R4EPI · aspina7 · Nov 5, 2025 · Nov 5, 2025 · Nov 5, 2025 · Nov 5, 2025
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -11,3 +11,5 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^doc$
+^Meta$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,18 +1,14 @@
-# NOTE: This workflow is overkill for most R packages
-# check-standard.yaml is likely a better choice
-# usethis::use_github_action("check-standard") will install it.
-#
-# 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
+# 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:
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - master
+    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -24,85 +20,33 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,  cov: 'true', r: 'release'}
-          - {os: windows-latest,cov: 'false', r: 'release'}
-          - {os: windows-latest,cov: 'false', r: '3.6'}
-          - {os: ubuntu-16.04,  cov: 'false', r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest", http-user-agent: "R/4.0.0 (ubuntu-16.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-16.04,  cov: 'false', r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,  cov: 'false', r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,  cov: 'false', r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,  cov: 'false', r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {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:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - 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-pandoc@master
-
-      - 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@v1
+      - 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 system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "16.04"), sep = "\n")')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Cover
-        if: matrix.config.cov == 'true'
-        run: covr::codecov()
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,46 +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: master
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  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@master
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - 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@v1
+      - 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")
-        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 "[email protected]"
-          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/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,63 @@
+# 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.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    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::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v5
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/.gitignore b/.gitignore
@@ -7,3 +7,5 @@
 README.html
 inst/rmarkdown/templates/*/skeleton/*.xlsx
 docs
+/doc/
+/Meta/
diff --git a/.travis.yml b/.travis.yml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Type: Package
 Package: sitrep
-Title: Report templates and helper functions for applied epidemiology
+Title: Report Templates And Helper Functions For Applied Epidemiology
 Version: 0.2.3
 Authors@R: 
     c(person(given = "Alexander",
@@ -31,16 +31,20 @@ Authors@R:
              role = "ctb"),
       person(given = "Neale",
              family = "Batra",
-             role = "ctb"))
+             role = "ctb"), 
+    person("Applied Epi Incorporated", 
+           role = "cph"), 
+    person("Medecins Sans Frontieres Operational Centre Amsterdam", 
+           role = "fnd"))
 Description: A meta-package that loads the complete sitrep ecosystem for applied 
     epidemiology analysis. This package provides report templates and automatically 
-    loads companion packages: epitabulate (for epidemiological tables), epidict 
-    (for data dictionaries), epikit (for epidemiological utilities), and apyramid 
-    (for age-sex pyramids). Simply load sitrep to access all functions from the 
-    ecosystem.
+    loads companion packages, including epitabulate (for epidemiological tables), 
+    epidict (for data dictionaries), epikit (for epidemiological utilities), 
+    and apyramid (for age-sex pyramids). Simply load sitrep to access all 
+    functions from the ecosystem.
 License: GPL-3
 BugReports: https://github.com/R4EPI/sitrep/issues
-URL: https://github.com/R4EPI/sitrep,
+URL: https://github.com/R4EPI/sitrep/,
     https://r4epi.github.io/sitrep/
 Depends: 
     R (>= 3.2)
@@ -106,4 +110,3 @@ Collate:
     'sitrep-package.R'
     'check_templates.R'
     'metapackage_functions.R'
-
diff --git a/LICENSE.md b/LICENSE.md
@@ -553,7 +553,7 @@ and each file should have at least the “copyright” line and a pointer to
 where the full notice is found.
 
     <one line to give the program's name and a brief idea of what it does.>
-    Copyright (C) 2019 Zhian N. Kamvar, Annick Lenglet
+    Copyright (C) 2019 Applied Epi Incorporated
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -573,7 +573,7 @@ Also add information on how to contact you by electronic and paper mail.
 If the program does terminal interaction, make it output a short notice like this
 when it starts in an interactive mode:
 
-    sitrep Copyright (C) 2019 Zhian N. Kamvar, Annick Lenglet
+    sitrep Copyright (C) 2019 Applied Epi Incorporated
     This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
     This is free software, and you are welcome to redistribute it
     under certain conditions; type 'show c' for details.

diff --git a/R/metapackage_functions.R b/R/metapackage_functions.R
@@ -393,7 +393,7 @@ ignore_unused_imports <- function() {
   epidict::dict_rename_helper
   epidict::gen_data
   epidict::msf_dict
-  epidict::msf_dict_rename_helper
+  # epidict::msf_dict_rename_helper
   epidict::read_dict
   epikit::add_weights_cluster
   epikit::add_weights_strata
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,3 +11,5 @@ @@
     ^_pkgdown\.yml$
     ^docs$
     ^pkgdown$
+    ^doc$
+    ^Meta$