From fa684a9a3bfc6ae66d39ac18471743b53b23e4d2 Mon Sep 17 00:00:00 2001
From: Dong Xi <38050865+xidongdxi@users.noreply.github.com>
Date: Fri, 20 Mar 2026 22:09:16 -0400
Subject: [PATCH 1/3] fix issue 90 by changing precision

---
 .gitignore                |   2 ++
 R/graph_test_closure.R    |  11 ++++++++---
 tests/testthat/Rplots.pdf | Bin 9091 -> 0 bytes
 3 files changed, 10 insertions(+), 3 deletions(-)
 delete mode 100644 tests/testthat/Rplots.pdf

diff --git a/.gitignore b/.gitignore
index a18da5b7..7d133ee0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,3 +12,5 @@ inst/doc
 *~$*docx
 *~$*xlsx
 *~$*pptx
+Rplots.pdf
+.DS_Store
diff --git a/R/graph_test_closure.R b/R/graph_test_closure.R
index ba59b8f0..c8cb1b50 100644
--- a/R/graph_test_closure.R
+++ b/R/graph_test_closure.R
@@ -306,14 +306,19 @@ graph_test_closure <- function(graph,
   # The adjusted p-value for an *intersection* is the smallest adjusted p-value
   # for the groups it contains
   adjusted_p_intersection <- apply(adjusted_p, 1, min)
-  reject_intersection <-
-    adjusted_p_intersection <= (alpha + .Machine$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
diff --git a/tests/testthat/Rplots.pdf b/tests/testthat/Rplots.pdf
deleted file mode 100644
index adba4e38b42531db1adc63edca02c50d1d885aa6..0000000000000000000000000000000000000000
GIT binary patch
literal 0
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M(P(HSm88)A2XRxyVE_OC


From b907f0b957ff8b5d07fd3de370b1bab678ff267a Mon Sep 17 00:00:00 2001
From: Dong Xi <38050865+xidongdxi@users.noreply.github.com>
Date: Fri, 20 Mar 2026 23:02:21 -0400
Subject: [PATCH 2/3] updated other files for 0.2.9

---
 CRAN-SUBMISSION                |  2 +-
 DESCRIPTION                    |  4 ++--
 NEWS.md                        |  5 +++++
 codemeta.json                  |  8 ++++----
 cran-comments.md               |  5 +++++
 vignettes/generate-closure.Rmd | 15 ++++++++-------
 6 files changed, 25 insertions(+), 14 deletions(-)

diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
index 6bb573f1..7347c74b 100644
--- a/CRAN-SUBMISSION
+++ b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 0.2.8
+Version: 0.2.9
 Date: 2025-05-07 03:10:43 UTC
 SHA: 86213d2cf7bf8a29ac608260f2fd935e7fc2fd7d
diff --git a/DESCRIPTION b/DESCRIPTION
index 3ebc6abb..ba31978f 100644
--- a/DESCRIPTION
+++ b/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
diff --git a/NEWS.md b/NEWS.md
index 031f2daa..2e2d7d2f 100644
--- a/NEWS.md
+++ b/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
\ No newline at end of file
diff --git a/codemeta.json b/codemeta.json
index 594ff230..b9e12742 100644
--- a/codemeta.json
+++ b/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"
diff --git a/cran-comments.md b/cran-comments.md
index 2c20cdd4..39dcbf74 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,3 +1,8 @@
+# Version 0.2.9
+
+- This is the ninth submission to CRAN.
+- Closed Issue #90 by changing the precision for parametric tests
+
 # Version 0.2.8
 
 - This is the eighth submission to CRAN.
diff --git a/vignettes/generate-closure.Rmd b/vignettes/generate-closure.Rmd
index 8b4e1516..bb3d6ecc 100644
--- a/vignettes/generate-closure.Rmd
+++ b/vignettes/generate-closure.Rmd
@@ -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)
 

From 89e4d4d5ee1d0f436188ae47caf7927ff2f1c1f3 Mon Sep 17 00:00:00 2001
From: Dong Xi <38050865+xidongdxi@users.noreply.github.com>
Date: Fri, 20 Mar 2026 23:13:02 -0400
Subject: [PATCH 3/3] Updated cran-comments.md

---
 cran-comments.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/cran-comments.md b/cran-comments.md
index 39dcbf74..e6f1192e 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -3,6 +3,10 @@
 - 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.