type: <fix> message: <minor fixes>

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

@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/pkgdown.yaml

@@ -1,48 +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
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    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@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Deploy package
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - 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

.github/workflows/pr-commands.yaml

@@ -0,0 +1,79 @@
+# 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:
+  issue_comment:
+    types: [created]
+
+name: Commands
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add \*.R
+          git commit -m 'Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test-coverage.yaml

@@ -1,48 +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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
 
-      - name: Query dependencies
+      - name: Test coverage
         run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         shell: Rscript {0}
 
-      - name: Restore R package cache
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
+      - name: Show testthat output
+        if: always()
         run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - name: Test coverage
-        run: covr::codecov(type = 'all')
-        shell: Rscript {0}
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

R/center_mlm.R

@@ -11,7 +11,7 @@
 #' @export
 #'
 #' @examples
-#' center_mlm(iris,ends_with('Length',group = 'Species')
+#' center_mlm(iris,dplyr::ends_with('Length'),group = 'Species')
 #'
 center_mlm = function(data,cols,group,keep_original = TRUE){
   data_names = names(data)
@@ -20,7 +20,7 @@ center_mlm = function(data,cols,group,keep_original = TRUE){
   group_name = data %>% dplyr::select(!!enquo(group)) %>% names()
 
   mean_data = data %>%
-    dplyr::group_by(across(!!group)) %>% 
+    dplyr::group_by(dplyr::across(!!group)) %>% 
     dplyr::summarise(dplyr::across(!!cols,~mean(.,na.rm = T))) %>%
     dplyr::mutate(dplyr::across(!!cols, function(x) { (x - mean(x,na.rm = TRUE))})) %>% 
     dplyr::ungroup() %>% 
@@ -37,7 +37,7 @@ center_mlm = function(data,cols,group,keep_original = TRUE){
   }
 
   return_data = dplyr::full_join(centered_data,mean_data,by = group_name) %>% 
-    dplyr::select(c(all_of(data_names),dplyr::ends_with('group_c'),dplyr::ends_with('_mean'),dplyr::everything()))
+    dplyr::select(c(dplyr::all_of(data_names),dplyr::ends_with('group_c'),dplyr::ends_with('_mean'),dplyr::everything()))
 
 
   return(return_data)    

R/dummy_coding.R

@@ -8,32 +8,21 @@
 #' @export
 #'
 #' @examples
-#' effect_coding(iris,Species)
-#' Dummy Coding
-#'
-#' @param data data.frame object 
-#' @param cols vector or tidyselect syntax or helpers. column(s) that need to be re-coded
-#'
-#' @return
-#' return a data.frame with factors being effect coded
-#' @export
-#'
-#' @examples
 #' dummy_coding(iris,Species)
 #' 
 dummy_coding <- function(data,cols) {
-  cols_names = data %>% select(!!enquo(cols)) %>% names()
+  cols_names = data %>%dplyr::select(!!enquo(cols)) %>% names()
   return_df = data
   for (group in cols_names) {
-    group_name = data %>% select(!!enquo(group)) %>% names()
-    distinct_group = data %>% distinct(across(!!enquo(group))) %>% pull(.) %>% as.character()
-    distinct_group_num = data %>% distinct(across(!!enquo(group))) %>% nrow()
-    contrasts_df = data.frame(contr.treatment(distinct_group_num,base = distinct_group_num))
+    group_name = data %>%dplyr::select(!!enquo(group)) %>% names()
+    distinct_group = data %>% dplyr::distinct(dplyr::across(!!enquo(group))) %>%dplyr::pull(.) %>% as.character()
+    distinct_group_num = data %>% dplyr::distinct(dplyr::across(!!enquo(group))) %>% nrow()
+    contrasts_df = data.frame(stats::contr.treatment(distinct_group_num,base = distinct_group_num))
     colnames(contrasts_df) = paste0(group_name,'_',distinct_group[1:nrow(contrasts_df)-1],'_dum')
     dummy_coded_df = contrasts_df %>% 
-      mutate(group = distinct_group) %>% 
-      rename(!!enquo(group):=group)
-    return_df = full_join(return_df,dummy_coded_df)
+     dplyr::mutate(group = distinct_group) %>% 
+     dplyr::rename(!!enquo(group):=group)
+    return_df =dplyr::full_join(return_df,dummy_coded_df)
   }
   return(return_df)
 }

R/effect_coding.R

@@ -9,6 +9,7 @@
 #'
 #' @examples
 #' effect_coding(iris,Species)
+#' 
 effect_coding = function(data,cols,factor = TRUE){
   if (factor == TRUE) {
     names = data %>% dplyr::select(!!enquo(cols)) %>% colnames(.)
@@ -18,18 +19,18 @@ effect_coding = function(data,cols,factor = TRUE){
     }
     return(return_df) 
   } else if(factor == FALSE){
-    cols_names = data %>% select(!!enquo(cols)) %>% names()
+    cols_names = data %>%dplyr::select(!!enquo(cols)) %>% names()
     return_df = data
     for (group in cols_names) {
-      group_name = data %>% select(!!enquo(group)) %>% names()
-      distinct_group = data %>% distinct(across(!!enquo(group))) %>% pull(.) %>% as.character()
-      distinct_group_num = data %>% distinct(across(!!enquo(group))) %>% nrow()
-      contrasts_df = data.frame(contr.sum(distinct_group_num))
+      group_name = data %>% dplyr::select(!!enquo(group)) %>% names()
+      distinct_group = data %>% dplyr::distinct(dplyr::across(!!enquo(group))) %>%dplyr::pull(.) %>% as.character()
+      distinct_group_num = data %>% dplyr::distinct(dplyr::across(!!enquo(group))) %>% nrow()
+      contrasts_df = data.frame(stats::contr.sum(distinct_group_num))
       colnames(contrasts_df) = paste0(group_name,'_',distinct_group[1:nrow(contrasts_df)-1],'_eff')
       dummy_coded_df = contrasts_df %>% 
-        mutate(group = distinct_group) %>% 
-        rename(!!enquo(group):=group)
-      return_df = full_join(return_df,dummy_coded_df)
+       dplyr::mutate(group = distinct_group) %>% 
+       dplyr::rename(!!enquo(group):=group)
+      return_df =dplyr::full_join(return_df,dummy_coded_df)
     }
     return(return_df)