R cmd check and io website

.Rbuildignore

@@ -0,0 +1 @@
+^LICENSE\.md$

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,54 @@
+# 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
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          #r-version: 4.4.1
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with: 
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          error-on: '"error"'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,46 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub Pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs  # Jekyll outputs to the _site folder by default

.gitignore

@@ -0,0 +1,3 @@
+src/rsvie.so
+src/RunInterventions.o
+src/RcppExports.o

DESCRIPTION

@@ -5,39 +5,44 @@ Authors@R:
     person("David", "Hodgson", , "david.hodgson@lshtm.ac.uk", role = c("aut", "cre"),
            comment = c(ORCID = "YOUR-ORCID-ID"))
 Description: What the package does (one paragraph).
-License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
-    license
+License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Depends:
     R (>= 4.2)
 Imports: 
+    methods,
     here,
     lubridate,
     ggplot2,
     Rcpp,
     patchwork,
     RcppEigen,
-    Rcpp,
     dplyr,
     forcats,
     tidyr,
     pacman,
     RColorBrewer,
     EnvStats,
     BH,
-    magrittr
+    magrittr,
+    data.table,
+    furrr,
+    future, 
+    purrr, 
+    readr,
+    stringr
 Suggests:
-    gifski,
-    learnr,
+    knitr,
+    rmarkdown,
     usethis,
     roxygen2,
     devtools,
-    magrittr,
     testthat (>= 3.0.0)
 LinkingTo:
     Rcpp,
     RcppEigen,
     BH
+VignetteBuilder: knitr
 Config/testthat/edition: 3