Merge pull request #362 from easystats/copilot/fix-p-value-stars-display

Fix conditional formatting rule ordering for openxlsx2 v1.21 compatibility

Author: rempsyc

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: correlation
 Title: Methods for Correlation Analysis
-Version: 0.8.8
+Version: 0.8.8.1
 Authors@R:
     c(person(given = "Dominique",
              family = "Makowski",
@@ -88,7 +88,7 @@ VignetteBuilder:
     knitr
 Encoding: UTF-8
 Language: en-US
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3
 Config/Needs/website:

NEWS.md

@@ -1,3 +1,11 @@
+# correlation 0.8.9
+
+## Bug Fixes
+
+- `cormatrix_to_excel()` now works correctly with openxlsx2 v1.16+. Fixed
+  conditional formatting rule ordering to accommodate openxlsx2's new waterfall
+  strategy (#361).
+
 # correlation 0.8.8
 
 - `correlation()` gains a `missing=` argument, similar to `stats::cor(use=)`, for controlling how missing data is handled.

R/cormatrix_to_excel.R

@@ -41,13 +41,17 @@
 #' \dontshow{
 #' setwd(.old_wd)
 #' }
-cormatrix_to_excel <- function(data,
-                               filename,
-                               overwrite = TRUE,
-                               print.mat = TRUE,
-                               ...) {
+cormatrix_to_excel <- function(
+  data,
+  filename,
+  overwrite = TRUE,
+  print.mat = TRUE,
+  ...
+) {
   if (missing(filename)) {
-    insight::format_error("Argument 'filename' required (as per CRAN policies).")
+    insight::format_error(
+      "Argument 'filename' required (as per CRAN policies)."
+    )
   }
 
   insight::check_if_installed("openxlsx2")
@@ -241,52 +245,61 @@ cormatrix_to_excel <- function(data,
   wb$add_worksheet("p_values")$add_data(x = p_val)
 
   # create conditional formatting for the stars (as well as colours as we have no)
-  # one star
   # Compute the cell range for styling
   dims_fmt <- openxlsx2::wb_dims(cols = all.columns, rows = all.columns)
+
+  # gray diagonal (most specific, must be first to win for r = 1)
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 <= .2, r_values!B2 > 0, p_values!B2 < .05)",
-    style = "one_star_pink"
+    rule = "r_values!B2 = 1",
+    style = "gray_style"
   )
+
+  # three stars (p < .001) - most specific color ranges first
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 >= .2, p_values!B2 < .05)",
-    style = "one_star_peach"
+    rule = "AND(r_values!B2 >= .4, p_values!B2 < .001)",
+    style = "three_stars_red"
   )
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 >= .4, p_values!B2 < .05)",
-    style = "one_star_red"
+    rule = "AND(r_values!B2 >= .2, p_values!B2 < .001)",
+    style = "three_stars_peach"
   )
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 >= -.2, r_values!B2 < 0, p_values!B2 < .05)",
-    style = "one_star_lightblue"
+    rule = "AND(r_values!B2 <= .2, r_values!B2 > 0, p_values!B2 < .001)",
+    style = "three_stars_pink"
   )
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 <= -.2, p_values!B2 < .05)",
-    style = "one_star_midblue"
+    rule = "AND(r_values!B2 <= -.4, p_values!B2 < .001)",
+    style = "three_stars_darkblue"
   )
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 <= -.4, p_values!B2 < .05)",
-    style = "one_star_darkblue"
+    rule = "AND(r_values!B2 <= -.2, p_values!B2 < .001)",
+    style = "three_stars_midblue"
+  )
+  wb$add_conditional_formatting(
+    "r_values",
+    dims = dims_fmt,
+    rule = "AND(r_values!B2 >= -.2, r_values!B2 < 0, p_values!B2 < .001)",
+    style = "three_stars_lightblue"
   )
 
-  # two stars
+  # two stars (p < .01) - most specific color ranges first
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 <= .2, r_values!B2 > 0, p_values!B2 < .01)",
-    style = "two_stars_pink"
+    rule = "AND(r_values!B2 >= .4, p_values!B2 < .01)",
+    style = "two_stars_red"
   )
   wb$add_conditional_formatting(
     "r_values",
@@ -297,14 +310,14 @@ cormatrix_to_excel <- function(data,
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 >= .4, p_values!B2 < .01)",
-    style = "two_stars_red"
+    rule = "AND(r_values!B2 <= .2, r_values!B2 > 0, p_values!B2 < .01)",
+    style = "two_stars_pink"
   )
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 >= -.02, r_values!B2 < 0, p_values!B2 < .01)",
-    style = "two_stars_lightblue"
+    rule = "AND(r_values!B2 <= -.4, p_values!B2 < .01)",
+    style = "two_stars_darkblue"
   )
   wb$add_conditional_formatting(
     "r_values",
@@ -315,74 +328,68 @@ cormatrix_to_excel <- function(data,
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 <= -.4, p_values!B2 < .01)",
-    style = "two_stars_darkblue"
+    rule = "AND(r_values!B2 >= -.2, r_values!B2 < 0, p_values!B2 < .01)",
+    style = "two_stars_lightblue"
   )
 
-  # three stars
+  # one star (p < .05) - most specific color ranges first
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 <= .2, r_values!B2 > 0, p_values!B2 < .001)",
-    style = "three_stars_pink"
+    rule = "AND(r_values!B2 >= .4, p_values!B2 < .05)",
+    style = "one_star_red"
   )
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 >= .2, p_values!B2 < .001)",
-    style = "three_stars_peach"
+    rule = "AND(r_values!B2 >= .2, p_values!B2 < .05)",
+    style = "one_star_peach"
   )
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 >= .4, p_values!B2 < .001)",
-    style = "three_stars_red"
+    rule = "AND(r_values!B2 <= .2, r_values!B2 > 0, p_values!B2 < .05)",
+    style = "one_star_pink"
   )
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 >= -.2, r_values!B2 < 0, p_values!B2 < .001)",
-    style = "three_stars_lightblue"
+    rule = "AND(r_values!B2 <= -.4, p_values!B2 < .05)",
+    style = "one_star_darkblue"
   )
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 <= -.2, p_values!B2 < .001)",
-    style = "three_stars_midblue"
+    rule = "AND(r_values!B2 <= -.2, p_values!B2 < .05)",
+    style = "one_star_midblue"
   )
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
-    rule = "AND(r_values!B2 <= -.4, p_values!B2 < .001)",
-    style = "three_stars_darkblue"
+    rule = "AND(r_values!B2 >= -.2, r_values!B2 < 0, p_values!B2 < .05)",
+    style = "one_star_lightblue"
   )
 
-  # Other formatting
-  wb$add_conditional_formatting(
-    "r_values",
-    dims = dims_fmt,
-    rule = "AND(r_values!B2 = 1)",
-    style = "gray_style"
-  )
+  # no stars (for non-significant correlations)
   wb$add_conditional_formatting(
     "r_values",
     dims = dims_fmt,
     rule = "AND(p_values!B2 >= .05)",
     style = "no_star"
   )
 
-  # p-values
+  # p-values (most specific first)
   wb$add_conditional_formatting(
     "p_values",
     dims = dims_fmt,
-    rule = "< 10",
-    style = "p_style"
+    rule = "== 0",
+    style = "gray_style"
   )
   wb$add_conditional_formatting(
     "p_values",
     dims = dims_fmt,
-    rule = "< .05",
-    style = "p_style1"
+    rule = "< .001",
+    style = "p_style3"
   )
   wb$add_conditional_formatting(
     "p_values",
@@ -393,14 +400,14 @@ cormatrix_to_excel <- function(data,
   wb$add_conditional_formatting(
     "p_values",
     dims = dims_fmt,
-    rule = "< .001",
-    style = "p_style3"
+    rule = "< .05",
+    style = "p_style1"
   )
   wb$add_conditional_formatting(
     "p_values",
     dims = dims_fmt,
-    rule = "== 0",
-    style = "gray_style"
+    rule = "< 10",
+    style = "p_style"
   )
 
   ## Freeze Panes
@@ -409,7 +416,8 @@ cormatrix_to_excel <- function(data,
 
   # Save Excel
   cat(paste0(
-    "\n\n [Correlation matrix '", filename,
+    "\n\n [Correlation matrix '",
+    filename,
     ".xlsx' has been saved to working directory (or where specified).]"
   ))
   openxlsx2::wb_save(wb, file = paste0(filename, ".xlsx"), overwrite = TRUE)

man/cor_smooth.Rd

@@ -5,9 +5,9 @@
     Output
       # Correlation Matrix (pearson-method)
       
-      Parameter1 | Parameter2 |    r |       95% CI | t(9) |         p
-      ----------------------------------------------------------------
-      x1         |         x2 | 1.00 | [1.00, 1.00] |  Inf | < .001***
+      Parameter1 | Parameter2 | r |       95% CI | t(9) |         p
+      -------------------------------------------------------------
+      x1         |         x2 | 1 | [1.00, 1.00] |  Inf | < .001***
       
       p-value adjustment method: Holm (1979)
       Observations: 11
@@ -19,9 +19,9 @@
     Output
       # Correlation Matrix (pearson-method)
       
-      Parameter1 | Parameter2 |    r |       95% CI | t(9) |         p
-      ----------------------------------------------------------------
-      var1       |       var2 | 1.00 | [1.00, 1.00] |  Inf | < .001***
+      Parameter1 | Parameter2 | r |       95% CI | t(9) |         p
+      -------------------------------------------------------------
+      var1       |       var2 | 1 | [1.00, 1.00] |  Inf | < .001***
       
       p-value adjustment method: Holm (1979)
       Observations: 11