Create documentation website using GitHub Pages

.Rbuildignore

@@ -3,3 +3,7 @@
 ^LICENSE\.md$
 ^data-raw$
 ^README\.Rmd$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,47 @@
+# 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:
+
+name: R-CMD-check.yaml
+
+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: ubuntu-latest,   r: 'release'}
+
+    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: ${{ 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")'

.github/workflows/pkgdown.yaml

@@ -0,0 +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]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+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

@@ -6,3 +6,4 @@
 *.pdf
 
 inst/doc
+docs

DESCRIPTION

@@ -10,7 +10,7 @@ License: Apache License (>= 2)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-URL: https://github.com/SAFEHR-data/omopcept
+URL: https://SAFEHR-data.github.io/omopcept/
 BugReports: https://github.com/SAFEHR-data/omopcept/issues
 Depends: 
     R (>= 3.5.0)

README.Rmd

@@ -19,6 +19,7 @@ knitr::opts_chunk$set(
 # omopcept
 
 <!-- badges: start -->
+[![R-CMD-check](https://github.com/SAFEHR-data/omopcept/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/SAFEHR-data/omopcept/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 **Active development 2025, breaking changes possible**     

README.md

@@ -5,6 +5,8 @@
 # omopcept
 
 <!-- badges: start -->
+
+[![R-CMD-check](https://github.com/SAFEHR-data/omopcept/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/SAFEHR-data/omopcept/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 **Active development 2025, breaking changes possible**
@@ -153,16 +155,16 @@ omop_names("chemotherapy", v_ids="LOINC")
 #> # A tibble: 71 × 10
 #>    concept_id concept_name              domain_id vocabulary_id concept_class_id
 #>         <int> <chr>                     <chr>     <chr>         <chr>           
-#>  1   45882419 A proper value is applic… Meas Val… LOINC         Answer          
-#>  2   45882273 Information is not avail… Meas Val… LOINC         Answer          
-#>  3   45884441 No information whatsoeve… Meas Val… LOINC         Answer          
-#>  4   45884440 No proper value is appli… Meas Val… LOINC         Answer          
-#>  5   45881771 Received cancer chemothe… Meas Val… LOINC         Answer          
-#>  6   45884510 Chemotherapy/medication … Meas Val… LOINC         Answer          
-#>  7   36309148 Currently receiving chem… Meas Val… LOINC         Answer          
-#>  8    1035179 Chemotherapy - IV         Meas Val… LOINC         Answer          
-#>  9    1035159 Chemotherapy - Oral       Meas Val… LOINC         Answer          
-#> 10    1035128 Chemotherapy - Other      Meas Val… LOINC         Answer          
+#>  1    1035179 Chemotherapy - IV         Meas Val… LOINC         Answer          
+#>  2    1035159 Chemotherapy - Oral       Meas Val… LOINC         Answer          
+#>  3    1035128 Chemotherapy - Other      Meas Val… LOINC         Answer          
+#>  4   45882480 Chemotherapy, NOS         Meas Val… LOINC         Answer          
+#>  5   45876436 Chemotherapy Administered Meas Val… LOINC         Answer          
+#>  6   45884295 Unknown if any chemother… Meas Val… LOINC         Answer          
+#>  7   45880125 No chemotherapy administ… Meas Val… LOINC         Answer          
+#>  8   45879751 Chemotherapy              Meas Val… LOINC         Answer          
+#>  9   45882373 Chemotherapy spill        Meas Val… LOINC         Answer          
+#> 10   45878374 Chemotherapy, single age… Meas Val… LOINC         Answer          
 #> # ℹ 61 more rows
 #> # ℹ 5 more variables: standard_concept <chr>, concept_code <chr>,
 #> #   valid_start_date <date>, valid_end_date <date>, invalid_reason <chr>
@@ -171,16 +173,16 @@ omop_names("chemotherapy", v_ids=c("LOINC","SNOMED"), d_ids=c("Observation","Pro
 #> # A tibble: 316 × 10
 #>    concept_id concept_name              domain_id vocabulary_id concept_class_id
 #>         <int> <chr>                     <chr>     <chr>         <chr>           
-#>  1    3046488 Chemotherapy [Minimum Da… Observat… LOINC         Survey          
-#>  2   40768860 Cancer chemotherapy rece… Observat… LOINC         Clinical Observ…
-#>  3   36303659 Guidance for chemoemboli… Procedure LOINC         Clinical Observ…
-#>  4    1024644 Guidance for chemoemboli… Observat… LOINC         LOINC Component 
-#>  5    1030274 Chemotherapy              Observat… LOINC         LOINC Component 
-#>  6    1034150 Chemotherapy in last 14 … Observat… LOINC         LOINC Component 
-#>  7    1034151 Chemotherapy in last 14 … Observat… LOINC         LOINC Component 
-#>  8    3010410 Chemotherapy records      Observat… LOINC         Clinical Observ…
-#>  9    3011998 Date 1st chemotherapy tr… Observat… LOINC         Clinical Observ…
-#> 10   40758122 Chemotherapy in last 14 … Observat… LOINC         Survey          
+#>  1   36305649 Chemotherapy infusion st… Observat… LOINC         Clinical Observ…
+#>  2   36305185 Chemotherapy infusion st… Observat… LOINC         Clinical Observ…
+#>  3   36305554 Chemotherapy infusion st… Observat… LOINC         Clinical Observ…
+#>  4   36305537 Chemotherapy infusion st… Observat… LOINC         Clinical Observ…
+#>  5   36660670 Cancer chemotherapy rece… Observat… LOINC         Clinical Observ…
+#>  6    3046488 Chemotherapy [Minimum Da… Observat… LOINC         Survey          
+#>  7   40768860 Cancer chemotherapy rece… Observat… LOINC         Clinical Observ…
+#>  8   36303659 Guidance for chemoemboli… Procedure LOINC         Clinical Observ…
+#>  9    1024644 Guidance for chemoemboli… Observat… LOINC         LOINC Component 
+#> 10    1004252 Flag for Date 1st chemot… Observat… LOINC         LOINC Component 
 #> # ℹ 306 more rows
 #> # ℹ 5 more variables: standard_concept <chr>, concept_code <chr>,
 #> #   valid_start_date <date>, valid_end_date <date>, invalid_reason <chr>
@@ -237,6 +239,12 @@ relations <- omop_relations(sharp$concept_id,
 
 omop_graph(relations, saveplot=FALSE, graphtitle=NULL, 
            legendshow=FALSE, nodetxtsize=5, textcolourvar="step")
+#> 
+#> The downloaded binary packages are in
+#>  /var/folders/pl/k11lm9710hlgl02nvzx4z9wr0000gp/T//RtmpDoD4KN/downloaded_packages
+#> 
+#> The downloaded binary packages are in
+#>  /var/folders/pl/k11lm9710hlgl02nvzx4z9wr0000gp/T//RtmpDoD4KN/downloaded_packages
 ```
 
 <img src="man/figures/README-omop_graph-1.png" width="100%" />

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://catalamarti.github.io/omopcept/
+template:
+  bootstrap: 5
+