Merge pull request #208 from rsquaredacademy/develop

olsrr 0.6.0

.Rbuildignore

@@ -16,3 +16,4 @@
 ^debug\.log$
 ^\.github$
 ^CODE_OF_CONDUCT\.md$
+^revdep$

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

@@ -1,14 +1,10 @@
-# 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
 
@@ -22,63 +18,33 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {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: 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:
-      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: r-lib/actions/setup-r@v1
+      - 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-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

.github/workflows/test-coverage.yaml

@@ -1,48 +1,31 @@
+# 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
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
-
-      - 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
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@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-
+          use-public-rspm: true
 
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov()
+        run: covr::codecov(quiet = FALSE)
         shell: Rscript {0}

DESCRIPTION

@@ -17,20 +17,21 @@ Imports:
     gridExtra,
     nortest,
     stats,
-    utils
+    utils,
+    xplorerr
 Suggests:
     covr,
     descriptr,
     knitr,
     rmarkdown,
     testthat,
-    vdiffr,
-    xplorerr
+    vdiffr
 License: MIT + file LICENSE
 URL: https://olsrr.rsquaredacademy.com/, https://github.com/rsquaredacademy/olsrr
 BugReports: https://github.com/rsquaredacademy/olsrr/issues
 Encoding: UTF-8
 LazyData: true
 VignetteBuilder: knitr
-RoxygenNote: 7.1.1
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
 Config/testthat/edition: 3

NEWS.md

@@ -1,10 +1,22 @@
-# olsrr 0.5.3.9000
+# olsrr 0.6.0
+
+This is a minor release for bug fixes and other enhancements.
 
 ## New Features
 
-- Force variables in/out in variable selection procedures
-- Hierarchical selection
-- Variable selection using r-squared and adjusted r-squared
+- hierarchical selection can be enables when using `p` values as variable selection metric
+
+## Enhancements
+
+- force variables to be included or excluded from the model at all stages of variable selection
+- Variable selection methods allow use of the following metrics:
+    - p value
+    - akaike information criterion (aic)
+    - schwarz bayesian criterion (sbc)
+    - sawa bayesian criterion (sbic)
+    - r-square
+    - adjusted r-square
+- Choose threshold for determining influential observations in `ols_plot_dffits()`
 
 ## Bug Fixes
 

R/ols-bartlett-test.R

@@ -27,8 +27,10 @@
 #'
 #' @examples
 #' # using grouping variable
-#' library(descriptr)
-#' ols_test_bartlett(mtcarz, 'mpg', group_var = 'cyl')
+#' if (require("descriptr")) {
+#'   library(descriptr)
+#'   ols_test_bartlett(mtcarz, 'mpg', group_var = 'cyl')
+#' }
 #'
 #' # using variables
 #' ols_test_bartlett(hsb, 'read', 'write')

R/ols-cooks-d-barplot.R

@@ -5,8 +5,11 @@
 #' fitted values of the model.
 #'
 #' @param model An object of class \code{lm}.
-#' @param type An integer between 1 and 5 selecting one of the 6 methods for computing the threshold.
-#' @param print_plot logical; if \code{TRUE}, prints the plot else returns a plot object.
+#' @param type An integer between 1 and 5 selecting one of the 5 methods for
+#'     computing the threshold.
+#' @param threshold Threshold for detecting outliers.
+#' @param print_plot logical; if \code{TRUE}, prints the plot else returns a
+#'     plot object.
 #'
 #' @details
 #' Cook's distance was introduced by American statistician R Dennis Cook in
@@ -51,6 +54,8 @@
 #' @examples
 #' model <- lm(mpg ~ disp + hp + wt, data = mtcars)
 #' ols_plot_cooksd_bar(model)
+#' ols_plot_cooksd_bar(model, type = 4)
+#' ols_plot_cooksd_bar(model, threshold = 0.2)
 #'
 #' @importFrom stats cooks.distance
 #' @importFrom ggplot2 geom_bar coord_flip ylim geom_hline geom_label
@@ -59,15 +64,19 @@
 #'
 #' @export
 #'
-ols_plot_cooksd_bar <- function(model, type = 1, print_plot = TRUE) {
+ols_plot_cooksd_bar <- function(model, type = 1, threshold = NULL, print_plot = TRUE) {
 
   check_model(model)
 
   k <- ols_prep_cdplot_data(model, type)
   d <- ols_prep_outlier_obs(k)
   f <- ols_prep_cdplot_outliers(k)
+
+  if (is.null(threshold)) {
+      threshold <- k$ts
+  }
 
-  y_max <- max(k$maxx, k$ts)
+  y_max <- max(k$maxx, threshold)
   y_lim <- y_max + (y_max * 0.1)
 
   # geoms
@@ -76,33 +85,33 @@ ols_plot_cooksd_bar <- function(model, type = 1, print_plot = TRUE) {
     geom_bar(width = 0.5, stat = "identity", aes(fill = fct_color)) +
     geom_text(hjust = -0.2, nudge_x = 0.05, size = 2, na.rm = TRUE) +
     geom_hline(yintercept = 0) +
-    geom_hline(yintercept = k$ts, colour = "red") 
+    geom_hline(yintercept = threshold, colour = "red")
 
   # annotations
   p <-
     p +
     annotate("text", x = Inf, y = Inf, hjust = 1.2, vjust = 2,
       family = "serif", fontface = "italic", colour = "darkred",
-      label = paste("Threshold:", round(k$ts, 3))) 
+      label = paste("Threshold:", round(threshold, 3)))
 
   # scales
-  p <- 
+  p <-
     p +
-    scale_fill_manual(values = c("blue", "red")) 
+    scale_fill_manual(values = c("blue", "red"))
 
   # guides
-  p <- 
+  p <-
     p +
     labs(fill = "Observation") +
     xlab("Observation") +
-    ylab("Cook's D") + 
-    ggtitle("Cook's D Bar Plot") + 
-    ylim(0, y_lim) 
+    ylab("Cook's D") +
+    ggtitle("Cook's D Bar Plot") +
+    ylim(0, y_lim)
 
   if (print_plot) {
     suppressWarnings(print(p))
   } else {
-    return(list(plot = p, outliers = f, threshold = k$ts))
+    return(list(plot = p, outliers = f, threshold = threshold))
   }
 
-}
+}

R/ols-cooks-d-chart.R

@@ -6,6 +6,7 @@
 #'
 #' @param model An object of class \code{lm}.
 #' @param type An integer between 1 and 5 selecting one of the 6 methods for computing the threshold.
+#' @param threshold Threshold for detecting outliers.
 #' @param print_plot logical; if \code{TRUE}, prints the plot else returns a plot object.
 #'
 #' @details
@@ -51,35 +52,41 @@
 #' @examples
 #' model <- lm(mpg ~ disp + hp + wt, data = mtcars)
 #' ols_plot_cooksd_chart(model)
+#' ols_plot_cooksd_chart(model, type = 4)
+#' ols_plot_cooksd_chart(model, threshold = 0.2)
 #'
 #' @importFrom ggplot2 geom_linerange
 #'
 #' @seealso [ols_plot_cooksd_bar()]
 #'
 #' @export
 #'
-ols_plot_cooksd_chart <- function(model, type = 1, print_plot = TRUE) {
+ols_plot_cooksd_chart <- function(model, type = 1, threshold = NULL, print_plot = TRUE) {
 
   check_model(model)
 
   k <- ols_prep_cdplot_data(model, type)
   d <- ols_prep_outlier_obs(k)
   f <- ols_prep_cdplot_outliers(k)
 
+  if (is.null(threshold)) {
+      threshold <- k$ts
+  }
+
   p <- 
     ggplot(d, aes(x = obs, y = cd, label = txt, ymin = min(cd), ymax = cd)) +
     geom_linerange(colour = "blue") + 
     geom_point(shape = 1, colour = "blue") +
     geom_text(vjust = -1, size = 3, family = "serif", fontface = "italic",
               colour = "darkred", na.rm = TRUE) +
-    geom_hline(yintercept = k$ts, colour = "red") 
+    geom_hline(yintercept = threshold, colour = "red") 
 
   # annotations
   p <- 
     p +
     annotate("text", x = Inf, y = Inf, hjust = 1.2, vjust = 2,
       family = "serif", fontface = "italic", colour = "darkred",
-      label = paste("Threshold:", round(k$ts, 3)))
+      label = paste("Threshold:", round(threshold, 3)))
 
   # guides
   p <-
@@ -92,7 +99,7 @@ ols_plot_cooksd_chart <- function(model, type = 1, print_plot = TRUE) {
   if (print_plot) {
     suppressWarnings(print(p))
   } else {
-    return(list(plot = p, outliers = f, threshold = k$ts))
+    return(list(plot = p, outliers = f, threshold = threshold))
   }
 
-}
+}

R/ols-launch-app.R

@@ -7,8 +7,6 @@
 #' @export
 #'
 ols_launch_app <- function() {
-
-	check_suggests('xplorerr')
 	xplorerr::app_linear_regression()
 }