casaultb · EOGrady21 · Feb 20, 2026 · Feb 20, 2026 · Feb 20, 2026 · Feb 20, 2026
diff --git a/.github/workflows/R-CMD-CHECK.yaml b/.github/workflows/R-CMD-CHECK.yaml
@@ -0,0 +1,44 @@
+# 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: windows-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      PKG_SYSREQS: false
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
+            any::devtools
+          needs: check
+
+      - name: Install package
+        run: devtools::install()
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov(quiet = FALSE)
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          error-on: '"error"'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,48 +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
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - 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}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@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 dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
-        shell: Rscript {0}
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install package
-        run: R CMD INSTALL .
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
 
-      - name: Deploy package
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.travis.yml b/.travis.yml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -34,12 +34,15 @@ Suggests:
     testthat (>= 2.1.0),
     knitr,
     rmarkdown,
+    ggplot2,
+    grid,
+    tools,
+    usethis,
+    covr
 URL: https://casaultb.github.io/azmpdata, https://github.com/casaultb/azmpdata
 BugReports: https://github.com/casaultb/azmpdata/issues
 Imports: 
     dplyr,
-    ggplot2,
-    grid,
     leaflet,
     lubridate,
     magrittr,
@@ -51,9 +54,7 @@ Imports:
     stringr,
     tidyr,
     tibble,
-    tools,
     utils,
-    usethis
 Depends: 
     R (>= 3.5)
 VignetteBuilder: knitr
diff --git a/R/zzz.R b/R/zzz.R
@@ -2,9 +2,9 @@
 utils::globalVariables(c('year', 'value', 'month', 'day', 'year_dec', 'xmin', 'xmax', 'ymin', 'ymax', '.', 'ls_data', 'variable', 'tmp_variable', 'keyword', 'dataframe'))
 
 .onAttach <- function(libname, pkgname) {
-  # check if updates are available
+  # Check if updates are available
   update_check(gitPkg = 'casaultb/azmpdata')
-  message("\tazmpdata:: Indexing all available monthly azmpdata...")
-  assign("azmpMonthlyParams", area_indexer(doMonths=T, doParameters = T), envir = .GlobalEnv)
+  packageStartupMessage("\tazmpdata:: Indexing all available monthly azmpdata...")
+  assign("azmpMonthlyParams", area_indexer(doMonths = TRUE, doParameters = TRUE), envir = .GlobalEnv)
 }
 
diff --git a/README.Rmd b/README.Rmd
@@ -16,7 +16,8 @@ knitr::opts_chunk$set(
 # *azmpdata*
 
 <!-- badges: start -->
-[![Travis build status](https://travis-ci.org/casaultb/azmpdata.svg?branch=master)](https://travis-ci.org/casaultb/azmpdata)
+[![R-CMD-check](https://github.com/casaultb/azmpdata/actions/workflows/R-CMD-CHECK.yaml/badge.svg)](https://github.com/casaultb/azmpdata/actions/workflows/R-CMD-CHECK.yaml/badge.svg)
+
 <!-- badges: end -->
 
 The R package *azmpdata* provides a series of data products derived from raw data collected as part of the Atlantic Zone Monitoring Program ([AZMP](https://www.dfo-mpo.gc.ca/science/data-donnees/azmp-pmza/index-eng.html)). The data products provided in this package are used to generate the different figures contained in the Research Documents produced annually by Fisheries and Ocean Canada's Maritimes region.  The Research Documents describe the physical, chemical and biological conditions observed in Maritimes region since the inception of the AZMP program (see example documents for the [physical](http://www.dfo-mpo.gc.ca/csas-sccs/Publications/ResDocs-DocRech/2018/2018_016-eng.html) conditions and for the [optical, chemical and biological](http://www.dfo-mpo.gc.ca/csas-sccs/Publications/ResDocs-DocRech/2018/2018_017-eng.html) conditions).
@@ -26,8 +27,8 @@ The R package *azmpdata* provides a series of data products derived from raw dat
 The *azmpdata* R package can be installed from [GitHub](https://github.com) with:
 
 ``` r
-# install.packages("devtools")
-devtools::install_github("casaultb/azmpdata")
+library(remotes)
+remotes::install_github(repo = "casaultb/azmpdata", ref = "master", build_vignettes = TRUE)
 ```
 
 ## Datasets

diff --git a/README.md b/README.md
@@ -1,16 +1,16 @@
 azmpdata R package
 ================
 Benoit Casault, Emily Chisholm
-15 December, 2020
+20 February, 2026
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 # *azmpdata*
 
 <!-- badges: start -->
 
-[![Travis build
-status](https://travis-ci.org/casaultb/azmpdata.svg?branch=master)](https://travis-ci.org/casaultb/azmpdata)
+[![R-CMD-check](https://github.com/casaultb/azmpdata/actions/workflows/R-CMD-CHECK.yaml/badge.svg)](https://github.com/casaultb/azmpdata/actions/workflows/R-CMD-CHECK.yaml/badge.svg)
+
 <!-- badges: end -->
 
 The R package *azmpdata* provides a series of data products derived from
@@ -48,33 +48,47 @@ To access a dataset in data frame format:
 
 ``` r
 library(azmpdata)
-#> 
-#>  casaultb/azmpdata status:
-#>  (Package ver: 0.2019.0.9000) Up to date
-#>  (Data ver:2020-11-26) is up to date
+#> casaultb/azmpdata status:
+#>  (Package ver: 0.2019.0.9100) Up to date
+#>  (Data ver:2021-01-14 ) Up to date
+#>  azmpdata:: Indexing all available monthly azmpdata...
 data("Derived_Annual_Broadscale")
 head(Derived_Annual_Broadscale)
-#>   year          area density_gradient_0_50 temperature_at_sea_floor
-#> 1 1948 Scotion Shelf              -0.00139                       NA
-#> 2 1949 Scotion Shelf              -0.00968                       NA
-#> 3 1950 Scotion Shelf              -0.01883                       NA
-#> 4 1951 Scotion Shelf              -0.00092                       NA
-#> 5 1952 Scotion Shelf               0.00155                       NA
-#> 6 1953 Scotion Shelf              -0.00313                       NA
-#>   cold_intermediate_layer_volume minimum_temperature_in_cold_intermediate_layer
-#> 1                           <NA>                                           <NA>
-#> 2                           <NA>                                           <NA>
-#> 3                           <NA>                                           <NA>
-#> 4                           <NA>                                           <NA>
-#> 5                           <NA>                                           <NA>
-#> 6                           <NA>                                           <NA>
+#>   year              area density_gradient_0_50 sea_temperature_0 salinity_0
+#> 1 1948 scotian_shelf_box               0.02715              6.45      31.23
+#> 2 1949 scotian_shelf_box               0.01339              8.97      31.83
+#> 3 1950 scotian_shelf_box               0.00587              8.15      31.92
+#> 4 1951 scotian_shelf_box               0.02733              9.55      31.21
+#> 5 1952 scotian_shelf_box               0.03159              8.91      31.02
+#> 6 1953 scotian_shelf_box               0.02433              8.89      31.27
+#>   temperature_at_sea_floor cold_intermediate_layer_volume
+#> 1                       NA                             NA
+#> 2                       NA                             NA
+#> 3                       NA                             NA
+#> 4                       NA                             NA
+#> 5                       NA                             NA
+#> 6                       NA                             NA
+#>   minimum_temperature_in_cold_intermediate_layer north_atlantic_oscillation
+#> 1                                             NA                         NA
+#> 2                                             NA                         NA
+#> 3                                             NA                         NA
+#> 4                                             NA                         NA
+#> 5                                             NA                         NA
+#> 6                                             NA                         NA
+#>   sea_surface_temperature_from_satellite
+#> 1                                     NA
+#> 2                                     NA
+#> 3                                     NA
+#> 4                                     NA
+#> 5                                     NA
+#> 6                                     NA
 ```
 
 To access a dataset in csv format:
 
 ``` r
 system.file("extdata/csv", "Derived_Annual_Broadscale.csv", package = "azmpdata")
-#> [1] "C:/Users/ChisholmE/Documents/R/R-4.0.2/library/azmpdata/extdata/csv/Derived_Annual_Broadscale.csv"
+#> [1] "C:/Users/ogradye/AppData/Local/Temp/1/RtmpWY0v01/temp_libpath305426945375/azmpdata/extdata/csv/Derived_Annual_Broadscale.csv"
 ```
 
 ### Variable Organization
@@ -105,18 +119,18 @@ look as below:
 
 ``` r
 res <- variable_lookup(keywords = c('nitrate', 'phosphate'), search_help = TRUE)
-#> Joining, by = c("keyword", "variable", "dataframe")
+#> Joining with `by = join_by(keyword, variable, dataframe)`
 
 head(res)
-#> # A tibble: 6 x 3
+#> # A tibble: 6 × 3
 #>   keyword variable                  dataframe                   
 #>   <chr>   <chr>                     <chr>                       
 #> 1 nitrate integrated_nitrate_0_50   Derived_Annual_Sections     
 #> 2 nitrate integrated_nitrate_0_50   Derived_Annual_Stations     
 #> 3 nitrate integrated_nitrate_0_50   Derived_Occupations_Sections
-#> 4 nitrate integrated_nitrate_50_150 Derived_Annual_Sections     
-#> 5 nitrate integrated_nitrate_50_150 Derived_Annual_Stations     
-#> 6 nitrate integrated_nitrate_50_150 Derived_Occupations_Sections
+#> 4 nitrate integrated_nitrate_0_50   Derived_Occupations_Stations
+#> 5 nitrate integrated_nitrate_50_150 Derived_Annual_Sections     
+#> 6 nitrate integrated_nitrate_50_150 Derived_Annual_Stations
 ```
 
 #### Dataset Documentation

diff --git a/man/azmpdata-package.Rd b/man/azmpdata-package.Rd
diff --git a/man/azmpdata.Rd b/man/azmpdata.Rd