Merge 97a5720 into 63babd4

IndrajeetPatil · Dec 20, 2019 · 3fa57fc · 3fa57fc
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: ggstatsplot
 Title: 'ggplot2' Based Plots with Statistical Details
-Version: 0.1.4
+Version: 0.1.4.9000
 Authors@R: 
     c(person(given = "Indrajeet",
              family = "Patil",
@@ -31,7 +31,7 @@ BugReports: https://github.com/IndrajeetPatil/ggstatsplot/issues
 Depends: 
     R (>= 3.5.0)
 Imports:
-    broomExtra (>= 0.0.6),
+    broomExtra (>= 1.0.0),
     cowplot (>= 1.0.0),
     crayon (>= 1.3.4),
     dplyr (>= 0.8.3),
@@ -46,7 +46,7 @@ Imports:
     insight (>= 0.7.1),
     metaBMA (>= 0.6.2),
     metafor (>= 2.1-0),
-    pairwiseComparisons (>= 0.1.2),
+    pairwiseComparisons (>= 0.1.3),
     paletteer (>= 1.0.0),
     parameters (>= 0.3.0),
     psych (>= 1.8.12),
@@ -61,7 +61,6 @@ Imports:
 Suggests:
     broom,
     broom.mixed,
-    jmv,
     knitr,
     lme4,
     MASS,

diff --git a/NAMESPACE b/NAMESPACE
@@ -105,7 +105,6 @@ importFrom(metaBMA,meta_random)
 importFrom(metafor,rma)
 importFrom(pairwiseComparisons,p_adjust_text)
 importFrom(pairwiseComparisons,pairwise_comparisons)
-importFrom(pairwiseComparisons,pairwise_comparisons_caption)
 importFrom(pairwiseComparisons,pairwise_p)
 importFrom(paletteer,scale_color_paletteer_d)
 importFrom(paletteer,scale_fill_paletteer_d)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# ggstatsplot 0.1.4.9000
+
+MINOR CHANGES
+
+  - New dataset included: `bugs_wide`
+
 # ggstatsplot 0.1.4
 
 BUG FIXES

diff --git a/R/data.R b/R/data.R
@@ -237,3 +237,33 @@
 #' head(bugs_long)
 #' dplyr::glimpse(bugs_long)
 "bugs_long"
+
+
+#' @title Wide-format version of the "Bugs" dataset.
+#' @name bugs_wide
+#' @details This data set, "Bugs", provides the extent to which men and women
+#'   want to kill arthropods that vary in freighteningness (low, high) and
+#'   disgustingness (low, high). Each participant rates their attitudes towards
+#'   all anthropods. Subset of the data reported by Ryan et al. (2013).
+#'
+#' @format A data frame with 93 rows and 6 variables
+#' \itemize{
+#'   \item subject. Dummy identity number for each participant.
+#'   \item gender. Participant's gender (Female, Male).
+#'   \item region. Region of the world the participant was from.
+#'   \item education. Level of education.
+#'   \item ldlf,ldhf,hdlf,hdhf.The desire to kill an arthropod was indicated on
+#'   a scale from 0 to 10 in each condition of the experiment (**LDLF**: low
+#'   freighteningness and low disgustingness; **LFHD**: low freighteningness and
+#'   high disgustingness; **HFHD**: high freighteningness and low
+#'   disgustingness; **HFHD**: high freighteningness and high disgustingness).
+#' }
+#'
+#' @source
+#' \url{https://www.sciencedirect.com/science/article/pii/S0747563213000277}
+#'
+#' @examples
+#' dim(bugs_wide)
+#' head(bugs_wide)
+#' dplyr::glimpse(bugs_wide)
+"bugs_wide"
diff --git a/R/ggbarstats.R b/R/ggbarstats.R
@@ -46,22 +46,13 @@
 #' # association test (or contingency table analysis)
 #' ggstatsplot::ggbarstats(
 #'   data = mtcars,
-#'   main = vs,
-#'   condition = cyl,
+#'   x = vs,
+#'   y = cyl,
 #'   nboot = 10,
 #'   labels.legend = c("0 = V-shaped", "1 = straight"),
 #'   legend.title = "Engine"
 #' )
 #'
-#' # using `counts` argument
-#' library(jmv)
-#'
-#' ggstatsplot::ggbarstats(
-#'   data = as.data.frame(HairEyeColor),
-#'   x = Eye,
-#'   y = Hair,
-#'   counts = Freq
-#' )
 #' @export
 
 # defining the function

diff --git a/R/ggbetweenstats.R b/R/ggbetweenstats.R
@@ -129,7 +129,7 @@
 #' @importFrom paletteer scale_color_paletteer_d scale_fill_paletteer_d
 #' @importFrom ggsignif geom_signif
 #' @importFrom statsExpressions bf_ttest bf_oneway_anova
-#' @importFrom pairwiseComparisons pairwise_comparisons pairwise_comparisons_caption
+#' @importFrom pairwiseComparisons pairwise_comparisons
 #'
 #' @seealso \code{\link{grouped_ggbetweenstats}}, \code{\link{ggwithinstats}},
 #'  \code{\link{grouped_ggwithinstats}}
@@ -566,14 +566,7 @@ ggbetweenstats <- function(data,
       )
 
     # preparing the caption for pairwise comparisons test
-    caption <-
-      pairwiseComparisons::pairwise_comparisons_caption(
-        type = type,
-        var.equal = var.equal,
-        paired = FALSE,
-        p.adjust.method = p.adjust.method,
-        caption = caption
-      )
+    caption <- pairwise_caption(caption, unique(df_pairwise$test.details), p.adjust.method)
   }
 
   # ------------------------ annotations and themes -------------------------

diff --git a/R/ggpiestats.R b/R/ggpiestats.R
@@ -98,14 +98,6 @@
 #'   legend.title = "Engine"
 #' )
 #'
-#' # using `counts` argument
-#' library(jmv, warn.conflicts = FALSE)
-#'
-#' ggstatsplot::ggpiestats(
-#'   data = as.data.frame(HairEyeColor),
-#'   x = Eye,
-#'   counts = Freq
-#' )
 #' @export
 
 # defining the function

diff --git a/R/ggwithinstats.R b/R/ggwithinstats.R
@@ -19,7 +19,7 @@
 #'
 #' @importFrom rlang exec !! enquo :=
 #' @importFrom statsExpressions bf_ttest bf_oneway_anova
-#' @importFrom pairwiseComparisons pairwise_comparisons pairwise_comparisons_caption
+#' @importFrom pairwiseComparisons pairwise_comparisons
 #'
 #' @details
 #'
@@ -397,14 +397,7 @@ ggwithinstats <- function(data,
       )
 
     # preparing the caption for pairwise comparisons test
-    caption <-
-      pairwiseComparisons::pairwise_comparisons_caption(
-        type = type,
-        var.equal = TRUE,
-        paired = TRUE,
-        p.adjust.method = p.adjust.method,
-        caption = caption
-      )
+    caption <- pairwise_caption(caption, unique(df_pairwise$test.details), p.adjust.method)
   }
 
   # ------------------------ annotations and themes -------------------------

diff --git a/R/grouped_ggbarstats.R b/R/grouped_ggbarstats.R
@@ -24,18 +24,6 @@
 #'
 #' @examples
 #' \donttest{
-#' # with condition and with count data
-#' library(jmv)
-#'
-#' ggstatsplot::grouped_ggbarstats(
-#'   data = as.data.frame(HairEyeColor),
-#'   x = Hair,
-#'   y = Eye,
-#'   counts = Freq,
-#'   grouping.var = Sex
-#' )
-#'
-#' # the following will take slightly more amount of time
 #' # for reproducibility
 #' set.seed(123)
 #'
@@ -51,11 +39,8 @@
 #'   x = color,
 #'   y = clarity,
 #'   grouping.var = cut,
-#'   sampling.plan = "poisson",
 #'   title.prefix = "Quality",
 #'   bar.label = "both",
-#'   messages = FALSE,
-#'   perc.k = 1,
 #'   nrow = 2
 #' )
 #' }

diff --git a/R/grouped_ggpiestats.R b/R/grouped_ggpiestats.R
@@ -28,16 +28,6 @@
 #'   x = cyl
 #' )
 #'
-#' # without condition and with count data
-#' library(jmv)
-#'
-#' ggstatsplot::grouped_ggpiestats(
-#'   data = as.data.frame(HairEyeColor),
-#'   x = Hair,
-#'   counts = Freq,
-#'   grouping.var = Sex
-#' )
-#'
 #' # the following will take slightly more amount of time
 #' # for reproducibility
 #' set.seed(123)

diff --git a/R/helpers_ggbetweenstats_graphics.R b/R/helpers_ggbetweenstats_graphics.R
@@ -307,7 +307,8 @@ outlier_df <- function(data,
 #' library(ggplot2)
 #'
 #' # plot
-#' p <- ggplot(iris, aes(Species, Sepal.Length)) + geom_boxplot()
+#' p <- ggplot(iris, aes(Species, Sepal.Length)) +
+#'   geom_boxplot()
 #'
 #' # dataframe with pairwise comparison test results
 #' df_pair <- pairwiseComparisons::pairwise_comparisons(
@@ -393,6 +394,29 @@ ggsignif_adder <- function(plot,
   return(plot)
 }
 
+#' @name pairwise_caption
+#' @noRd
+
+pairwise_caption <- function(caption, test.description, p.adjust.method) {
+  substitute(
+    atop(
+      displaystyle(top.text),
+      expr = paste(
+        "Pairwise comparisons: ",
+        bold(test.description),
+        "; Adjustment (p-value): ",
+        bold(p.adjust.method.text)
+      )
+    ),
+    env = list(
+      top.text = caption,
+      test.description = test.description,
+      p.adjust.method.text = p_adjust_text(p.adjust.method)
+    )
+  )
+}
+
+
 #' @name ggsignif_xy
 #' @importFrom utils combn
 #'

diff --git a/README.Rmd b/README.Rmd
@@ -424,9 +424,7 @@ ggstatsplot::ggwithinstats(
   y = Taste,
   sort = "descending", # ordering groups along the x-axis based on
   sort.fun = median, # values of `y` variable
-  pairwise.comparisons = TRUE,
-  pairwise.display = "s",
-  pairwise.annotation = "p",
+  pairwise.comparisons = TRUE, # show pairwise comparison test results
   title = "Wine tasting",
   caption = "Data from: `WRS2` R package",
   ggtheme = ggthemes::theme_fivethirtyeight(),

diff --git a/README.md b/README.md
@@ -7,9 +7,9 @@
 | --------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | [![CRAN\_Release\_Badge](http://www.r-pkg.org/badges/version-ago/ggstatsplot)](https://CRAN.R-project.org/package=ggstatsplot)                                  | [![Travis Build Status](https://travis-ci.org/IndrajeetPatil/ggstatsplot.svg?branch=master)](https://travis-ci.org/IndrajeetPatil/ggstatsplot)                                               | [![Daily downloads badge](https://cranlogs.r-pkg.org/badges/last-day/ggstatsplot?color=blue)](https://CRAN.R-project.org/package=ggstatsplot)     | [![GitHub version](https://img.shields.io/badge/GitHub-0.1.3.9000-orange.svg?style=flat-square)](https://github.com/IndrajeetPatil/ggstatsplot/)               | [![Website](https://img.shields.io/badge/website-ggstatsplot-orange.svg?colorB=E91E63)](https://indrajeetpatil.github.io/ggstatsplot/)                          |
 | [![CRAN Checks](https://cranchecks.info/badges/summary/ggstatsplot)](https://cran.r-project.org/web/checks/check_results_ggstatsplot.html)                      | [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/IndrajeetPatil/ggstatsplot?branch=master&svg=true)](https://ci.appveyor.com/project/IndrajeetPatil/ggstatsplot) | [![Weekly downloads badge](https://cranlogs.r-pkg.org/badges/last-week/ggstatsplot?color=blue)](https://CRAN.R-project.org/package=ggstatsplot)   | [![Forks](https://img.shields.io/badge/forks-85-blue.svg)](https://github.com/IndrajeetPatil/ggstatsplot/)                                                     | [![Rdoc](https://www.rdocumentation.org/badges/version/ggstatsplot)](https://www.rdocumentation.org/packages/ggstatsplot)                                       |
-| [![minimal R version](https://img.shields.io/badge/R%3E%3D-3.5.0-6666ff.svg)](https://cran.r-project.org/)                                                      | [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/)                                                                               | [![Monthly downloads badge](https://cranlogs.r-pkg.org/badges/last-month/ggstatsplot?color=blue)](https://CRAN.R-project.org/package=ggstatsplot) | [![Github Issues](https://img.shields.io/badge/issues-24-red.svg)](https://github.com/IndrajeetPatil/ggstatsplot/issues)                                       | [![vignettes](https://img.shields.io/badge/vignettes-0.1.3-orange.svg?colorB=FF5722)](https://CRAN.R-project.org/package=ggstatsplot/vignettes/)                |
+| [![minimal R version](https://img.shields.io/badge/R%3E%3D-3.5.0-6666ff.svg)](https://cran.r-project.org/)                                                      | [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/)                                                                               | [![Monthly downloads badge](https://cranlogs.r-pkg.org/badges/last-month/ggstatsplot?color=blue)](https://CRAN.R-project.org/package=ggstatsplot) | [![Github Issues](https://img.shields.io/badge/issues-23-red.svg)](https://github.com/IndrajeetPatil/ggstatsplot/issues)                                       | [![vignettes](https://img.shields.io/badge/vignettes-0.1.3-orange.svg?colorB=FF5722)](https://CRAN.R-project.org/package=ggstatsplot/vignettes/)                |
 | [![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/IndrajeetPatil/ggstatsplot.svg)](https://github.com/IndrajeetPatil/ggstatsplot) | [![Coverage Status](https://coveralls.io/repos/github/IndrajeetPatil/ggstatsplot/badge.svg?branch=master)](https://coveralls.io/github/IndrajeetPatil/ggstatsplot?branch=master)             | [![Total downloads badge](https://cranlogs.r-pkg.org/badges/grand-total/ggstatsplot?color=blue)](https://CRAN.R-project.org/package=ggstatsplot)  | [![Github Stars](https://img.shields.io/github/stars/IndrajeetPatil/ggstatsplot.svg?style=social&label=Github)](https://github.com/IndrajeetPatil/ggstatsplot) | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2074621.svg)](https://doi.org/10.5281/zenodo.2074621)                                                       |
-| [![Licence](https://img.shields.io/badge/licence-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)                                                | [![Codecov test coverage](https://codecov.io/gh/IndrajeetPatil/ggstatsplot/branch/master/graph/badge.svg)](https://codecov.io/gh/IndrajeetPatil/ggstatsplot?branch=master)                   | [![HitCount](http://hits.dwyl.io/IndrajeetPatil/ggstatsplot.svg)](http://hits.dwyl.io/IndrajeetPatil/ggstatsplot)                                 | [![Last-changedate](https://img.shields.io/badge/last%20change-2019--12--18-yellowgreen.svg)](https://github.com/IndrajeetPatil/ggstatsplot/commits/master)    | [![GitHub last commit](https://img.shields.io/github/last-commit/IndrajeetPatil/ggstatsplot.svg)](https://github.com/IndrajeetPatil/ggstatsplot/commits/master) |
+| [![Licence](https://img.shields.io/badge/licence-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)                                                | [![Codecov test coverage](https://codecov.io/gh/IndrajeetPatil/ggstatsplot/branch/master/graph/badge.svg)](https://codecov.io/gh/IndrajeetPatil/ggstatsplot?branch=master)                   | [![HitCount](http://hits.dwyl.io/IndrajeetPatil/ggstatsplot.svg)](http://hits.dwyl.io/IndrajeetPatil/ggstatsplot)                                 | [![Last-changedate](https://img.shields.io/badge/last%20change-2019--12--20-yellowgreen.svg)](https://github.com/IndrajeetPatil/ggstatsplot/commits/master)    | [![GitHub last commit](https://img.shields.io/github/last-commit/IndrajeetPatil/ggstatsplot.svg)](https://github.com/IndrajeetPatil/ggstatsplot/commits/master) |
 | [![status](https://tinyverse.netlify.com/badge/ggstatsplot)](https://CRAN.R-project.org/package=ggstatsplot)                                                    | [![R build status](https://github.com/IndrajeetPatil/ggstatsplot/workflows/R-CMD-check/badge.svg)](https://github.com/IndrajeetPatil/ggstatsplot)                                            | [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/ggstatsplot/community)                                           | [![Project Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)                                                     | [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/IndrajeetPatil/ggstatsplot/issues) |
 
 # Raison d’être
@@ -217,7 +217,7 @@ ggstatsplot::ggplot_converter
 #> function(plot) {
 #>   cowplot::ggdraw() + cowplot::draw_grob(grid::grobTree(plot))
 #> }
-#> <bytecode: 0x000000002d4a7830>
+#> <bytecode: 0x000000002d953a70>
 #> <environment: namespace:ggstatsplot>
 ```
 
@@ -437,9 +437,7 @@ ggstatsplot::ggwithinstats(
   y = Taste,
   sort = "descending", # ordering groups along the x-axis based on
   sort.fun = median, # values of `y` variable
-  pairwise.comparisons = TRUE,
-  pairwise.display = "s",
-  pairwise.annotation = "p",
+  pairwise.comparisons = TRUE, # show pairwise comparison test results
   title = "Wine tasting",
   caption = "Data from: `WRS2` R package",
   ggtheme = ggthemes::theme_fivethirtyeight(),

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -65,4 +65,5 @@ reference:
       - intent_morality
       - iris_long
       - VR_dilemma
+      - bugs_wide
       - bugs_long
diff --git a/codemeta.json b/codemeta.json
@@ -14,7 +14,7 @@
   ],
   "issueTracker": "https://github.com/IndrajeetPatil/ggstatsplot/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.1.4",
+  "version": "0.1.4.9000",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -87,18 +87,6 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=broom.mixed"
     },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "jmv",
-      "name": "jmv",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=jmv"
-    },
     {
       "@type": "SoftwareApplication",
       "identifier": "knitr",
@@ -231,7 +219,7 @@
       "@type": "SoftwareApplication",
       "identifier": "broomExtra",
       "name": "broomExtra",
-      "version": ">= 0.0.6",
+      "version": ">= 1.0.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -418,7 +406,7 @@
       "@type": "SoftwareApplication",
       "identifier": "pairwiseComparisons",
       "name": "pairwiseComparisons",
-      "version": ">= 0.1.2",
+      "version": ">= 0.1.3",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",

diff --git a/data-raw/bugs_wide.R b/data-raw/bugs_wide.R
@@ -0,0 +1,16 @@
+# loading the needed libraries
+library(jmv)
+library(tibble)
+library(tidyr)
+
+# loading dataset
+data("bugs", package = "jmv")
+
+# converting to long format
+bugs_wide <- tibble::as_tibble(bugs)
+
+# all column names in lower case
+names(bugs_wide) <- tolower(names(bugs_wide))
+
+# saving the data
+save(bugs_wide, file = "data/bugs_wide.rdata")
diff --git a/data/bugs_wide.rdata b/data/bugs_wide.rdata
diff --git a/docs/404.html b/docs/404.html