699 remove multiplot (#700)

* Remove multiplot

* Correct typo

* Correcting typo in argument to assert_integerish

NAMESPACE

@@ -341,7 +341,6 @@ export(maxDose)
 export(maxSize)
 export(mcmc)
 export(minSize)
-export(multiplot)
 export(nextBest)
 export(ngrid)
 export(plotDualResponses)
@@ -521,9 +520,6 @@ importFrom(graphics,lines)
 importFrom(graphics,matlines)
 importFrom(graphics,matplot)
 importFrom(graphics,plot)
-importFrom(grid,grid.newpage)
-importFrom(grid,pushViewport)
-importFrom(grid,viewport)
 importFrom(gridExtra,arrangeGrob)
 importFrom(kableExtra,add_footnote)
 importFrom(kableExtra,add_header_above)

NEWS.md

@@ -1,4 +1,5 @@
 # Version 1.0.9000.9133
+* Removed `multiplot` function.  Use Please use equivalent functionality in other packages, such as `cowplot` or `ggpubr`.
 * Added new `DataGrouped` and `DesignGrouped` classes with corresponding model `LogisticLogNormalGrouped` to support simultaneous dose escalation with monotherapy and combination therapy arms.
 * Created the `CrmPackClass` class as the ultimate ancestor of all other 
 `crmPack` classes to allow identification of crmPack classes and simpler 

R/Rules-class.R

@@ -2698,7 +2698,8 @@ setClass(
 #' @example examples/Rules-class-CohortSizeRange.R
 #'
 CohortSizeRange <- function(intervals, cohort_size) {
-  assert_integerish(cohort_size, lower = 1, any.missing = FALSE)
+  # Cohort size 0 is needed to allow for no-placebo designs
+  assert_integerish(cohort_size, lower = 0, any.missing = FALSE)
 
   .CohortSizeRange(
     intervals = intervals,
@@ -2759,7 +2760,8 @@ CohortSizeRange <- function(intervals, cohort_size) {
 #'
 CohortSizeDLT <- function(intervals, cohort_size) {
   assert_integerish(intervals, lower = 0, any.missing = FALSE)
-  assert_integerish(cohort_size, lower = 1, any.missing = FALSE)
+  # Cohort size 0 is needed to allow for no-placebo designs
+  assert_integerish(cohort_size, lower = 0, any.missing = FALSE)
 
   .CohortSizeDLT(
     intervals = as.integer(intervals),
@@ -2810,7 +2812,8 @@ CohortSizeDLT <- function(intervals, cohort_size) {
 #' @example examples/Rules-class-CohortSizeConst.R
 #'
 CohortSizeConst <- function(size) {
-  assert_integerish(size, min = 1)
+  # Cohort size 0 is needed to allow for no-placebo designs
+  assert_integerish(size, lower = 0)
   .CohortSizeConst(size = as.integer(size))
 }
 
@@ -2859,7 +2862,8 @@ CohortSizeConst <- function(size) {
 #' @example examples/Rules-class-CohortSizeParts.R
 #'
 CohortSizeParts <- function(cohort_sizes) {
-  assert_integerish(cohort_sizes, min = 1, any.missing = FALSE)
+  # Cohort size 0 is needed to allow for no-placebo designs
+  assert_integerish(cohort_sizes, lower = 0, any.missing = FALSE)
   .CohortSizeParts(cohort_sizes = as.integer(cohort_sizes))
 }
 

R/helpers.R

@@ -219,63 +219,6 @@ crmPackHelp <- function() {
   utils::help(package = "crmPack", help_type = "html")
 }
 
-#' Multiple plot function
-#'
-#' ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects).
-#' If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
-#' then plot 1 will go in the upper left, 2 will go in the upper right, and
-#' 3 will go all the way across the bottom.
-#'
-#' @param \dots Objects to be passed
-#' @param plotlist a list of additional objects
-#' @param rows Number of rows in layout
-#' @param layout A matrix specifying the layout. If present, \code{rows}
-#' is ignored.
-#'
-#' @return Used for the side effect of plotting
-#' @importFrom grid grid.newpage pushViewport viewport
-#' @export
-multiplot <- function(..., plotlist = NULL, rows = 1, layout = NULL) {
-  # Make a list from the ... arguments and plotlist
-  plots <- c(list(...), plotlist)
-
-  numPlots <- length(plots)
-
-  # If layout is NULL, then use 'cols' to determine layout
-  if (is.null(layout)) {
-    # Make the panel
-    # ncol: Number of columns of plots
-    # nrow: Number of rows needed, calculated from # of cols
-    layout <- matrix(seq(1, rows * ceiling(numPlots / rows)),
-      nrow = rows, ncol = ceiling(numPlots / rows),
-      byrow = TRUE
-    )
-  }
-
-  if (numPlots == 1) {
-    print(plots[[1]])
-  } else {
-    # Set up the page
-    grid::grid.newpage()
-    grid::pushViewport(grid::viewport(layout = grid::grid.layout(
-      nrow(layout),
-      ncol(layout)
-    )))
-
-    # Make each plot, in the correct location
-    for (i in seq_len(numPlots))
-    {
-      # Get the i,j matrix positions of the regions that contain this subplot
-      matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE))
-
-      print(plots[[i]], vp = grid::viewport(
-        layout.pos.row = matchidx$row,
-        layout.pos.col = matchidx$col
-      ))
-    }
-  }
-}
-
 ##' Taken from utils package (print.vignette)
 ##'
 ##' @importFrom tools file_ext

_pkgdown.yaml

@@ -416,7 +416,6 @@ reference:
       - matchTolerance
       - maxSize
       - minSize
-      - multiplot
       - or-Stopping-Stopping
       - or-Stopping-StoppingAny
       - or-StoppingAny-Stopping