Merge pull request #77 from olivroy/upkeep

Upkeep - fix doc issues + update CI + drop crayon

.Rbuildignore

@@ -21,4 +21,5 @@
 ^hex\.png$
 ^LICENSE\.md$
 ^\.github$
-^pkgdown$
+^pkgdown$
+^interactions\.Rproj$

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

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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:
@@ -8,6 +8,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -18,7 +20,7 @@ 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 +31,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,26 +43,10 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
-
-      - name: Set CRAN mirror
-        run: echo "options(repos = c(CRAN='https://cloud.r-project.org/'))" > ~/.Rprofile
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Install lme4 from source to fix Matrix errors
-        run: | 
-          install.packages('lme4', type = 'source')
-        shell: Rscript {0}
-
       - uses: r-lib/actions/check-r-package@v2
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
         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/pkgdown.yaml

@@ -1,29 +1,31 @@
-# Jacob copied from https://github.com/r-lib/pkgdown/blob/main/.github/workflows/pkgdown.yaml 
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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]
     tags: ['*']
   pull_request:
-    branches: [master, main]
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
-    if: github.event_name == 'push' || github.event.pull_request.head.repo.fork == false
     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 }}
-      NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
-      NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
-      isPush: ${{ github.event_name == 'push' }}
-
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
-
-      - uses: r-lib/actions/setup-tinytex@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -38,7 +40,7 @@ jobs:
 
       - name: Install package
         run: R CMD INSTALL .
-
+  
       - name: Build and deploy pkgdown site
         if: contains(env.isPush, 'true')
         run: |
@@ -50,7 +52,7 @@ jobs:
         run: |
           pkgdown::build_site()
         shell: Rscript {0}
-
+  
       - name: Create index file
         if: contains(env.isPush, 'false')
         run: |

.github/workflows/test-coverage.yaml

@@ -8,43 +8,54 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          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: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -16,8 +16,8 @@ URL: https://interactions.jacob-long.com
 BugReports: https://github.com/jacob-long/interactions/issues 
 License: MIT + file LICENSE
 Encoding: UTF-8
-Imports: ggplot2,
-  crayon,
+Imports:
+  ggplot2 (>= 3.4.0),
   cli,
   generics,
   jtools (>= 2.0.3),
@@ -26,17 +26,17 @@ Imports: ggplot2,
 Suggests:
   broom,
   cowplot,
-  ggstance,
+  broom.mixed,
   glue,
   huxtable (>= 3.0.0),
   lme4,
   margins,
   sandwich,
   survey,
-    knitr,
-    rmarkdown,
-    testthat,
-    vdiffr
+  knitr,
+  rmarkdown,
+  testthat,
+  vdiffr
 Enhances:
   brms,
   rstanarm

NAMESPACE

@@ -37,11 +37,6 @@ import(jtools)
 import(rlang)
 importFrom(cli,cat_rule)
 importFrom(cli,rule)
-importFrom(crayon,bold)
-importFrom(crayon,inverse)
-importFrom(crayon,italic)
-importFrom(crayon,red)
-importFrom(crayon,underline)
 importFrom(generics,glance)
 importFrom(generics,tidy)
 importFrom(stats,aggregate)

R/interact_plot.R

@@ -136,8 +136,8 @@
 #'   appears above the legend. If \code{NULL}, the name of the moderating
 #'   variable is used.
 #'
-#' @param colors See [jtools_colors] for details on the types of arguments
-#'    accepted. Default is "CUD Bright" for factor
+#' @param colors See [`jtools_colors`][jtools::jtools_colors] for details on the
+#'    types of arguments accepted. Default is "CUD Bright" for factor
 #'    moderators, "Blues" for +/- SD and user-specified \code{modx.values}
 #'    values.
 #'
@@ -446,11 +446,14 @@ interact_plot <- function(model, pred, modx, modx.values = NULL, mod2 = NULL,
   # Check for factor predictor and send to plot_cat() if so
   if (!is.numeric(d[[pred]])) {
     # Warn users that this is kinda janky
-    msg_wrap("Detected factor predictor. Plotting with cat_plot() instead.
-              Consult cat_plot() documentation (?cat_plot) for full details
-              on how to specify models with categorical predictors. If you 
-              experience errors or unexpected results, try using cat_plot() 
-              directly.")
+    cli::cli_inform(c(
+      x = "Detected factor predictor.",
+      i = "Plotting with cat_plot() instead.",
+      i = "See {.help interactions::cat_plot} for full details on 
+         how to specify models with categorical predictors.",
+      i = "If you  experience errors or unexpected results, try using 
+           cat_plot() directly."
+    ))
     # Gather arguments for plot_cat()
     args <- list(predictions = pm, pred = pred, modx = modx, mod2 = mod2,
                   data = d, modx.values = modxvals2, mod2.values = mod2vals2,

R/johnson_neyman.R

@@ -622,17 +622,16 @@ johnson_neyman <- function(model, pred, modx, vmat = NULL, alpha = 0.05,
 }
 
 #' @export
-#' @importFrom crayon bold inverse underline
 
 print.johnson_neyman <- function(x, ...) {
 
   atts <- attributes(x)
 
   # Describe whether sig values are inside/outside the interval
   if (atts$inside == FALSE) {
-    inout <- inverse("OUTSIDE")
+    inout <- cli::style_inverse("OUTSIDE")
   } else {
-    inout <- inverse("INSIDE")
+    inout <- cli::style_inverse("INSIDE")
   }
 
   b_format <- num_print(x$bounds, atts$digits)
@@ -641,13 +640,16 @@ print.johnson_neyman <- function(x, ...) {
   pmsg <- paste("p <", alpha)
 
   # Print the output
-  cat(bold(underline("JOHNSON-NEYMAN INTERVAL")), "\n\n")
+  cli::cat_line(
+    cli::style_bold(cli::style_underline("JOHNSON-NEYMAN INTERVAL")),
+    "\n"
+  )
   if (all(is.finite(x$bounds))) {
     cat_wrap("When ", atts$modx, " is ", inout, " the interval [",
              b_format[1], ", ", b_format[2], "], the slope of ", atts$pred,
              " is ", pmsg, ".", brk = "\n\n")
-    cat_wrap(italic("Note: The range of observed values of", atts$modx,
-        "is "), "[", m_range[1], ", ", m_range[2], "]", brk = "\n\n")
+    cat_wrap(cli::style_italic("Note: The range of observed values of ", atts$modx,
+        " is "), "[", m_range[1], ", ", m_range[2], "]", brk = "\n\n")
   } else {
     cat_wrap("The Johnson-Neyman interval could not be found.
         Is the p value for your interaction term below

R/simple_margins.R

@@ -247,7 +247,6 @@ sim_margins <- function(model, pred, modx, mod2 = NULL, modx.values = NULL,
 
 #' @export
 #' @importFrom cli cat_rule rule
-#' @importFrom crayon red bold italic
 
 print.sim_margins <- function(x, ...) {
 
@@ -308,7 +307,10 @@ print.sim_margins <- function(x, ...) {
     }
 
     # Clearly label simple slopes
-    cat(bold(underline("SIMPLE MARGINS")), "\n\n")
+    cli::cat_line(
+      cli::style_bold(cli::style_underline("SIMPLE MARGINS")),
+      "\n"
+    )
 
     for (i in seq_along(x$modx.values)) {
 
@@ -329,8 +331,8 @@ print.sim_margins <- function(x, ...) {
         modx_label <- paste0(m[i, x$modx])
       }
 
-      cat(italic(paste0("Average marginal effect of ", x$pred, " when ",
-                        x$modx, " = ", modx_label, ": \n\n")))
+      cli::cat_line(cli::style_italic(paste0("Average marginal effect of ", x$pred, " when ",
+                        x$modx, " = ", modx_label, ": \n")))
       print(md_table(slopes, digits = x$digits, format = "pandoc",
                      row.names = FALSE, sig.digits = FALSE))
 

R/simple_slopes.R

@@ -775,7 +775,6 @@ sim_slopes <- function(model, pred, modx, mod2 = NULL, modx.values = NULL,
 
 #' @export
 #' @importFrom cli cat_rule rule
-#' @importFrom crayon red bold italic
 
 print.sim_slopes <- function(x, ...) {
 
@@ -859,7 +858,10 @@ print.sim_slopes <- function(x, ...) {
     }
 
     # Clearly label simple slopes
-    cat(bold(underline("SIMPLE SLOPES ANALYSIS")), "\n\n")
+    cli::cat_line(
+      cli::style_bold(cli::style_underline("SIMPLE SLOPES ANALYSIS")),
+      "\n"
+    )
 
     for (i in seq_along(x$modx.values)) {
 
@@ -882,7 +884,7 @@ print.sim_slopes <- function(x, ...) {
       # Print conditional intercept
       if (x$cond.int == TRUE | fac_pred == TRUE) {
         pred_lab <- if (fac_pred) {slopes[["Coef."]]} else {x$pred}
-        cat(italic(paste0("When ", x$modx, " = ", modx_label, ": \n\n")))
+        cli::cat_line(cli::style_italic(paste0("When ", x$modx, " = ", modx_label, ": \n")))
         if (x$cond.int) {
           ints <- m$ints[i,2:ncol(m$slopes)]
           slopes <- as.data.frame(rbind(slopes, ints))
@@ -895,8 +897,8 @@ print.sim_slopes <- function(x, ...) {
         print(md_table(slopes %not% "Coef.", digits = x$digits,
                        format = "pandoc", sig.digits = FALSE))
       } else {
-        cat(italic(paste0("Slope of ", x$pred, " when ", x$modx, " = ",
-                          modx_label, ": \n\n")))
+        cli::cat_line(cli::style_italic(paste0("Slope of ", x$pred, " when ", x$modx, " = ",
+                          modx_label, ": \n")))
         print(md_table(slopes, digits = x$digits, format = "pandoc",
                        row.names = FALSE, sig.digits = FALSE))
       }
@@ -1036,7 +1038,7 @@ nobs.sim_slopes <- function(object, ...) {
 #' @param x The [sim_slopes()] object.
 #' @param format The method for sharing the slope and associated uncertainty.
 #'  Default is `"{estimate} ({std.error})"`. See the instructions for the
-#'  `error_format` argument of [export_summs()] for more on your
+#'  `error_format` argument of [jtools::export_summs()] for more on your
 #'  options.
 #' @param sig.levels A named vector in which the values are potential p value
 #'  thresholds and the names are significance markers (e.g., "*") for when