Improve test helper and reporting reliability

r_functionality.R

@@ -911,8 +911,10 @@ checkAssumptionsForAnova <- function(data, y, factors) {
     return("You must take the non-parametric ANOVA as Levene’s test is significant (p < 0.05).")
   }
 
-  print("You may take parametric ANOVA (function anova_test). See https://www.datanovia.com/en/lessons/anova-in-r/#check-assumptions-1 for more information.")
-}
+  message("You may take parametric ANOVA (function anova_test). See https://www.datanovia.com/en/lessons/anova-in-r/#check-assumptions-1 for more information.")
+
+  invisible(NULL)
+}
 
 
 #' Generate the Latex-text based on the NPAV by Lüpsen (see \url{http://www.uni-koeln.de/~luepsen/R/}).
@@ -1113,40 +1115,46 @@ reportNPAVChi <- function(model, dv = "Testdependentvariable", write_to_clipboar
         stringtowrite <- paste0("The NPAV found a significant main effect of \\", trimws(model$descriptions[i]), " on ", dv, " (\\chisq~(1)=", Chivalue, ", ",  pValue, ")")
       }
 
-      effect_size_text <- ""
-      if (!is.null(sample_size) && is.numeric(sample_size) && sample_size > 0) {
-        effect_size <- tryCatch(
-          effectsize::chisq_to_w(
-            chi = Chivalue,
-            n = sample_size,
-            ci = 0.95
-          ),
-          error = function(e) NULL
-        )
-
-        if (!is.null(effect_size)) {
-          effect_size <- as.data.frame(effect_size)
-          w_value <- effect_size$Cohens_w
-          ci_low <- effect_size$CI_low
-          ci_high <- effect_size$CI_high
-          if (!is.null(w_value) && !is.na(w_value)) {
-            effect_size_text <- paste0(
-              ", $w=",
-              sprintf("%.2f", w_value)
-            )
-            if (!is.null(ci_low) && !is.null(ci_high) && !any(is.na(c(ci_low, ci_high)))) {
-              effect_size_text <- paste0(
-                effect_size_text,
-                " [",
-                sprintf("%.2f", ci_low),
-                ", ",
-                sprintf("%.2f", ci_high),
-                "]"
-              )
-            }
-          }
-        }
-      }
+      effect_size_text <- ""
+      if (!is.null(sample_size) && is.numeric(sample_size) && sample_size > 0) {
+        effect_size <- tryCatch(
+          effectsize::chisq_to_w(
+            chi = Chivalue,
+            n = sample_size,
+            ci = 0.95
+          ),
+          error = function(e) NULL
+        )
+
+        w_value <- sqrt(Chivalue / sample_size)
+        ci_low <- NULL
+        ci_high <- NULL
+
+        if (!is.null(effect_size)) {
+          effect_size <- as.data.frame(effect_size)
+          w_value <- effect_size$Cohens_w %||% w_value
+          ci_low <- effect_size$CI_low
+          ci_high <- effect_size$CI_high
+        }
+
+        if (!is.null(w_value) && !is.na(w_value)) {
+          effect_size_text <- paste0(
+            ", $w=",
+            sprintf("%.2f", w_value)
+          )
+
+          if (!is.null(ci_low) && !is.null(ci_high) && !any(is.na(c(ci_low, ci_high)))) {
+            effect_size_text <- paste0(
+              effect_size_text,
+              " [",
+              sprintf("%.2f", ci_low),
+              ", ",
+              sprintf("%.2f", ci_high),
+              "]"
+            )
+          }
+        }
+      }
 
       stringtowrite <- paste0(stringtowrite, effect_size_text, ". ")
 
@@ -1838,15 +1846,24 @@ reportDunnTestTable <- function(d = NULL, data, iv = "testiv", dv = "testdv", or
   # Format effect size
   table$r <- formatC(table$r, digits = 2, format = "f")
 
-  # Adjust the xtable call to handle the modified columns
-  xtable_obj <- xtable(table, 
-                       digits = c(0, 0, 4, 0, 0),
-                       caption = paste0("Post-hoc comparisons for independent variable \\", iv, 
-                                        " and dependent variable \\", dv, 
-                                        ". Positive Z-values mean that the first-named level is sig. higher than the second-named. For negative Z-values, the opposite is true. Effect size reported as rank-biserial correlation (r)."), 
-                       label = paste0("tab:posthoc-", iv, "-", dv))
-
-  print(xtable_obj, type = "latex", size = latexSize, caption.placement = "top", include.rownames = FALSE)
+  # Adjust the xtable call to handle the modified columns
+  if (requireNamespace("xtable", quietly = TRUE)) {
+    xtable_obj <- xtable::xtable(table,
+                         digits = c(0, 0, 4, 0, 0),
+                         caption = paste0("Post-hoc comparisons for independent variable \\", iv,
+                                          " and dependent variable \\", dv,
+                                          ". Positive Z-values mean that the first-named level is sig. higher than the second-named. For negative Z-values, the opposite is true. Effect size reported as rank-biserial correlation (r)."),
+                         label = paste0("tab:posthoc-", iv, "-", dv))
+
+    print(xtable_obj, type = "latex", size = latexSize, caption.placement = "top", include.rownames = FALSE)
+  } else {
+    cat(paste0(
+      "Post-hoc comparisons for independent variable \", iv,
+      " and dependent variable \", dv,
+      ". Positive Z-values mean that the first-named level is sig. higher than the second-named. For negative Z-values, the opposite is true. Effect size reported as rank-biserial correlation (r).\n"
+    ))
+    print(table)
+  }
 }
 
 #' Report statistical details for ggstatsplot.

tests/testthat/test_r_functionality.R

@@ -73,7 +73,10 @@ posthoc_stats <- list(
 
 basic_plot <- ggplot2::ggplot(sample_df, ggplot2::aes(x = ConditionID, y = value)) + ggplot2::geom_point()
 
-with_mock <- testthat::with_mocked_bindings
+# Helper wrapper to avoid relying on pkgload/devtools metadata when mocking
+with_mock <- function(..., .env = parent.frame()) {
+  testthat::with_mocked_bindings(..., .package = "base", .env = .env)
+}
 
 
 #### basic utilities ---------------------------------------------------------