Documentation of function pull added

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rpact
 Title: Confirmatory Adaptive Clinical Trial Design and Analysis
-Version: 4.0.0.9238
-Date: 2024-03-28
+Version: 4.0.0.9239
+Date: 2024-04-05
 Authors@R: c(
 	person(
 		given = "Gernot", 

NAMESPACE

@@ -11,6 +11,7 @@ S3method(as.data.frame,TrialDesignSet)
 S3method(as.list,Dictionary)
 S3method(as.matrix,FieldSet)
 S3method(as.vector,Dictionary)
+S3method(kable,ParameterSet)
 S3method(knit_print,ParameterSet)
 S3method(knit_print,SummaryFactory)
 S3method(length,TrialDesignSet)
@@ -114,7 +115,6 @@ export(getStageResults)
 export(getTestActions)
 export(getWideFormat)
 export(kable)
-export(kable.ParameterSet)
 export(mvnprd)
 export(mvstud)
 export(plotTypes)

R/class_analysis_dataset.R

@@ -457,7 +457,7 @@ writeDatasets <- function(datasets, file, ..., append = FALSE, quote = TRUE, sep
         if (length(args) == 2 && !is.null(design)) {
             dataset <- .getDatasetFromArgs(...)
             if (!is.null(dataset)) {
-                dataset <- dataset$clone(deep = TRUE) # TODO was $copy shallow
+                dataset <- dataset$clone(deep = TRUE) 
                 dataset$.design <- design
                 return(dataset)
             }

R/class_core_parameter_set.R

@@ -1642,15 +1642,22 @@ print.ParameterSet <- function(x, ..., markdown = NA) {
     return(invisible(x))
 }
 
+#' 
+#' @rdname pull.ParameterSet
+#' 
 #' @export 
+#' 
 pull <- function(x, var) UseMethod("pull")
 
 #'
+#' @title
 #' Extract a single parameter
 #' 
+#' @description
 #' Pull a parameter from a parameter set.
 #' 
-#' @param  var A variable specified as: 
+#' @param x The \code{\link{ParameterSet}} object to pull from.
+#' @param var A variable specified as: 
 #'  - a literal variable name 
 #'  - a positive integer, giving the position counting from the left 
 #'  - a negative integer, giving the position counting from the right. 
@@ -1680,7 +1687,6 @@ pull.ParameterSet <- function(x, var = -1) {
     if (var == 0) {
         stop(C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT, "'x' (", x, ") must != 0")
     }
-    x <- addTrace(x, "pull", var)
     if (var < 0) {
         var <- length(x) + 1 - var
     }
@@ -1751,6 +1757,13 @@ knit_print.ParameterSet <- function(x, ...) {
     return(knitr::asis_output(result))
 }
 
+#' 
+#' @rdname kable.ParameterSet
+#' 
+#' @export 
+#' 
+kable <- function(x, ...) UseMethod("kable")
+
 #'
 #' @title
 #' Create output in Markdown
@@ -1795,20 +1808,3 @@ kable.ParameterSet <- function(x, ...) {
     .assertPackageIsInstalled("knitr")
     knitr::kable(x, ...)
 }
-
-#'
-#' @title
-#' Create tables in Markdown
-#'
-#' @description
-#' The \code{kable()} function returns a single table for a single object that inherits from class \code{\link{ParameterSet}}.
-#'
-#' @details
-#' Generic to represent a parameter set in Markdown.
-#'
-#' @param x The object that inherits from \code{\link{ParameterSet}}.
-#' @param  ... Other arguments (see \code{\link[knitr]{kable}}).
-#'
-#' @export
-#'
-setGeneric("kable", kable.ParameterSet)

R/f_analysis_base.R

@@ -50,7 +50,7 @@ NULL
 
     return(list(
         design = design,
-        dataInput = dataInput$clone(deep = TRUE) # TODO was $copy shallow
+        dataInput = dataInput$clone(deep = TRUE) 
     ))
 }
 

inst/doc/rpact_getting_started.html

@@ -12,7 +12,7 @@
 
 <meta name="author" content="Friedrich Pahlke and Gernot Wassmer" />
 
-<meta name="date" content="2024-03-28" />
+<meta name="date" content="2024-04-05" />
 
 <title>Getting started with rpact</title>
 
@@ -239,7 +239,7 @@
 
 <h1 class="title toc-ignore">Getting started with rpact</h1>
 <h4 class="author">Friedrich Pahlke and Gernot Wassmer</h4>
-<h4 class="date">2024-03-28</h4>
+<h4 class="date">2024-04-05</h4>