Initial package infrastructure

.Rbuildignore

@@ -13,3 +13,4 @@
 ^docs$
 ^pkgdown$
 ^tools$
+^scratch\.R$

.github/workflows/dependency-change.yaml

@@ -0,0 +1,83 @@
+# 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
+# Adapted from Epiverse packages: https://github.com/epiverse-trace
+on:
+  pull_request:
+    paths:
+      - 'DESCRIPTION'
+
+name: Analyze dependency changes
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  pull-requests: write
+
+jobs:
+  dependency-changes:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: any::pak, glue, gh
+
+      - name: Analyze dependency changes
+        shell: Rscript {0}
+        run: |
+          deps_base <- pak::pkg_deps("${{ github.repository }}@${{ github.base_ref }}", dependencies = TRUE) |>
+            subset(!directpkg) |>
+            subset(is.na(priority))
+          # We install from PR number rather than branch to deal with the case
+          # of PR coming from forks
+          deps_head <- pak::pkg_deps("${{ github.repository }}#${{ github.event.number }}", dependencies = TRUE) |>
+            subset(!directpkg) |>
+            subset(is.na(priority))
+
+          deps_added <- deps_head |>
+            subset(!ref %in% deps_base$ref)
+
+          deps_removed <- deps_base |>
+            subset(!ref %in% deps_head$ref)
+
+          if (nrow(deps_added) + nrow(deps_removed) > 0) {
+
+            message("Dependencies have changed! Analyzing...")
+
+            if (nrow(deps_added) > 0) {
+              nudge <- "Reach out on slack (`#code-review` or `#help` channels) to double check if there are base R alternatives to the new dependencies.\n"
+            } else {
+              nudge <- ""
+            }
+
+            msg <- glue::glue(
+              .sep = "\n",
+              "This pull request:",
+              "- Adds {nrow(deps_added)} new dependencies (direct and indirect)",
+              "- Adds {length(unique(deps_added$sysreqs))} new system dependencies",
+              "- Removes {nrow(deps_removed)} existing dependencies (direct and indirect)",
+              "- Removes {length(unique(deps_removed$sysreqs))} existing system dependencies",
+              "",
+              nudge,
+              "(Note that results may be inaccurate if you branched from an outdated version of the target branch.)"
+            )
+
+            message("Posting results as a pull request comment.")
+
+            gh::gh(
+              "POST /repos/{repo}/issues/{issue_number}/comments",
+              repo = "${{ github.repository }}",
+              issue_number = "${{ github.event.number }}",
+              body = msg
+            )
+
+          }

.github/workflows/render-readme.yaml

@@ -0,0 +1,97 @@
+# Adapted from Epiverse packages: https://github.com/epiverse-trace
+# Reproduce locally by running:
+# ```r
+# pak::pak(c("any::rmarkdown", "any::usethis", "."))
+# writeLines(
+#   knitr::knit_expand(
+#     "README.Rmd",
+#     packagename = read.dcf("DESCRIPTION", "Package"),
+#     gh_repo = usethis:::github_remote_list()$repo_spec
+#   ),
+#   "README_expanded.Rmd"
+# )
+# rmarkdown::render(
+#   "README_expanded.Rmd",
+#   output_file = "README.md",
+#   output_dir = "."
+# )
+# unlink("README_expanded.Rmd")
+# ```
+name: render-readme
+
+# Controls when the action will run. Triggers include:
+#
+# - button trigger from github action page
+# - on changes to readme.Rmd
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      # This may seem like a no-op but it prevents triggering on tags
+      # We use '**' rather '*' to accomodate names like 'dev/branch-1'
+      - '**'
+    paths:
+      - 'README.Rmd'
+      - '.github/workflows/render_readme.yml'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: write
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  render-readme:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repos
+        uses: actions/checkout@v4
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Setup pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rmarkdown, local::.
+
+      - name: Compile the readme
+        run: |
+          writeLines(
+            knitr::knit_expand(
+              "README.Rmd",
+              packagename = read.dcf("DESCRIPTION", "Package"),
+              gh_repo = Sys.getenv("GITHUB_REPOSITORY")
+            ),
+            "README_expanded.Rmd"
+          )
+          rmarkdown::render(
+            "README_expanded.Rmd",
+            output_file = "README.md",
+            output_dir = "."
+          )
+        shell: Rscript {0}
+
+      - name: Commit files
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Action"
+          git add README.md
+          # Also add README figures if they exist
+          if [ -d man/figures ]
+          then
+            git add man/figures/
+          fi
+          git diff-index --quiet HEAD || git commit -m "Automatic readme update"
+          git pull --rebase origin ${{ github.ref.name }}
+          git push origin || echo "No changes to push"

.github/workflows/update-copyright-year.yaml

@@ -0,0 +1,38 @@
+# Adapted from Epiverse packages: https://github.com/epiverse-trace
+name: Update copyright year(s) in license file
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 3 1 1 *'
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: FantasticFiasco/action-update-license-year@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          path: | 
+            LICENSE.md
+          prBody: >
+           This PR updates the copyright license for this new year! If you're reading this while you're celebrating, enjoy! Don't worry about this one :blush:
+
+           ![Happy new year!](https://media.giphy.com/media/HyDfNCZlTn5iU/giphy.gif?cid=ecf05e4777yl7dbo1xfha6bx1z5lrl13uq7biv6rs9dqsyoh&ep=v1_gifs_search&rid=giphy.gif&ct=g)
+      - uses: FantasticFiasco/action-update-license-year@v3
+        with:
+            token: ${{ secrets.GITHUB_TOKEN }}
+            path: | 
+              LICENSE
+            prBody: >
+             This PR updates the copyright license for this new year! If you're reading this while you're celebrating, enjoy! Don't worry about this one :blush:
+
+             ![Happy new year!](https://media.giphy.com/media/HyDfNCZlTn5iU/giphy.gif?cid=ecf05e4777yl7dbo1xfha6bx1z5lrl13uq7biv6rs9dqsyoh&ep=v1_gifs_search&rid=giphy.gif&ct=g)
+            transform: (?<=YEAR:\s)(?<from>\d{4})?-?(\d{4})?

.gitignore

@@ -49,3 +49,4 @@ po/*~
 rsconnect/
 inst/doc
 docs
+scratch.R

.lintr

@@ -1,6 +1,5 @@
 linters: all_linters(
     indentation_linter = NULL, # unstable as of lintr 3.1.0
-    extraction_operator_linter = NULL, # lints auto-generated vignette setup chunks
     implicit_integer_linter = NULL, # turn off due to multiple integerish values used
     duplicate_argument_linter = NULL, # due to cli_bullets
     object_name_linter = NULL, # due to S3 methods
@@ -20,8 +19,5 @@ exclusions: list(
     ),
     "vignettes" = list(
       undesirable_function_linter = Inf
-    ),
-    # do no attempt to lint auto-generated files
-    "R/RcppExports.R",
-    "R/cpp11.R"
+    )
   )

DESCRIPTION

@@ -1,15 +1,23 @@
-Package: vimc.rpkg.template
-Title: Your Package Title in Title Case
+Package: vimcheck
+Title: Diagnostics for Vaccination Modelling Burden and Impact Estimates
 Version: 0.0.0.9000
 Authors@R: c(
     person("Pratik", "Gupte", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5294-7819")),
+    person("Katy", "Gaythorpe", role = "aut",
+           comment = c(ORCID = "0000-0003-3734-9081")),
+    person("Xiang", "Li", role = "aut",
+           comment = c(ORCID = "0000-0002-5945-159X")),
+    person("Zoe", "Gibney", role = "aut"),
     person("Imperial College of Science, Technology and Medicine", role = c("cph", "fnd"))
   )
-Description: Your package description. It must end with a period (".") and
-    include relevant bibliographical references if applicable, using the
-    following format: Author et al. (2023) <doi:10.5281/zenodo.6619350>.
+Description: Run diagnostics on burden estimates submitted to the Vaccine
+    Impact Modelling Consortium (VIMC), and impacts estimated by VIMC, as
+    described in Echeverria-Londono et al.  (2021)
+    <doi:10.1186/s12889-021-12040-9>.
 License: MIT + file LICENSE
+URL: https://github.com/vimc/vimcheck, https://vimc.github.io/vimcheck/
+BugReports: https://github.com/vimc/vimcheck/issues
 Suggests: 
     knitr,
     rmarkdown,

NAMESPACE

@@ -1,3 +1,2 @@
 # Generated by roxygen2: do not edit by hand
 
-export(get_manual_mean)

NEWS.md

@@ -1,5 +1,5 @@
-# vimc.rpkg.template 0.0.1
+# vimcheck 0.0.1
 
-* This project now includes a
-   [`NEWS.md`](https://r-pkgs.org/other-markdown.html#sec-news) file to inform
-   users about changes and new features.
+- Added GHA workflows to notify of changed dependencies, auto-render `README.md` from `README.Rmd`, and update the copyright year annually.
+
+- Added reference to VIMC paper (Echeverria-Londono et al. 2021).

README.Rmd

@@ -1,6 +1,6 @@
 ---
 output: github_document
-# add bibliography here
+bibliography: vignettes/resources/references.json
 link-citations: true
 ---
 
@@ -15,40 +15,25 @@ knitr::opts_chunk$set(
 )
 ```
 
-# vimc.rpkg.template: TAGLINE
+# vimcheck: Diagnostics for vaccination modelling burden and impact estimates
 
 <!-- badges: start -->
 [![Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept)
-[![R build status](https://github.com/vimc/vimc.rpkg.template/workflows/R-CMD-check/badge.svg)](https://github.com/vimc/vimc.rpkg.template/actions/workflows/R-CMD-check.yaml)
-[![Codecov test coverage](https://codecov.io/gh/vimc/vimc.rpkg.template/branch/main/graph/badge.svg)](https://app.codecov.io/gh/vimc/vimc.rpkg.template?branch=main)
-[![CRAN status](https://www.r-pkg.org/badges/version/vimc.rpkg.template)](https://CRAN.R-project.org/package=vimc.rpkg.template)
+[![R build status](https://github.com/vimc/vimcheck/workflows/R-CMD-check/badge.svg)](https://github.com/vimc/vimcheck/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/vimc/vimcheck/branch/main/graph/badge.svg)](https://app.codecov.io/gh/vimc/vimcheck?branch=main)
+[![CRAN status](https://www.r-pkg.org/badges/version/vimcheck)](https://CRAN.R-project.org/package=vimcheck)
 <!-- badges: end -->
 
-_vimc.rpkg.template_ is a template package and repository on which future VIMC R packages are based.
-
-To use this template, select _vimc.rpkg.template_ from the drop-down menu under **Repository template** when creating a new repository in the VIMC GitHub organisation.
-Replace all instances of `"vimc.rpkg.template"` with your package name. Make sure to also:
-
-1. Edit the `DESCRIPTION` as appropriate with the correct package information, including authors;
-
-2. Edit the files in `R/`, `tests/`, and `vignettes/` to suit your package;
-
-3. Add spell check by running `usethis::use_spell_check(lang = "en-GB")`;
-
-4. Remove these instructions from `README.Rmd`, and re-render the `.md` file using `devtools::render_readme()`.
+_vimcheck_ is an R package for running diagnostic checks on burden estimates submitted to the Vaccine Impact Modelling Consortium (VIMC), and on impact estimates calculated by VIMC.
 
 ## Installation
 
-**NOTE:** Remove or comment out installation sources as appropriate.
-
-**Remember** to add the package to the [VIMC R-universe](https://github.com/vimc/vimc.r-universe.dev).
-
-You can install the development version of _vimc.rpkg.template_ from the VIMC R-universe with:
+You can install the development version of _vimcheck_ from the VIMC R-universe with:
 
 ```r
 installation from R-universe
 install.packages(
-  "vimc.rpkg.template", 
+  "vimcheck", 
   repos = c(
     "https://vimc.r-universe.dev", "https://cloud.r-project.org"
   )
@@ -59,18 +44,15 @@ or from GitHub [GitHub](https://github.com/) with:
 
 ``` r
 install.packages("pak")
-pak::pak("vimc/vimc.rpkg.template")
+pak::pak("vimc/vimcheck")
 ```
 
 ## Quick start
 
-Add a simple example of using the package's main feature(s) here, with a minimum amount of code.
-If preparatory or plotting steps are needed, prefer to hide them to keep focus on the package functionality.
+WIP.
 
 ## Related projects
 
-Add information and links to related projects, such as research papers or packages, here.
+VIMC impact assessment workflows are described in @echeverria-londono2021.
 
 ## References
-
-Space for references: REMOVE this text.