Merge pull request #9 from oxford-pharmacoepi/issue_7

add website

.Rbuildignore

@@ -4,3 +4,6 @@
 ^\.github$
 ^README\.Rmd$
 ^data-raw$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

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

@@ -18,11 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {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:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pkgdown.yaml

@@ -0,0 +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: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    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@v4
+
+      - 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::.
+          needs: website
+
+      - 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/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -3,3 +3,4 @@
 .Rdata
 .httr-oauth
 .DS_Store
+docs

DESCRIPTION

@@ -17,6 +17,7 @@ Imports:
     CDMConnector (>= 1.3.0),
     checkmate,
     cli,
+    CohortCharacteristics,
     dplyr,
     IncidencePrevalence (>= 0.7.0),
     lubridate,
@@ -28,3 +29,4 @@ Imports:
     visOmopResults
 Depends: 
     R (>= 2.10)
+URL: https://oxford-pharmacoepi.github.io/OmopSketch/

R/summariseEntryCharacteristics.R

@@ -34,7 +34,7 @@ summariseEntryCharacteristics <- function(cdm, byYear = FALSE) {
     strata <- list()
   }
   result <- cohort |>
-    PatientProfiles::summariseCharacteristics(strata = strata) |>
+    CohortCharacteristics::summariseCharacteristics(strata = strata) |>
     dplyr::filter(.data$variable_name != "Prior observation") |>
     dplyr::mutate(
       "variable_name" = dplyr::if_else(

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://oxford-pharmacoepi.github.io/OmopSketch/
+template:
+  bootstrap: 5
+