Merge pull request #29 from Merck/news

Standardize package name format and update news for gMCPLite 0.1.5 release

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: gMCPLite
 Title: Lightweight Graph Based Multiple Comparison Procedures
-Version: 0.1.4
+Version: 0.1.5
 Authors@R: c(
     person("Yalin", "Zhu", email = "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0003-3830-8660")),

NEWS.md

@@ -1,3 +1,12 @@
+# gMCPLite 0.1.5
+
+- In `hGraph()`, the `scale_fill_manual()` call now has the `guide`
+  argument explicitly named for compatibility with ggplot2 >= 3.5.0
+  (thanks, @teunbrand, #25).
+- Port essential upstream changes in gMCP 0.8-16, including a fix for
+  confidence interval calculations (#28).
+- Standardize package name style in documentation (#29).
+
 # gMCPLite 0.1.4
 
 - Use the `cairo_pdf()` device for better Unicode character plotting support

R/hgraph.R

@@ -18,7 +18,7 @@
 #' Create multiplicity graphs using ggplot2
 #'
 #' Plots a multiplicity graph defined by user inputs.
-#' The graph can also be used with the ***gMCP*** package to evaluate a set of
+#' The graph can also be used with the gMCP package to evaluate a set of
 #' nominal p-values for the tests of the hypotheses in the graph.
 #'
 #' @param nHypotheses number of hypotheses in graph

README.md

@@ -6,13 +6,13 @@
 [![Codecov test coverage](https://codecov.io/gh/Merck/gMCPLite/branch/main/graph/badge.svg)](https://app.codecov.io/gh/Merck/gMCPLite?branch=main)
 <!-- badges: end -->
 
-`gMCPLite` is a fork of `gMCP` for graph-based multiple comparison procedures,
+gMCPLite is a fork of gMCP for graph-based multiple comparison procedures,
 with the following features:
 
 - Kept a selected subset of the original functions.
-- Removed the `rJava` dependency and the Java-based graphical interface.
-- Added an `hGraph()` function for `ggplot2` visualizations.
-  It bridges `gMCP` result objects and `gsDesign` to produce
+- Removed the rJava dependency and the Java-based graphical interface.
+- Added an `hGraph()` function for ggplot2 visualizations.
+  It bridges gMCP result objects and gsDesign to produce
   multiple comparison graphs and sequential graph updates.
 
 ## Installation

_pkgdown.yml

@@ -5,6 +5,7 @@ url: https://merck.github.io/gMCPLite/
 template:
   bootstrap: 5
   bslib:
+    preset: "bootstrap"
     primary: "#00857c"
     navbar-light-brand-color: "#fff"
     navbar-light-brand-hover-color: "#fff"

vignettes/GraphicalMultiplicity.Rmd

@@ -30,12 +30,12 @@ knitr::opts_chunk$set(
 
 This document is intended to evaluate statistical significance for graphical multiplicity control when used with group sequential design [@MaurerBretz2013]. In particular, we demonstrate design and analysis of a complex oncology trial.
 There are many details building on the necessarily simple example provided by @MaurerBretz2013.
-The combination of tools provided by the **gMCPLite** and **gsDesign** packages is non-trivial, but developed in a way that is meant to be re-used in a straightforward fashion.
+The combination of tools provided by the gMCPLite and gsDesign packages is non-trivial, but developed in a way that is meant to be re-used in a straightforward fashion.
 This has been found to be particularly valuable to provide a prompt and verifiable conclusion in multiple trials such as @KEYNOTE048 where 14 hypotheses were evaluated using a template such as this.
 
 Given the complexity involved, substantial effort has been taken to provide methods to check hypothesis testing.
 
-- The initial testing is done by using sequential p-values [@LiuAnderson2008] which can then be plugged into standard graphical hypothesis testing R package, **gMCP** [@Bretz2009].
+- The initial testing is done by using sequential p-values [@LiuAnderson2008] which can then be plugged into standard graphical hypothesis testing R package, gMCP [@Bretz2009].
 - The graphical testing produces a sequence including the original multiplicity graph, followed by updated multiplicity graphs, each with a single hypothesis rejected from the previous graph.
 - The final graph, assuming not all hypotheses were rejected, provides the final Type I error available for testing each hypothesis that was not rejected.
 - Updated group sequential bounds for each hypothesis at the largest alpha-level it was evaluated can be checked vs. nominal p-values at each analysis to verify the testing conclusions reached with the above methods.
@@ -653,7 +653,7 @@ options(old)
 ## Session information
 
 You can use `sessionInfo()` to document the versions of R and R packages used to render this document.
-Note, in particular, that version 3.1 or later of the **gsDesign** package is needed.
+Note, in particular, that version 3.1 or later of the gsDesign package is needed.
 
 ## References
 

vignettes/hGraph.Rmd

@@ -30,13 +30,13 @@ library(dplyr)
 library(gridExtra)
 ```
 
-With `gsDesign` version 3.1, we have added a function to support graphical multiplicity methods using ***`ggplot2`***, this function is migrated to the `gMCPLite` package now.
+With gsDesign version 3.1, we have added a function to support graphical multiplicity methods using ggplot2, this function is migrated to the gMCPLite package now.
 
-The graphical method is introduced nicely in @Bretz2011 and originally supported by the ***`gMCP`*** packages (@gMCP), and now ***`gMCPLite`*** package.
+The graphical method is introduced nicely in @Bretz2011 and originally supported by the gMCP packages (@gMCP), and now gMCPLite package.
 It was extended to group sequential design by @MaurerBretz2013.
-While the ***`gMCPLite`***
-package supports graphics, here we add the `hGraph()` function to create multiplicity graphs using the ***`ggplot2`*** package as a convenience for those desiring this format.
-We demonstrate basic formatting in this article and demonstrate use with ***`gMCPLite`*** in the other article.
+While the gMCPLite
+package supports graphics, here we add the `hGraph()` function to create multiplicity graphs using the ggplot2 package as a convenience for those desiring this format.
+We demonstrate basic formatting in this article and demonstrate use with gMCPLite in the other article.
 
 Use of `hGraph()` is organized as follows: