Merge branch 'master' into MichaelChirico-patch-1

.Rbuildignore

@@ -1 +1,2 @@
 ^\.github$
+^codecov\.yml$

.github/.gitignore

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

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

@@ -8,9 +8,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -24,20 +25,20 @@ jobs:
         config:
           - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
-          # use 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: '4.1'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
 
+          # use 4.0 or 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: 'oldrel-4'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -46,6 +47,7 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
+          working-directory: pkg/caret
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -56,4 +58,5 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
           working-directory: pkg/caret

.github/workflows/pr-commands.yaml

@@ -4,7 +4,9 @@ on:
   issue_comment:
     types: [created]
 
-name: Commands
+name: pr-commands.yaml
+
+permissions: read-all
 
 jobs:
   document:
@@ -13,8 +15,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -51,8 +55,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

.github/workflows/test-coverage.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,38 +16,50 @@ jobs:
       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
+          working-directory: pkg/caret
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
           working-directory: pkg/caret
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
             path = "pkg/caret",
-            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 if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+          working-directory: pkg/caret
+
       - 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

README.md

@@ -1,5 +1,5 @@
-[![R-CMD-check](https://github.com/topepo/caret/workflows/R-CMD-check/badge.svg)](https://github.com/topepo/caret/actions)
-[![Coverage Status](https://coveralls.io/repos/topepo/caret/badge.svg?branch=master)](https://coveralls.io/r/topepo/caret?branch=master)
+![R-CMD-check](https://github.com/topepo/caret/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/topepo/caret/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/topepo/caret/graph/badge.svg)](https://app.codecov.io/gh/topepo/caret)
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/caret)](http://cran.r-project.org/web/packages/caret)
 [![Downloads](http://cranlogs.r-pkg.org/badges/caret)](http://cran.rstudio.com/package=caret)
 

pkg/caret/DESCRIPTION

@@ -107,11 +107,10 @@ Suggests:
     rmarkdown,
     rpart,
     spls,
-    subselect,
     superpc,
     testthat (>= 0.9.1),
     themis (>= 0.1.3)
 VignetteBuilder: 
     knitr
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2

pkg/caret/R/calibration.R

@@ -16,8 +16,8 @@
 #' \code{envir} argument in \code{eval}, e.g., a list or an environment) containing values for any
 #' variables in the formula, as well as \code{groups} and \code{subset} if applicable. If not found in
 #' \code{data}, or if \code{data} is unspecified, the variables are looked for in the environment of the
-#' formula. This argument is not used for \code{xyplot.calibration}. For {ggplot.calibration}, \code{data}
-#' should be an object of class "\code{calibration}"."
+#' formula. This argument is not used for \code{xyplot.calibration}. For \code{ggplot.calibration}, \code{data}
+#' should be an object of class "\code{calibration}".
 #'
 #' @param class a character string for the class of interest
 #'

pkg/caret/R/findCorrelation.R

@@ -6,13 +6,13 @@ findCorrelation_fast <- function(x, cutoff = .90, verbose = FALSE){
   averageCorr <- as.numeric(as.factor(averageCorr))
   x[lower.tri(x, diag = TRUE)] <- NA
   combsAboveCutoff <- which(abs(x) > cutoff)
-  
+
   colsToCheck <- ceiling(combsAboveCutoff / nrow(x))
   rowsToCheck <- combsAboveCutoff %% nrow(x)
-  
+
   colsToDiscard <- averageCorr[colsToCheck] > averageCorr[rowsToCheck]
   rowsToDiscard <- !colsToDiscard
-  
+
   if(verbose){
     colsFlagged <- pmin(ifelse(colsToDiscard, colsToCheck, NA),
                         ifelse(rowsToDiscard, rowsToCheck, NA), na.rm = TRUE)
@@ -22,7 +22,7 @@ findCorrelation_fast <- function(x, cutoff = .90, verbose = FALSE){
                    '\n \t Flagging column', colsFlagged, '\n'
     ))
   }
-  
+
   deletecol <- c(colsToCheck[colsToDiscard], rowsToCheck[rowsToDiscard])
   deletecol <- unique(deletecol)
   deletecol
@@ -31,29 +31,29 @@ findCorrelation_fast <- function(x, cutoff = .90, verbose = FALSE){
 findCorrelation_exact <- function(x, cutoff = 0.90, verbose = FALSE)
 {
   varnum <- dim(x)[1]
-  
+
   if (!isTRUE(all.equal(x, t(x)))) stop("correlation matrix is not symmetric")
   if (varnum == 1) stop("only one variable given")
-  
+
   x <- abs(x)
-  
+
   # re-ordered columns based on max absolute correlation
   originalOrder <- 1:varnum
-  
+
   averageCorr <- function(x) mean(x, na.rm = TRUE)
   tmp <- x
   diag(tmp) <- NA
-  
+
   maxAbsCorOrder <- order(apply(tmp, 2, averageCorr), decreasing = TRUE)
   x <- x[maxAbsCorOrder, maxAbsCorOrder]
   newOrder <- originalOrder[maxAbsCorOrder]
   rm(tmp)
-  
+
   deletecol <- rep(FALSE, varnum)
-  
+
   x2 <- x
   diag(x2) <- NA
-  
+
   for (i in 1:(varnum - 1)) {
     if(!any(x2[!is.na(x2)] > cutoff)){
       if (verbose) cat("All correlations <=", cutoff, "\n")
@@ -62,13 +62,13 @@ findCorrelation_exact <- function(x, cutoff = 0.90, verbose = FALSE)
     if (deletecol[i]) next
     for (j in (i + 1):varnum) {
       if (!deletecol[i] & !deletecol[j]) {
-        
+
         if (x[i, j] > cutoff) {
           mn1 <- mean(x2[i,], na.rm = TRUE)
           mn2 <- mean(x2[-j,], na.rm = TRUE)
-          if(verbose) cat("Compare row", newOrder[i], 
-                          " and column ", newOrder[j], 
-                          "with corr ", round(x[i,j], 3), "\n")  
+          if(verbose) cat("Compare row", newOrder[i],
+                          " and column ", newOrder[j],
+                          "with corr ", round(x[i,j], 3), "\n")
           if (verbose) cat("  Means: ", round(mn1, 3), "vs", round(mn2, 3))
           if (mn1 > mn2) {
             deletecol[i] <- TRUE
@@ -92,28 +92,22 @@ findCorrelation_exact <- function(x, cutoff = 0.90, verbose = FALSE)
 
 
 #' Determine highly correlated variables
-#' 
+#'
 #' This function searches through a correlation matrix and returns a vector of
 #' integers corresponding to columns to remove to reduce pair-wise
 #' correlations.
-#' 
+#'
 #' The absolute values of pair-wise correlations are considered. If two
 #' variables have a high correlation, the function looks at the mean absolute
 #' correlation of each variable and removes the variable with the largest mean
 #' absolute correlation.
-#' 
+#'
 #' Using \code{exact = TRUE} will cause the function to re-evaluate the average
 #' correlations at each step while \code{exact = FALSE} uses all the
 #' correlations regardless of whether they have been eliminated or not. The
 #' exact calculations will remove a smaller number of predictors but can be
 #' much slower when the problem dimensions are "big".
-#' 
-#' There are several function in the \pkg{subselect} package
-#' (\code{\link[subselect:eleaps]{leaps}},
-#' \code{\link[subselect:genetic]{genetic}},
-#' \code{\link[subselect:anneal]{anneal}}) that can also be used to accomplish
-#' the same goal but tend to retain more predictors.
-#' 
+#'
 #' @param x A correlation matrix
 #' @param cutoff A numeric value for the pair-wise absolute correlation cutoff
 #' @param verbose A boolean for printing the details
@@ -130,38 +124,38 @@ findCorrelation_exact <- function(x, cutoff = 0.90, verbose = FALSE)
 #' \code{\link[subselect:anneal]{anneal}}, \code{\link{findLinearCombos}}
 #' @keywords manip
 #' @examples
-#' 
-#' R1 <- structure(c(1, 0.86, 0.56, 0.32, 0.85, 0.86, 1, 0.01, 0.74, 0.32, 
+#'
+#' R1 <- structure(c(1, 0.86, 0.56, 0.32, 0.85, 0.86, 1, 0.01, 0.74, 0.32,
 #'                   0.56, 0.01, 1, 0.65, 0.91, 0.32, 0.74, 0.65, 1, 0.36,
-#'                   0.85, 0.32, 0.91, 0.36, 1), 
+#'                   0.85, 0.32, 0.91, 0.36, 1),
 #'                 .Dim = c(5L, 5L))
 #' colnames(R1) <- rownames(R1) <- paste0("x", 1:ncol(R1))
 #' R1
-#' 
+#'
 #' findCorrelation(R1, cutoff = .6, exact = FALSE)
 #' findCorrelation(R1, cutoff = .6, exact = TRUE)
 #' findCorrelation(R1, cutoff = .6, exact = TRUE, names = FALSE)
-#' 
-#' 
+#'
+#'
 #' R2 <- diag(rep(1, 5))
 #' R2[2, 3] <- R2[3, 2] <- .7
 #' R2[5, 3] <- R2[3, 5] <- -.7
 #' R2[4, 1] <- R2[1, 4] <- -.67
-#' 
+#'
 #' corrDF <- expand.grid(row = 1:5, col = 1:5)
 #' corrDF$correlation <- as.vector(R2)
 #' levelplot(correlation ~ row + col, corrDF)
-#' 
+#'
 #' findCorrelation(R2, cutoff = .65, verbose = TRUE)
-#' 
+#'
 #' findCorrelation(R2, cutoff = .99, verbose = TRUE)
-#' 
+#'
 #' @export findCorrelation
 findCorrelation <- function(x, cutoff = 0.90, verbose = FALSE, names = FALSE, exact = ncol(x) < 100) {
   if(names & is.null(colnames(x)))
     stop("'x' must have column names when `names = TRUE`")
-  out <- if(exact) 
-    findCorrelation_exact(x = x, cutoff = cutoff, verbose = verbose) else 
+  out <- if(exact)
+    findCorrelation_exact(x = x, cutoff = cutoff, verbose = verbose) else
       findCorrelation_fast(x = x, cutoff = cutoff, verbose = verbose)
   out
   if(names) out <- colnames(x)[out]