Merge pull request #120 from rsquaredacademy/develop

Migrations

.Rbuildignore

@@ -13,3 +13,4 @@
 ^hex_blorr\.png$
 ^cran-comments\.md$
 ^\.github$
+^Meta$

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

@@ -1,16 +1,14 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# 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:
-      - master
-      - develop
+    branches: [master, develop]
   pull_request:
-    branches:
-      - master
-      - develop
+    branches: [master, develop]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -22,63 +20,33 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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-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}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        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-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.github/workflows/test-coverage.yaml

@@ -1,48 +1,61 @@
+# 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:
-      - master
-      - develop
+    branches: [master, develop]
   pull_request:
-    branches:
-      - master
-      - develop
+    branches: [master, develop]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 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@v4
 
-      - 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, any::xml2
+          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")
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: codecov/codecov-action@v4
         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
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
         run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -3,3 +3,5 @@
 .RData
 .Ruserdata
 inst/doc
+/doc/
+/Meta/

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: blorr
 Type: Package
 Title: Tools for Developing Binary Logistic Regression Models
-Version: 0.3.0.9000
+Version: 0.3.1
 Authors@R: person("Aravind", "Hebbali", email = "[email protected]", role = c("aut", "cre"), 
     comment = c(ORCID = "0000-0001-9220-9669"))
 Description: Tools designed to make it easier for beginner and intermediate users to build and validate 
@@ -25,14 +25,15 @@ Suggests:
     knitr,
     magrittr,
     rmarkdown,
-    testthat,
+    testthat (>= 3.0.0),
     vdiffr,
     xplorerr
 License: MIT + file LICENSE
-URL: URL: https://blorr.rsquaredacademy.com/, https://github.com/rsquaredacademy/blorr
+URL: https://blorr.rsquaredacademy.com/, https://github.com/rsquaredacademy/blorr
 BugReports: https://github.com/rsquaredacademy/blorr/issues
 VignetteBuilder: knitr
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.0
+RoxygenNote: 7.3.2
 LinkingTo: Rcpp
+Config/testthat/edition: 3

R/blr-bivariate-analysis.R

@@ -335,10 +335,10 @@ plot.blr_segment_dist <- function(x, title = NA, xaxis_title = "Levels",
       breaks   = seq(0, 1, by = 0.1),
       labels   = paste0(seq(0, 1, by = 0.1) * 100, '%'),
       sec.axis = sec_axis(
-        trans  = ~.,
-        breaks = seq(0, 1, by = 0.1),
-        labels = paste0(seq(0, 1, by = 0.1) * 100, '%'),
-        name   = sec_yaxis_title))
+        transform = ~.,
+        breaks    = seq(0, 1, by = 0.1),
+        labels    = paste0(seq(0, 1, by = 0.1) * 100, '%'),
+        name      = sec_yaxis_title))
 
   if (print_plot) {
     print(p)

R/blr-blorr.R

@@ -5,8 +5,11 @@
 #' See the README on
 #' \href{https://github.com/rsquaredacademy/blorr}{GitHub}
 #'
+#' @keywords internal
 #' @docType package
 #' @name blorr
+#' @aliases blorr-package
+"_PACKAGE"
 NULL
 
 ## quiets concerns of R CMD check re: the .'s that appear in pipelines

R/blr-data-hsb.R

@@ -19,6 +19,6 @@
 #'   \item{honcomp}{1 if write > 60, else 0}
 #' }
 #'
-#' @source \url{http://www.ats.ucla.edu/stat/spss/whatstat/whatstat.htm}
+#' @source \url{https://www.openintro.org/data/index.php?data=hsb}
 #'
-"hsb2"
+"hsb2"

R/blr-gains-table.R

@@ -128,9 +128,7 @@ plot.blr_gains_table <- function(x, title = "Lift Chart", xaxis_title = "% Popul
 #' @param print_plot logical; if \code{TRUE}, prints the plot else returns a plot object.
 #'
 #' @references
-#' \url{https://doi.org/10.1198/tast.2009.08210}
-#'
-#' \url{https://www.ncbi.nlm.nih.gov/pubmed/843576}
+#' \url{https://pubmed.ncbi.nlm.nih.gov/843576/}
 #'
 #' @examples
 #' model <- glm(honcomp ~ female + read + science, data = hsb2,

R/blr-lorenz-curve.R

@@ -16,8 +16,6 @@
 #' Müller M, Rönz B (2000): Credit Scoring using Semiparametric Methods. In: Franke J, Härdle W, Stahl G (Eds.):
 #' Measuring Risk in Complex Stochastic Systems. New York, Springer-Verlag.
 #'
-#' \url{https://doi.org/10.2753/REE1540-496X470605}
-#'
 #' @examples
 #' model <- glm(honcomp ~ female + read + science, data = hsb2,
 #' family = binomial(link = 'logit'))

R/blr-pairs.R

@@ -6,11 +6,6 @@
 #'
 #' @return A tibble.
 #'
-#' @references
-#' \url{https://doi.org/10.1080/10485259808832744}
-#'
-#' \url{https://doi.org/10.1177/1536867X0600600302}
-#'
 #' @examples
 #' model <- glm(honcomp ~ female + read + science, data = hsb2,
 #' family = binomial(link = 'logit'))