Update docs (#357)

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

@@ -18,14 +18,14 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'devel', force_suggests: "0"}
-          - {os: windows-latest, r: 'devel'}
-          - {os: macOS-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: macOS-latest,   r: 'oldrel'}
-          - {os: windows-latest, r: 'oldrel'}
-          - {os: ubuntu-16.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - { os: macOS-latest,   r: 'devel',   force_suggests: "0" }
+          - { os: windows-latest, r: 'devel',   force_suggests: "1" }
+          - { os: macOS-latest,   r: 'release', force_suggests: "1" }
+          - { os: windows-latest, r: 'release', force_suggests: "1" }
+          - { os: ubuntu-16.04,   r: 'release', force_suggests: "1",  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest" }
+          - { os: macOS-latest,   r: 'oldrel',  force_suggests: "1" }
+          - { os: windows-latest, r: 'oldrel',  force_suggests: "1" }
+          - { os: ubuntu-16.04,   r: 'oldrel',  force_suggests: "1" , rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest" }
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -86,7 +86,14 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - name: Check
+      - name: Check with printing
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+          CAN_PRINT: "TRUE"
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Check as CRAN
         env:
           _R_CHECK_CRAN_INCOMING_: false
         run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")

.github/workflows/pkgdown.yaml

@@ -44,5 +44,7 @@ jobs:
         run: R CMD INSTALL .
 
       - name: Deploy package
+        env:
+          CAN_PRINT: "TRUE"
         run: pkgdown::deploy_to_branch(new_process = FALSE)
         shell: Rscript {0}

.github/workflows/test-coverage.yaml

@@ -42,5 +42,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Test coverage
+        env:
+          CAN_PRINT: "TRUE"
         run: covr::codecov()
         shell: Rscript {0}

DESCRIPTION

@@ -59,9 +59,11 @@ Suggests:
     roxygen2,
     testthat,
     crosstalk,
-    knitr
+    knitr,
+    spelling
 Roxygen: list(markdown = FALSE)
 RoxygenNote: 7.1.0
 VignetteBuilder: knitr
 SystemRequirements: openssl
 Encoding: UTF-8
+Language: en-US

NEWS.md

@@ -1,10 +1,37 @@
 GGally (development version)
 ---------------------
 
-### New Functions:
+### Vignettes
+* `vignette("ggally_plots")` - List of available high-level plots
+* `vignette("ggally_stats")` - Additional statistics for ggplot2
+* `vignette("ggbivariate")` - ggbivariate(): Plot an outcome with several potential explanatory variables
+* `vignette("ggcoef")` - ggcoef(): Model coefficients
+* `vignette("ggduo")` - ggduo(): Two-grouped plot matrix
+* `vignette("ggmatrix")` - ggmatrix(): Plot matrix
+* `vignette("ggnetworkmap")` - ggnetworkmap(): Network + map plot
+* `vignette("ggnostic")` - ggnostic(): Model diagnostics plot matrix
+* `vignette("ggpairs")` - ggpairs(): Pairwise plot matrix
+* `vignette("ggscatmat")` - ggscatmat(): Numeric pairwise plot matrix
+* `vignette("ggsurv")` - ggsurv(): Survival curves
+* `vignette("ggtable")` - ggtable(): Cross-tabulated tables
+* `vignette("glyph")` - glyphs(): Glyph plot
+
+
+### New functions
+
+`ggbivariate()` (@larmarange, #324)
+* Display an outcome using several potential explanatory variables
+* `vignette("ggbivariate")`
+
+`ggtable()` (@larmarange, #351)
+* Cross-tabulated tables of discrete variables
+* `vignette("ggtable")`
 
 `ggally_autopoint()`, `ggally_autopointDiag()` (@larmarange, #325)
-* Make scatterplots compatible with both continuous and catgeorical variables using `ggforce::geom_autopoint()`.
+* Make scatterplots compatible with both continuous and categorical variables using `ggforce::geom_autopoint()`.
+
+`ggally_colbar()`, `ggally_rowbar()` (@larmarange, #324)
+* Plot column or row percentage using bar plots.
 
 `ggally_count()`, `ggally_countDiag()` (@larmarange, #321)
 * Plot the number of observations by using rectangles with proportional areas.
@@ -16,11 +43,11 @@ GGally (development version)
 * Display a cross-tabulated table.
 
 `ggally_statistic()` (#327)
-* A generialized version of `ggally_cor()`
+* A generalized version of `ggally_cor()`
 * Use this method to create functions similar to `ggally_cor()` that return any text value given and `x` and `y` vector of data
 
-`ggally_summarise_by()`
-* Display summary statisctics of a continuous variable for each value of a discrete variable.
+`ggally_summarise_by()` (@larmarange, #325)
+* Display summary statistics of a continuous variable for each value of a discrete variable.
 
 `ggally_table()` (@larmarange, #326)
 * Plot the number of observations as a table.
@@ -36,10 +63,13 @@ GGally (development version)
 `stat_cross` (@larmarange, #326)
 * Computes statistics of a 2-dimensional matrix using `broom::augment.htest`.
 
+`stat_prop` (@larmarange, #324)
+* Compute proportions according to custom denominator.
+
 `stat_weighted_mean` (@larmarange, #333)
 * Compute the mean of y aesthetic for each unique value of x, taking into account weight aesthetic if provided.
 
-### Features and Bug Fixes:
+### Major updates
 
 `ggally_cor()` (#327)
 * New implementation using `ggally_statistic()`
@@ -51,6 +81,8 @@ GGally (development version)
 * To use the old version, change your `ggally_cor` function calls to `ggally_cor_v1_5`.
 * Previously deprecated parameters have been removed
 
+### Features and bug fixes:
+
 `ggpairs()` (#331)
 * new `proportion` argument to control relative size of sub-plots
 * option `proportion = "auto"` for automatic guess based on the number of levels for discrete variables

R/deprecated.R

@@ -1,4 +1,4 @@
-#' Correlation from the Scatter Plot (deprecated)
+#' Correlation value plot
 #'
 #' (Deprecated. See \code{\link{ggally_cor}}.)
 #'
@@ -14,7 +14,7 @@
 #' @param corUse deprecated. Use parameter \code{use}
 #' @param displayGrid if TRUE, display aligned panel gridlines
 #' @param ... other arguments being supplied to geom_text
-#' @author Barret Schloerke \email{schloerke@@gmail.com}
+#' @author Barret Schloerke
 #' @importFrom stats complete.cases cor
 #' @seealso \code{\link{ggally_cor}}
 #' @export

R/find-combo.R

@@ -3,7 +3,7 @@
 #' Retrieves the type of plot that should be used for all combinations
 #'
 #' @param data data set to be used
-#' @author Barret Schloerke \email{schloerke@@gmail.com}
+#' @author Barret Schloerke
 #' @keywords internal
 plot_types <- function(data, columnsX, columnsY, allowDiag = TRUE) {
 
@@ -65,7 +65,7 @@ plot_types <- function(data, columnsX, columnsY, allowDiag = TRUE) {
   dataInfo
 }
 
-#' Find Plot Types
+#' Find plot types
 #'
 #' Retrieves the type of plot for the specific columns
 #'
@@ -75,7 +75,8 @@ plot_types <- function(data, columnsX, columnsY, allowDiag = TRUE) {
 #' @param type2 y column type
 #' @param isAllNa is.na(data)
 #' @param allowDiag allow for diag values to be returned
-#' @author Barret Schloerke \email{schloerke@@gmail.com}
+#' @author Barret Schloerke
+#' @keywords internal
 find_plot_type <- function(col1Name, col2Name, type1, type2, isAllNa, allowDiag) {
 
   # diag calculations