Merge pull request #71 from keaven/issue-68

Dependency clean up and function lifecycle management

DESCRIPTION

@@ -1,43 +1,45 @@
 Package: gsDesign
-Version: 3.3.0.9000
+Version: 3.4.0
 Title: Group Sequential Design
+Authors@R: person(given = "Keaven", family = "Anderson", email =
+          "[email protected]", role = c('aut','cre'))
 Description: Derives group sequential clinical trial designs and describes
     their properties. Particular focus on time-to-event, binary, and
     continuous outcomes. Largely based on methods described in
     Jennison, Christopher and Turnbull, Bruce W., 2000,
     "Group Sequential Methods with Applications to Clinical Trials"
     ISBN: 0-8493-0316-8.
-Authors@R: person(given = "Keaven", family = "Anderson", email =
-          "[email protected]", role = c('aut','cre'))
-Depends: R (>= 3.5.0), ggplot2 (>= 0.9.2)
 License: GPL (>= 3)
+Copyright: Copyright 2010, Merck Research Laboratories
 URL: https://keaven.github.io/gsDesign/, https://github.com/keaven/gsDesign
 BugReports: https://github.com/keaven/gsDesign/issues
 Encoding: UTF-8
+Depends:
+    R (>= 3.5.0)
 Imports:
-    stats,
+    dplyr,
+    ggplot2 (>= 0.9.2),
+    graphics,
     magrittr,
-    rlang,
     methods,
-    graphics,
-    tools,
-    dplyr,
+    rlang,
+    stats,
     tidyr,
+    tools,
     xtable
 Suggests:
+    covr,
+    gridExtra,
+    gt,
+    kableExtra,
     knitr,
-    scales,
+    mvtnorm,
+    ragg,
     rmarkdown,
-    gt,
+    scales,
     testthat,
-    covr,
-    gridExtra,
     tibble,
-    utils,
-    mvtnorm,
-    gMCP,
-    kableExtra,
-    ragg
-VignetteBuilder: knitr
-Copyright: Copyright 2010, Merck Research Laboratories
-RoxygenNote: 7.1.2
+    utils
+VignetteBuilder:
+    knitr
+RoxygenNote: 7.2.1

NEWS.md

@@ -1,13 +1,15 @@
-# gsDesign 3.3.0.9000
-
-- Removed restriction on gsCP() interim test statistic zi
+# gsDesign 3.4.0 (October, 2022)
 
+- Removed restriction on `gsCP()` interim test statistic zi (#63).
+- Removed gMCP dependency. Updated vignettes and linked to vignettes in gMCPLite (#69).
+- Added deprecation warning to `hGraph()` and suggested using `gMCPLite::hGraph()` instead (#70).
+- Moved ggplot2 from `Depends` to `Imports` (#56).
 
 # gsDesign 3.3.0 (May, 2022)
 
 - Addition of vignettes
-    - Demonstrate cure model and calendar-based analysis timing for time-to-event endpoint design
-    - Vaccine efficacy design using spending bounds and exact binomial boundary crossing probabilities
+  - Demonstrate cure model and calendar-based analysis timing for time-to-event endpoint design
+  - Vaccine efficacy design using spending bounds and exact binomial boundary crossing probabilities
 - Minor fix to labeling in print.gsProbability
 - Fixed error in sfStep
 - Updates to reduce R CMD check and other minor issues 

R/hgraph.R

@@ -1,7 +1,7 @@
 #' @title Create multiplicity graphs using ggplot2
 #'
 #' @description \code{hGraph()} plots a multiplicity graph defined by user inputs.
-#' 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
+#' The graph can also be used with the **gMCPLite** 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
 #' @param nameHypotheses hypothesis names
 #' @param alphaHypotheses alpha-levels or weights for ellipses
@@ -30,31 +30,8 @@
 #' @param wchar character for alphaHypotheses in ellipses
 #' @return A `ggplot` object with a multi-layer multiplicity graph
 #' @examples
-#' library(tidyr)
-#' # Defaults: note clockwise ordering
-#' hGraph(5)
-#' # Add colors (default is 3 gray shades)
-#' hGraph(3,fill=1:3)
-#' # Colorblind palette
-#' cbPalette <- c("#999999", "#E69F00", "#56B4E9", "#009E73",
-#'                "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
-#' hGraph(6,fill=as.factor(1:6),palette=cbPalette)
-#' # Use a hue palette
-#' hGraph(4,fill=factor(1:4),palette=scales::hue_pal(l=75)(4))
-#' # different alpha allocation, hypothesis names and transitions
-#' alphaHypotheses <- c(.005,.007,.013)
-#' nameHypotheses <- c("ORR","PFS","OS")
-#' m <- matrix(c(0,1,0,
-#'               0,0,1,
-#'               1,0,0),nrow=3,byrow=TRUE)
-#' hGraph(3,alphaHypotheses=alphaHypotheses,nameHypotheses=nameHypotheses,m=m)
-#' # Custom position and size of ellipses, change text to multi-line text
-#' # Adjust box width
-#' # add legend in middle of plot
-#' hGraph(3,x=sqrt(0:2),y=c(1,3,1.5),size=6,halfWid=.3,halfHgt=.3, trhw=0.6,
-#'        palette=cbPalette[2:4], fill = c(1, 2, 2),
-#'        legend.position = c(.6,.5), legend.name = "Legend:", labels = c("Group 1", "Group 2"),
-#'        nameHypotheses=c("H1:\n Long name","H2:\n Longer name","H3:\n Longest name"))
+#' # 'gsDesign::hGraph' is deprecated.
+#' # See the examples in 'gMCPLite::hGraph' instead.
 #' @details
 #' See vignette **Multiplicity graphs formatting using ggplot2** for explanation of formatting.
 #' @importFrom grDevices gray.colors
@@ -98,6 +75,7 @@ hGraph <- function(
   # following is temporary fix from intended {'\u03b1'} for Windows
   wchar = if(as.character(Sys.info()[1])=="Windows"){'w'}else{'w'}
 ){
+  .Deprecated("gMCPLite::hGraph", old = "gsDesign::hGraph")
   #####################################################################
   # Begin: Internal functions
   #####################################################################

tests/gsDesign_independent_code.R

@@ -1005,7 +1005,7 @@ Validate_comp_sprt_bnd <- function(alpha, beta, p0, p1, nmin, nmax) {
 #-------------------------------------------------------------------------------
 save_gg_plot <- function(code, width = 4, height = 4) {
   path <- tempfile(fileext = ".png")
-  ggsave(path, plot = code, width = width, height = height, dpi = 72, units = "in")
+  ggplot2::ggsave(path, plot = code, width = width, height = height, dpi = 72, units = "in")
   path
 }
 

tests/testthat/test-independent-test-hGraph.R

@@ -1,7 +1,7 @@
 source('../gsDesign_independent_code.R')
 #-------------------------------------------------------------------------------
 # hGraph : hGraph() plots a multiplicity graph defined by user inputs. The graph
-#          can also be used with the ***gMCP*** package to evaluate a set of 
+#          can also be used with the **gMCPLite** package to evaluate a set of 
 #          nominal p-values for the tests of the hypotheses in the graph
 #-------------------------------------------------------------------------------