v2.5.6 on CRAN

.Rbuildignore

@@ -10,4 +10,6 @@ tar.gz$
 ^appveyor\.yml$
 ^\.github$
 .DS_Store
-^revdep$
+^revdep$
+^CRAN-SUBMISSION$
+^cran-comments\.md$

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

@@ -1,16 +1,13 @@
-# 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:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -22,65 +19,32 @@ 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@v6
+
+      - 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 }}
 
-      - 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: Restore R package cache
-        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: |
-          options(crayon.enabled = TRUE)
-          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")'

CRAN-SUBMISSION

@@ -0,0 +1,4 @@
+Version: 2.5.6
+Date: 2026-10-08 00:08:26 UTC
+SHA:
+    87b4b813ad9c1f4b74734e775d016b4735864060

DESCRIPTION

@@ -1,17 +1,15 @@
 Package: rfPermute
 Type: Package
 Title: Estimate Permutation p-Values for Random Forest Importance Metrics
-Description: Estimate significance of importance metrics
-    for a Random Forest model by permuting the response
-    variable. Produces null distribution of importance
-    metrics for each predictor variable and p-value of
-    observed. Provides summary and visualization functions for 'randomForest' 
-    results.
-Version: 2.5.4
+Description: Estimate significance of importance metrics for a Random Forest 
+  model by permuting the response variable. Produces null distribution of 
+  importance metrics for each predictor variable and p-value of observed. 
+  Provides summary and visualization functions for 'randomForest' results.
+Version: 2.5.6
 Authors@R: c(
-  EA = person("Eric", "Archer", email = "eric.archer@noaa.gov", role = c("aut", "cre")))
-URL: https://github.com/EricArcher/rfPermute
-BugReports: https://github.com/EricArcher/rfPermute/issues
+  EA = person("Eric", "Archer", email = "eric.ivan.archer@gmail.com", role = c("aut", "cre")))
+URL: https://github.com/SWFSC/rfPermute
+BugReports: https://github.com/SWFSC/rfPermute/issues
 Depends:
     R (>= 4.1.0)
 Imports:
@@ -20,9 +18,9 @@ Imports:
     ggplot2 (>= 3.3),
     grDevices,
     gridExtra,
-    magrittr (>= 2.0),
     methods,
     parallel,
+    pROC,
     randomForest (>= 4.6),
     rlang,
     scales,
@@ -52,7 +50,8 @@ Collate:
     plotVotes.R
     balancedSampsize.R
     cleanRFdata.R
+    rfROC.R
 LazyData: TRUE
 License: GPL (>= 2)
 Encoding: UTF-8
-RoxygenNote: 7.3.2
+Config/roxygen2/version: 8.1.0

NAMESPACE

@@ -27,10 +27,14 @@ export(plotTrace)
 export(plotVotes)
 export(rfPermute)
 export(rfPermuteTutorial)
-importFrom(magrittr,"%>%")
+export(rfROC)
 importFrom(methods,new)
-importFrom(randomForest,importance)
-importFrom(randomForest,randomForest)
+importFrom(randomForest,
+  importance,
+  randomForest
+)
 importFrom(rlang,.data)
-importFrom(stats,na.fail)
-importFrom(stats,predict)
+importFrom(stats,
+  na.fail,
+  predict
+)

R/confusionMatrix.R

@@ -72,6 +72,7 @@ confusionMatrix <- function(x, conf.level = 0.95, threshold = NULL) {
   cm <- rbind(cm, Overall = rep(NA, ncol(cm)))
   pct.correct <- (correct.n / all.n) * 100
   cbind(
+    n = all.n,
     cm, 
     pct.correct = pct.correct[rownames(cm)], 
     ci[rownames(cm), , drop = FALSE],
@@ -88,8 +89,8 @@ plotConfMat <- function(x, title = NULL, plot = TRUE) {
   if(rf$type == "regression") stop("'rf' must be of a classification model")
 
   conf <- .confMat(rf)
-  pct.correct <- (100 * sum(diag(conf)) / sum(conf)) %>% 
-    round(0) %>% 
+  pct.correct <- (100 * sum(diag(conf)) / sum(conf)) |> 
+    round(0) |> 
     paste0("% correct")
   title <- if(is.null(title)) {
     pct.correct 
@@ -99,18 +100,18 @@ plotConfMat <- function(x, title = NULL, plot = TRUE) {
   freq <- rowSums(conf)
   rownames(conf) <- paste0(names(freq), " (", freq, ")")
 
-  p <- conf %>% 
-    prop.table(1) %>% 
-    as.data.frame %>% 
-    tibble::rownames_to_column("observed") %>% 
-    tidyr::gather("predicted", "prop", -.data$observed) %>% 
+  p <- conf |> 
+    prop.table(1) |> 
+    as.data.frame() |> 
+    tibble::rownames_to_column("observed") |> 
+    tidyr::gather("predicted", "prop", -.data$observed) |> 
     dplyr::mutate(
       observed = factor(.data$observed),
       observed = stats::reorder(.data$observed, dplyr::desc(.data$observed)),
       predicted = factor(.data$predicted)
-    ) %>% 
-    ggplot2::ggplot(ggplot2::aes_string("predicted", "observed")) +
-    ggplot2::geom_raster(ggplot2::aes_string(fill = "prop")) +
+    ) |> 
+    ggplot2::ggplot(ggplot2::aes(x = .data$predicted, y = .data$observed)) +
+    ggplot2::geom_raster(ggplot2::aes(fill = .data$prop)) +
     ggplot2::scale_fill_viridis_c(
       option = "magma", 
       direction = -1, 
@@ -121,7 +122,8 @@ plotConfMat <- function(x, title = NULL, plot = TRUE) {
     ggplot2::guides(fill = ggplot2::guide_colorbar(title = "Proportion")) +
     ggplot2::theme(
       axis.text.x.top = ggplot2::element_text(angle = 45, hjust = 0),
-      panel.background = ggplot2::element_blank()
+      panel.background = ggplot2::element_blank(),
+      legend.key.height = ggplot2::unit(1, 'null')
     )
 
   if(plot) print(p)

R/importance.R

@@ -137,12 +137,12 @@ plotImportance <- function(x, plot.type = c("bar", "heatmap"), imp.type = NULL,
         pval = if(inherits(x, "rfPermute")) {
           x$pval[rownames(imp.mat), i, sc]
         } else Inf
-      ) %>% 
-        tibble::rownames_to_column("pred") %>% 
+      ) |> 
+        tibble::rownames_to_column("pred") |> 
         dplyr::mutate(
           is.sig = .data$pval <= alpha,
           pred = stats::reorder(.data$pred, .data$imp)
-        ) %>% 
+        ) |> 
         dplyr::arrange(-.data$imp)
       if(sig.only) imp.df <- imp.df[imp.df$is.sig, ]
       n <- min(n, nrow(imp.df))
@@ -151,7 +151,7 @@ plotImportance <- function(x, plot.type = c("bar", "heatmap"), imp.type = NULL,
 
       ggplot2::ggplot(
         imp.df, 
-        ggplot2::aes_string(x = "pred", y = "imp", fill = "is.sig") 
+        ggplot2::aes(x = .data$pred, y = .data$imp, fill = .data$is.sig) 
       ) + 
         ggplot2::geom_bar(stat = "identity") +
         ggplot2::coord_flip() + 
@@ -174,17 +174,17 @@ plotImportance <- function(x, plot.type = c("bar", "heatmap"), imp.type = NULL,
     preds <- rev(rev(preds)[1:n])
     imp.df <- data.frame(imp.mat[preds, imp.type, drop = FALSE], check.names = FALSE)
     if(ranks) for(i in imp.type) imp.df[[i]] <- rank(-imp.df[[i]])
-    imp.df <- imp.df %>% 
-      tibble::rownames_to_column("pred") %>% 
-      tidyr::pivot_longer(-.data$pred, names_to = "type") %>% 
+    imp.df <- imp.df |> 
+      tibble::rownames_to_column("pred") |> 
+      tidyr::pivot_longer(-.data$pred, names_to = "type") |> 
       dplyr::mutate(
         type = factor(.data$type, levels = imp.type),
         pred = factor(.data$pred, levels = preds)
       )
 
     # create plot
-    g <- ggplot2::ggplot(imp.df, ggplot2::aes_string("type", "pred")) +
-      ggplot2::geom_raster(ggplot2::aes_string(fill = "value")) + 
+    g <- ggplot2::ggplot(imp.df, ggplot2::aes(x = .data$type, y = .data$pred)) +
+      ggplot2::geom_raster(ggplot2::aes(fill = .data$value)) + 
       ggplot2::theme(panel.background = ggplot2::element_blank())
     g <- g + if(ranks) {
       ggplot2::scale_fill_gradient2(
@@ -236,4 +236,4 @@ plotImportance <- function(x, plot.type = c("bar", "heatmap"), imp.type = NULL,
     }
   }
   invisible(imp.plot)
-}
+}

R/plotImpPreds.R

@@ -68,10 +68,10 @@ plotImpPreds <- function(x, df, class.col, imp.type = NULL, max.vars = 16,
   df$.class. <- factor(df[[class.col]])
   df <- df[, c(".class.", imp.vars)]
 
-  p <- df %>%
-    tidyr::pivot_longer(-.data$.class., names_to = "var") %>% 
-    dplyr::mutate(var = factor(.data$var, levels = imp.vars)) %>% 
-    ggplot2::ggplot(ggplot2::aes_string(".class.", "value")) +
+  p <- df |>
+    tidyr::pivot_longer(-.data$.class., names_to = "var") |> 
+    dplyr::mutate(var = factor(.data$var, levels = imp.vars)) |> 
+    ggplot2::ggplot(ggplot2::aes(x = .data$.class., y = .data$value)) +
     ggplot2::geom_violin(alpha = violin.alpha) +
     ggplot2::geom_jitter(size = size, alpha = point.alpha, width = 0.25, height = 0) +
     ggplot2::facet_wrap(~ var, scales = "free_y") +
@@ -80,4 +80,4 @@ plotImpPreds <- function(x, df, class.col, imp.type = NULL, max.vars = 16,
 
   if(plot) print(p)
   invisible(p)
-}
+}