Merge pull request #93 from openpharma/90-bug-graph_test_closure-provides-inconsistent-results-between-rejections-and-closed-tests

90 bug graph test closure provides inconsistent results between rejections and closed tests

Author: xidongdxi

.gitignore

@@ -12,3 +12,5 @@ inst/doc
 *~$*docx
 *~$*xlsx
 *~$*pptx
+Rplots.pdf
+.DS_Store

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 0.2.8
+Version: 0.2.9
 Date: 2025-05-07 03:10:43 UTC
 SHA: 86213d2cf7bf8a29ac608260f2fd935e7fc2fd7d

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: graphicalMCP
 Title: Graphical Multiple Comparison Procedures
-Version: 0.2.8
+Version: 0.2.9
 Authors@R: c(
     person("Dong", "Xi", , "dong.xi1@gilead.com", role = c("aut", "cre")),
     person("Ethan", "Brockmann", , "ethan.brockmann@atorusresearch.com", role = "aut"),
@@ -48,5 +48,5 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Language: en-US

NEWS.md

@@ -59,3 +59,8 @@
 
 * Corrected urls for references
 * Submission for CRAN release
+
+# graphicalMCP 0.2.9
+
+* Closed Issue #90 by changing the precision for parametric tests
+* Submission for CRAN release

R/graph_test_closure.R

@@ -306,14 +306,19 @@ graph_test_closure <- function(graph,
   # The adjusted p-value for an *intersection* is the smallest adjusted p-value
   # for the groups it contains
   adjusted_p_intersection <- apply(adjusted_p, 1, min)
-  reject_intersection <-
-    adjusted_p_intersection <= (alpha + .Machine$double.eps)
+
+  # When parametric tests are used, mvtnorm::pmvnorm introduces Monte Carlo
+  # error (controlled by abseps, default 1e-6). A small tolerance is added to
+  # rejection comparisons to avoid false non-rejections at the boundary.
+  tol <- if (any(test_types == "parametric")) 1e-6 else .Machine$double.eps
+
+  reject_intersection <- adjusted_p_intersection <= (alpha + tol)
 
   # The adjusted p-value for a *hypothesis* is the largest adjusted p-value for
   # the intersections containing that hypothesis
   adjusted_p_hypothesis <-
     apply(adjusted_p_intersection * matrix_intersections, 2, max, na.rm = TRUE)
-  reject_hypothesis <- adjusted_p_hypothesis <= alpha # Hypothesis test results
+  reject_hypothesis <- adjusted_p_hypothesis <= (alpha + tol)
 
   # Adjusted p-value details ---------------------------------------------------
   # Reported adjusted p-values shouldn't exceed 1

codemeta.json

@@ -7,13 +7,13 @@
   "codeRepository": "https://github.com/openpharma/graphicalMCP",
   "issueTracker": "https://github.com/openpharma/graphicalMCP/issues",
   "license": "Apache License 2",
-  "version": "0.2.8",
+  "version": "0.2.9",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.1.2 (2021-11-01)",
+  "runtimePlatform": "R version 4.4.3 (2025-02-28)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -318,7 +318,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "803.544KB",
+  "fileSize": "775.434KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",
@@ -339,7 +339,7 @@
       "url": "https://CRAN.R-project.org/package=graphicalMCP"
     }
   ],
-  "releaseNotes": "https://github.com/openpharma/graphicalMCP/blob/master/NEWS.md",
+  "releaseNotes": "https://github.com/openpharma/graphicalMCP/blob/main/NEWS.md",
   "readme": "https://github.com/openpharma/graphicalMCP/blob/main/README.md",
   "developmentStatus": "https://www.repostatus.org/#active",
   "relatedLink": "https://CRAN.R-project.org/package=graphicalMCP"

cran-comments.md

@@ -1,3 +1,12 @@
+# Version 0.2.9
+
+- This is the ninth submission to CRAN.
+- Closed Issue #90 by changing the precision for parametric tests
+
+## R CMD check results
+
+0 errors | 0 warnings | 0 notes
+
 # Version 0.2.8
 
 - This is the eighth submission to CRAN.

tests/testthat/Rplots.pdf

@@ -271,13 +271,14 @@ write.csv(
 
 ```{r power-conventional, include = FALSE, eval = FALSE}
 gcp_conventional <- function(
-    graph,
-    alpha = 0.025,
-    power_marginal = rep(alpha, length(graph$hypotheses)),
-    sim_n = 100,
-    sim_corr = diag(length(graph$hypotheses)),
-    sim_success = NULL,
-    verbose = FALSE) {
+  graph,
+  alpha = 0.025,
+  power_marginal = rep(alpha, length(graph$hypotheses)),
+  sim_n = 100,
+  sim_corr = diag(length(graph$hypotheses)),
+  sim_success = NULL,
+  verbose = FALSE
+) {
   hyp_names <- names(graph$hypotheses)
   num_hyps <- length(graph$hypotheses)