set up infrastruct

.Rbuildignore

@@ -2,3 +2,7 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^README\.Rmd$
+^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/.gitignore

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

.github/workflows/R-CMD-check.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:
+    branches: [main, master]
+
+name: R-CMD-check
+
+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: 'devel', http-user-agent: '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: ${{ 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

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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
+
+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/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -1 +1,2 @@
 .Rproj.user
+docs

DESCRIPTION

@@ -14,5 +14,5 @@ RoxygenNote: 7.2.3
 Imports: 
     stats,
     utils
-URL: https://github.com/capro-uio/freesurfer.lme
+URL: https://github.com/capro-uio/freesurfer.lme, http://www.capro.dev/freesurfer.lme/
 BugReports: https://github.com/capro-uio/freesurfer.lme/issues

NAMESPACE

@@ -1,3 +1,4 @@
 # Generated by roxygen2: do not edit by hand
 
 export(make_qdec)
+export(scale_vec)

R/qdec.R

@@ -45,6 +45,9 @@ make_qdec <- function(data, formula, path = NULL) {
 #' @param ... additional arguments to be passed to \code{\link{scale}}
 #'
 #' @return scaled vector
+#' @export
+#' @examples
+#' scale_vec(1:20)
 scale_vec <- function(x, ...) {
   # Error if x has more than one dimension
   if(!is.null(dim(x))){

README.Rmd

@@ -16,6 +16,7 @@ knitr::opts_chunk$set(
 # freesurfer.lme
 
 <!-- badges: start -->
+[![R-CMD-check](https://github.com/capro-uio/freesurfer.lme/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/capro-uio/freesurfer.lme/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 Running vertex-wise linear mixed effects models in [Freesurfer](https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) requires a specific file format. 

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: http://www.capro.dev/freesurfer.lme/
+template:
+  bootstrap: 5
+