Greenwood

.Rbuildignore

@@ -1,10 +1,12 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^codecov.yml$
 ^cran-comments.md$
 ^CRAN-RELEASE$
 ^doc$
 ^docs$
 ^figures$
+^\.github$
 ^Ideas for Future Work$
 ^Meta$
 ^pkgdown$

.github/.gitignore

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

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

@@ -0,0 +1,51 @@
+# 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]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -0,0 +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: [main, master]
+  pull_request:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - 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, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          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}
+
+      - 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: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -2,10 +2,23 @@ Package: ggResidpanel
 Type: Package
 Title: Panels and Interactive Versions of Diagnostic Plots using 'ggplot2'
 Version: 0.3.0.9000
-Authors@R: c(person("Katherine", "Goode", email = "[email protected]", role = c("aut", "cre")),
-    person("Kathleen", "Rey", email = "[email protected]", role = c("aut")))
-Description: An R package for creating diagnostic plots for models. The package allows for the 
-    creation of panels of plots and interactive plots.
+Authors@R: c(
+  person(
+    "Katherine", "Goode", 
+    email = "[email protected]", 
+    role = c("aut", "cre")
+  ),
+  person(
+    "Kathleen", "Rey", 
+    email = "[email protected]", 
+    role = c("aut")),
+  person(
+    "Greenwood", "Mark", 
+    email = "[email protected]", 
+    role = c("ctb"))
+  )
+Description: An R package for creating diagnostic plots for models. The package
+  allows for the creation of panels of plots and interactive plots.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
@@ -16,11 +29,12 @@ Imports:
   grDevices,
   grid,
   MASS,
+  methods,
   plotly,
   qqplotr,
   stats,
   stringr
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.2
 Suggests: 
   dplyr,
   forcats,
@@ -31,8 +45,9 @@ Suggests:
   randomForest,
   rmarkdown,
   rpart,
-  testthat,
+  testthat (>= 3.0.0),
   vdiffr,
   wesanderson
 VignetteBuilder: knitr
 Depends: R (>= 3.0.0)
+Config/testthat/edition: 3

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(resid_auxpanel)
+export(resid_calibrate)
 export(resid_compare)
 export(resid_interact)
 export(resid_panel)
@@ -10,7 +11,8 @@ importFrom(cowplot,draw_label)
 importFrom(cowplot,ggdraw)
 importFrom(cowplot,plot_grid)
 importFrom(ggplot2,aes)
-importFrom(ggplot2,aes_string)
+importFrom(ggplot2,after_stat)
+importFrom(ggplot2,coord_fixed)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,expand_limits)
@@ -30,6 +32,7 @@ importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggplotGrob)
 importFrom(ggplot2,ggplot_build)
 importFrom(ggplot2,labs)
+importFrom(ggplot2,scale_color_gradient2)
 importFrom(ggplot2,scale_x_continuous)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,stat_function)
@@ -43,6 +46,7 @@ importFrom(ggplot2,ylab)
 importFrom(grDevices,extendrange)
 importFrom(grid,gpar)
 importFrom(grid,textGrob)
+importFrom(methods,is)
 importFrom(plotly,"%>%")
 importFrom(plotly,ggplotly)
 importFrom(plotly,layout)
@@ -54,9 +58,12 @@ importFrom(qqplotr,stat_qq_point)
 importFrom(stats,cooks.distance)
 importFrom(stats,dnorm)
 importFrom(stats,fitted)
+importFrom(stats,formula)
 importFrom(stats,hatvalues)
+importFrom(stats,lm)
 importFrom(stats,lowess)
 importFrom(stats,model.frame)
 importFrom(stats,resid)
 importFrom(stats,sd)
+importFrom(stats,simulate)
 importFrom(stringr,str_sub)

NEWS.md

@@ -1,3 +1,32 @@
+# ggResidpanel 0.4.0
+
+## Major 
+
+- Added resid_calibrate
+- For lm model:
+  - Standardized residuals are now the default instead of raw residuals
+  - Fixed issue when leverage is equal to 1 when computing standardized residuals - report Pearson residuals instead
+- Added alpha value in all functions
+- Adjustments to Cook's D plots
+  - "Return a warning if any of the leverage values are equal to 1 and add lines to plot"
+  - Need to add more descriptions here
+- In plot_constlev, removed "Compute the values for the lowess curve"
+- In plot_lev, :
+  - "Create the cutoff SAS uses with Cook's D"
+  - "Count number over cutoff"
+  - Adjusted the way constant leverage is handled
+  - Added Cook's D values
+  - When creating hat values, "Add more resolution for large n"
+- In plot_ls, "If smoother is set to true, do not add it to the plot"
+- Adjustments to the smoother options across various plot types
+
+## Minor
+
+- Typo fixes in documentation
+- Small fixes to code for better practices
+- Small updates to plot_hist grid
+- Clean up of some plot labels
+
 # ggResidpanel 0.3.0
 
 ## Major:

R/helper_checks.R

@@ -149,20 +149,3 @@ check_leverage <- function(model, plots){
   }
 
 }
-
-# Return a warning about choosing the number of bins if a histogram is included
-# and the number of bins has not been specified and return the default option if
-# not specified
-# check_bins <- function(plots, bins){
-#
-#   if("default" %in% plots | "SAS" %in% plots | "all" %in% plots | "hist" %in% plots){
-#     if(is.na(bins)){
-#       bins = 30
-#       warning("By default, bins = 30 in the histogram of residuals. If necessary,
-#             specify an appropriate number of bins.")
-#     }
-#   }
-#
-#   return(bins)
-#
-# }

R/helper_plotly_label.R

@@ -197,11 +197,11 @@ if(class(model)[1]%in%c("lm", "glm")){
   #Trim variables that are numeric and contain a decimal
   #down to 3 decimal places
   # for(i in 1:ncol(plotly_data)){
-  #   #First part checks for rows in teh column that contain a decimal
-  #   #if they do not contian a decimal, do nothing to them.
+  #   #First part checks for rows in the column that contain a decimal
+  #   #if they do not contain a decimal, do nothing to them.
   #
   #   #The second part checks to see if the row values are value numbers
-  #   #A cateogrical value could contain a period
+  #   #A categorical value could contain a period
   #   plotly_data[grepl("\\.", as.character(plotly_data[,i]))&!is.na(as.numeric(plotly_data[,i])),i] <- round(as.numeric(as.character(plotly_data[grepl("\\.", as.character(plotly_data[,i]))&!is.na(as.numeric(plotly_data[,i])),i])), 3)
   # }
 

R/helper_resid.R

@@ -6,14 +6,20 @@ helper_resid <- function(type = NA, model){
   # lm residuals
   if(class(model)[1] == "lm"){
 
-    # Default: raw residuals
-    if(is.na(type) | type == "response"){
-      return(resid(model, type = "response"))
+    # Default: standardized residuals
+    if(is.na(type) | type == "standardized"){
+      if (any(!is.finite(stdres(model)))){
+        warning("Leverage 1 observation(s) encountered, reporting Pearson Residuals")
+        return(resid(model, type = "response") / summary(model)$sigma)
+      } else {
+      return(stdres(model))
+      }
     }else if(type == "pearson"){
       return(resid(model, type = "response") / summary(model)$sigma)
-    }else if(type == "standardized"){
-      return(stdres(model))
+    }else if(type == "response"){
+      return(resid(model, "response"))
     }
+
 
   # glm residuals
   } else if (class(model)[1] == "glm"){

R/plot_auxboxplot.R

@@ -14,7 +14,8 @@ plot_auxboxplot <- function(resid, theme, axis.text.size, title.text.size, title
   ## Creation of Plot ---------------------------------------------------------------
 
   # Create the boxplot of residuals
-  plot <- ggplot(model_values, aes_string(x = " ", y = "Residual")) +
+  plot <- 
+    ggplot(model_values, aes(x = " ", y = {{Residual}})) +
     geom_boxplot(width = .5) +
     geom_point(alpha = 0) +
     labs(x = " ", y = "Residuals")
@@ -28,7 +29,7 @@ plot_auxboxplot <- function(resid, theme, axis.text.size, title.text.size, title
     plot <- plot + theme_grey()
   }
 
-  # Set text size of title and axis lables, determine whether to include a title,
+  # Set text size of title and axis labels, determine whether to include a title,
   # and return plot
   if (title.opt == TRUE){
     plot +