,which.packet)
+importFrom(lattice,xyplot)
+importFrom(magrittr,"%>%")
+importFrom(optimx,optimx)
+importFrom(stats,AIC)
+importFrom(stats,as.formula)
+importFrom(stats,complete.cases)
+importFrom(stats,dmultinom)
+importFrom(stats,dnorm)
+importFrom(stats,filter)
+importFrom(stats,glm)
+importFrom(stats,glm.control)
+importFrom(stats,integrate)
+importFrom(stats,lm)
+importFrom(stats,logLik)
+importFrom(stats,median)
+importFrom(stats,na.omit)
+importFrom(stats,optim)
+importFrom(stats,pbinom)
+importFrom(stats,pf)
+importFrom(stats,plogis)
+importFrom(stats,pnorm)
+importFrom(stats,predict)
+importFrom(stats,pt)
+importFrom(stats,qf)
+importFrom(stats,qlogis)
+importFrom(stats,qnorm)
+importFrom(stats,qt)
+importFrom(stats,quasi)
+importFrom(stats,reshape)
+importFrom(stats,rnorm)
+importFrom(stats,sd)
+importFrom(stats,setNames)
+importFrom(stats,uniroot)
+importFrom(stats,update)
+importFrom(tibble,column_to_rownames)
+importFrom(utils,head)
+importFrom(utils,modifyList)
+importFrom(utils,read.csv)
+importFrom(utils,read.delim)
+importFrom(utils,tail)