ggbarstats p instead of asterisk

IndrajeetPatil · Dec 2, 2020 · a3074ab · a3074ab · lintr-bot · Dec 2, 2020
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diff --git a/NAMESPACE b/NAMESPACE
@@ -71,7 +71,6 @@ importFrom(ipmisc,"%<>%")
 importFrom(ipmisc,"%>%")
 importFrom(ipmisc,as_tibble)
 importFrom(ipmisc,enframe)
-importFrom(ipmisc,signif_column)
 importFrom(ipmisc,specify_decimal_p)
 importFrom(ipmisc,stats_type_switch)
 importFrom(ipmisc,tibble)

diff --git a/NEWS.md b/NEWS.md
@@ -25,10 +25,10 @@ BUG FIXES
 
   - Setting `mean.path = FALSE` in `ggwithinstats` produced incorrect colors for
     points (#470). This bug was introduced in `0.6.5` and is now fixed.
-    
+
   - If user had set `options(scipen = 999)` in their session, the *p*-value
-    formatting for `ggpiestats` and `ggcoefstats` looked super-ugly (#478).
-    This has been fixed.
+    formatting for `ggpiestats` and `ggcoefstats` looked super-ugly (#478). This
+    has been fixed.
 
 MAJOR CHANGES
 
@@ -38,7 +38,7 @@ MAJOR CHANGES
   - `ggpiestats` and `ggbarstats` don't support returning dataframes. See FAQ
     vignette on how to get these dataframes:
     <https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/faq.html#faq-1>
-    
+
   - `ggpiestats` and `ggbarstats` were not supposed to support returning Bayes
     Factor for paired contingency table analysis, which is not supported in
     `BayesFactor` itself.
@@ -47,6 +47,10 @@ MAJOR CHANGES
     degrees of freedom are not available for `t`-statistic, they are displayed
     to be `Inf`, in keeping with `easystats` conventions.
 
+  - Instead of showing significance of *p*-values with APA's asterisks
+    conventions, `ggbarstats` now instead shows the actual *p*-values from
+    one-sample proportion tests.
+
 NEW FEATURES
 
   - More models supported in `ggcoefstats`: `Glm`.

diff --git a/R/ggbarstats.R b/R/ggbarstats.R
@@ -203,14 +203,10 @@ ggbarstats <- function(data,
     p <- p +
       ggplot2::geom_text(
         data = df_proptest,
-        mapping = ggplot2::aes(
-          x = {{ y }},
-          y = 1.05,
-          label = significance,
-          fill = NULL
-        ),
-        size = 5,
-        na.rm = TRUE
+        mapping = ggplot2::aes(x = {{ y }}, y = 1.05, label = .p.label, fill = NULL),
+        size = 2.8,
+        na.rm = TRUE,
+        parse = TRUE
       )
   }
 
@@ -219,12 +215,7 @@ ggbarstats <- function(data,
     p <- p +
       ggplot2::geom_text(
         data = df_proptest,
-        mapping = ggplot2::aes(
-          x = {{ y }},
-          y = -0.05,
-          label = N,
-          fill = NULL
-        ),
+        mapping = ggplot2::aes(x = {{ y }}, y = -0.05, label = N, fill = NULL),
         size = 4,
         na.rm = TRUE
       )

diff --git a/R/ggpiestats.R b/R/ggpiestats.R
@@ -12,8 +12,9 @@
 #'   (a goodness of fit test) will be run for the `x` variable. Otherwise an
 #'   appropriate association test will be run. This argument can not be `NULL`
 #'   for `ggbarstats` function.
-#' @param proportion.test Decides whether proportion test for `x` variable is
-#'   to be carried out for each level of `y` (Default: `TRUE`).
+#' @param proportion.test Decides whether proportion test for `x` variable is to
+#'   be carried out for each level of `y` (Default: `TRUE`). In `ggbarstats`,
+#'   only *p*-values from this test will be displayed.
 #' @param perc.k Numeric that decides number of decimal places for percentage
 #'   labels (Default: `0`).
 #' @param label Character decides what information needs to be displayed

diff --git a/R/global_vars.R b/R/global_vars.R
@@ -30,7 +30,8 @@ utils::globalVariables(
     "term",
     "df",
     ".label",
-    ".counts"
+    ".counts",
+    ".p.label"
   ),
   package = "ggstatsplot",
   add = FALSE

diff --git a/R/helpers_ggbetweenstats_graphics.R b/R/helpers_ggbetweenstats_graphics.R
@@ -14,7 +14,7 @@
 #' @importFrom dplyr select group_by matches mutate rowwise group_modify arrange ungroup
 #' @importFrom rlang !! enquo ensym :=
 #' @importFrom tidyr drop_na
-#' @importFrom ipmisc specify_decimal_p signif_column
+#' @importFrom ipmisc specify_decimal_p
 #'
 #' @examples
 #' # this internal function may not have much utility outside of the package

diff --git a/R/helpers_ggcatstats_graphics.R b/R/helpers_ggcatstats_graphics.R
@@ -44,8 +44,7 @@ df_descriptive <- function(data,
 
 # creating a dataframe with counts
 cat_counter <- function(data, x, y = NULL, ...) {
-  data %>%
-    dplyr::group_by(.data = ., {{ y }}, {{ x }}, .drop = TRUE) %>%
+  dplyr::group_by(.data = data, {{ y }}, {{ x }}, .drop = TRUE) %>%
     dplyr::tally(x = ., name = "counts") %>%
     dplyr::mutate(.data = ., perc = (counts / sum(counts)) * 100) %>%
     dplyr::ungroup(.) %>%
@@ -60,18 +59,16 @@ cat_counter <- function(data, x, y = NULL, ...) {
 #'
 #' @noRd
 
-# combine info about sample size plus
-df_proptest <- function(data, x, y, k = 3L, ...) {
+# combine info about sample size plus proportion test
+df_proptest <- function(data, x, y, k = 2L, ...) {
   dplyr::full_join(
     # descriptives
     x = cat_counter(data = data, x = {{ y }}) %>%
       dplyr::mutate(N = paste0("(n = ", .prettyNum(counts), ")")),
     # proportion tests
     y = dplyr::group_by(data, {{ y }}) %>%
       dplyr::group_modify(.f = ~ chisq_test_safe(., {{ x }})) %>%
-      dplyr::ungroup(.) %>%
-      ipmisc::signif_column(data = ., p = p.value) %>%
-      dplyr::filter(.data = ., !is.na(significance)),
+      dplyr::ungroup(.),
     by = rlang::as_name(rlang::ensym(y))
   ) %>%
     dplyr::rowwise() %>%
@@ -87,7 +84,8 @@ df_proptest <- function(data, x, y, k = 3L, ...) {
         "', ~italic(n)==",
         counts,
         ")"
-      )
+      ),
+      .p.label = paste0("list(~italic(p)=='", specify_decimal_p(p.value, k, TRUE), "')")
     ) %>%
     dplyr::ungroup()
 }

diff --git a/README.Rmd b/README.Rmd
@@ -736,6 +736,8 @@ ggstatsplot::ggbarstats(
 )
 ```
 
+(The *p*-values from one-sample proportion test are displayed on top of each bar.)
+
 And, needless to say, there is also a `grouped_` variant of this function-
 
 ```{r ggbarstats2, fig.height = 12, fig.width = 10}

diff --git a/README.md b/README.md
@@ -825,6 +825,9 @@ ggstatsplot::ggbarstats(
 
 <img src="man/figures/README-ggbarstats1-1.png" width="100%" />
 
+(The *p*-values from one-sample proportion test are displayed on top of
+each column.)
+
 And, needless to say, there is also a `grouped_` variant of this
 function-
 

diff --git a/docs/articles/web_only/faq.html b/docs/articles/web_only/faq.html
diff --git a/docs/articles/web_only/faq_files/figure-html/ggbar_colors-1.png b/docs/articles/web_only/faq_files/figure-html/ggbar_colors-1.png
diff --git a/docs/articles/web_only/gallery_files/figure-html/gallery2-1.png b/docs/articles/web_only/gallery_files/figure-html/gallery2-1.png
diff --git a/docs/articles/web_only/ggbetweenstats.html b/docs/articles/web_only/ggbetweenstats.html
diff --git a/docs/articles/web_only/ggcorrmat.html b/docs/articles/web_only/ggcorrmat.html
diff --git a/docs/articles/web_only/ggdotplotstats.html b/docs/articles/web_only/ggdotplotstats.html
diff --git a/docs/articles/web_only/gghistostats.html b/docs/articles/web_only/gghistostats.html
diff --git a/docs/articles/web_only/gghistostats_files/figure-html/grouped1-1.png b/docs/articles/web_only/gghistostats_files/figure-html/grouped1-1.png
diff --git a/docs/articles/web_only/gghistostats_files/figure-html/psychact3-1.png b/docs/articles/web_only/gghistostats_files/figure-html/psychact3-1.png
diff --git a/docs/articles/web_only/ggpiestats.html b/docs/articles/web_only/ggpiestats.html
diff --git a/docs/articles/web_only/ggscatterstats.html b/docs/articles/web_only/ggscatterstats.html
diff --git a/docs/articles/web_only/ggwithinstats.html b/docs/articles/web_only/ggwithinstats.html
diff --git a/docs/articles/web_only/other_resources.html b/docs/articles/web_only/other_resources.html
diff --git a/docs/articles/web_only/other_resources_files/header-attrs-2.5.3/header-attrs.js b/docs/articles/web_only/other_resources_files/header-attrs-2.5.3/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -19,7 +19,7 @@ articles:
   web_only/purrr_examples: purrr_examples.html
   web_only/session_info: session_info.html
   web_only/theme_ggstatsplot: theme_ggstatsplot.html
-last_built: 2020-12-01T23:14Z
+last_built: 2020-12-02T18:57Z
 urls:
   reference: https://indrajeetpatil.github.io/ggstatsplot//reference
   article: https://indrajeetpatil.github.io/ggstatsplot//articles

diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
diff --git a/docs/reference/figures/README-ggbarstats1-1.png b/docs/reference/figures/README-ggbarstats1-1.png
diff --git a/docs/reference/figures/README-ggbarstats2-1.png b/docs/reference/figures/README-ggbarstats2-1.png
diff --git a/docs/reference/figures/README-ggscatterstats2-1.png b/docs/reference/figures/README-ggscatterstats2-1.png
diff --git a/docs/reference/ggbarstats-1.png b/docs/reference/ggbarstats-1.png
-Original file line number
+Diff line change
@@ Expand Up / @@ -736,6 +736,8 @@ ggstatsplot::ggbarstats( @@
     )
     ```
+    (The *p*-values from one-sample proportion test are displayed on top of each bar.)
     And, needless to say, there is also a `grouped_` variant of this function-
     ```{r ggbarstats2, fig.height = 12, fig.width = 10}
@@ Expand Down @@