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class_core_parameter_set.R
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class_core_parameter_set.R
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## |
## | *Parameter set classes*
## |
## | This file is part of the R package rpact:
## | Confirmatory Adaptive Clinical Trial Design and Analysis
## |
## | Author: Gernot Wassmer, PhD, and Friedrich Pahlke, PhD
## | Licensed under "GNU Lesser General Public License" version 3
## | License text can be found here: https://www.r-project.org/Licenses/LGPL-3
## |
## | RPACT company website: https://www.rpact.com
## | rpact package website: https://www.rpact.org
## |
## | Contact us for information about our services: info@rpact.com
## |
## | File version: $Revision: 7962 $
## | Last changed: $Date: 2024-05-31 13:41:37 +0200 (Fr, 31 Mai 2024) $
## | Last changed by: $Author: pahlke $
## |
#' @include class_dictionary.R
#' @include f_core_constants.R
#' @include f_core_assertions.R
NULL
#'
#' @name FieldSet
#'
#' @title
#' Field Set
#'
#' @description
#' Basic class for field sets.
#'
#' @details
#' The field set implements basic functions for a set of fields.
#'
#' @include class_core_plot_settings.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
FieldSet <- R6::R6Class("FieldSet",
public = list(
.parameterTypes = NULL,
.showParameterTypeEnabled = NULL,
.catLines = NULL,
.deprecatedFieldNames = NULL,
.getFieldNames = function() {
classNames <- class(self)
classNames <- classNames[classNames != "R6"]
classNames <- base::rev(classNames)
fieldNames <- unlist(lapply(classNames, function(x) {
names(base::get(x)$public_fields)
}))
startFieldNameIndices <- grepl("^\\.", fieldNames)
fieldNames <- c(fieldNames[startFieldNameIndices], fieldNames[!startFieldNameIndices])
return(fieldNames)
},
.getVisibleFieldNames = function() {
fieldNames <- self$.getFieldNames()
fieldNames <- fieldNames[!startsWith(fieldNames, ".")]
fieldNames <- fieldNames[!(fieldNames %in% self$.deprecatedFieldNames)]
return(fieldNames)
},
.resetCat = function() {
self$.catLines <- character()
},
.cat = function(..., file = "", sep = "", fill = FALSE, labels = NULL,
append = FALSE, heading = 0, tableColumns = 0, consoleOutputEnabled = TRUE,
na = NA_character_) {
if (consoleOutputEnabled) {
cat(..., file = file, sep = sep, fill = fill, labels = labels, append = append)
return(invisible())
}
args <- list(...)
line <- ""
if (length(args) > 0) {
if (tableColumns > 0) {
values <- unlist(args, use.names = FALSE)
values <- values[values != "\n"]
for (i in 1:length(values)) {
values[i] <- gsub("\n", "", values[i])
}
if (!is.null(na) && length(na) == 1 && !is.na(na)) {
len <- min(nchar(values))
naStr <- paste0(trimws(na), " ")
while (nchar(naStr) < len) {
naStr <- paste0(" ", naStr)
}
values[is.na(values) | nchar(trimws(values)) == 0] <- naStr
}
line <- paste0(values, collapse = "| ")
if (trimws(line) != "" && !grepl("\\| *$", line)) {
line <- paste0(line, "|")
}
line <- paste0("| ", line)
extraCells <- tableColumns - length(values)
if (extraCells > 0 && trimws(line) != "") {
line <- paste0(line, paste0(rep(" |", extraCells), collapse = ""))
}
line <- paste0(line, "\n")
} else {
line <- paste0(args, collapse = sep)
listItemEnabled <- grepl("^ ", line)
headingBaseNumber <- as.integer(getOption("rpact.print.heading.base.number",
C_HEADING_BASE_NUMBER_DEFAULT))
if (is.na(headingBaseNumber)) {
headingBaseNumber <- C_HEADING_BASE_NUMBER_DEFAULT
}
if (headingBaseNumber < -2) {
warning(
"Illegal option ", sQuote("rpact.print.heading.base.number"),
" (", headingBaseNumber, ") was set to ", C_HEADING_BASE_NUMBER_DEFAULT
)
headingBaseNumber <- C_HEADING_BASE_NUMBER_DEFAULT
}
if (headingBaseNumber > 4) {
warning(
"Illgeal option ", sQuote("rpact.print.heading.base.number"),
" (", headingBaseNumber, ") was set to 4 because it was too large"
)
headingBaseNumber <- 4L
}
if (heading > 0) {
if (headingBaseNumber %in% c(-1, -2)) {
lineBreak <- ""
if (grepl("\n *$", line)) {
lineBreak <- "\n\n"
}
fontStyle <- ifelse(headingBaseNumber == -1, "**", "*")
line <- paste0(fontStyle, sub(": *", "", trimws(line)), fontStyle, lineBreak)
} else {
headingCmd <- paste0(rep("#", heading + headingBaseNumber + 1), collapse = "")
lineBreak <- ""
if (grepl("\n *$", line)) {
lineBreak <- "\n\n"
}
line <- paste0(headingCmd, " ", sub(": *", "", trimws(line)), lineBreak)
}
} else {
parts <- strsplit(line, " *: ")[[1]]
if (length(parts) == 2) {
line <- paste0("*", trimws(parts[1]), "*: ", parts[2])
}
}
if (listItemEnabled) {
if (grepl("^ ", line)) {
line <- sub("^ ", "* ", line)
} else {
line <- paste0("* ", line)
}
}
}
}
if (length(self$.catLines) == 0) {
self$.catLines <- line
} else {
self$.catLines <- c(self$.catLines, line)
}
return(invisible())
},
.getFields = function(values) {
flds <- self$.getFieldNames()
if (!missing(values)) {
flds <- flds[flds %in% values]
}
result <- setNames(vector("list", length(flds)), flds)
for (fld in flds) {
result[[fld]] <- self[[fld]]
}
return(result)
}
)
)
#'
#' @name ParameterSet
#'
#' @title
#' Parameter Set
#'
#' @description
#' Basic class for parameter sets.
#'
#' @details
#' The parameter set implements basic functions for a set of parameters.
#'
#' @include f_core_constants.R
#' @include f_core_utilities.R
#' @include f_parameter_set_utilities.R
#' @include f_analysis_utilities.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
ParameterSet <- R6::R6Class("ParameterSet",
inherit = FieldSet,
public = list(
initialize = function(..., .showParameterTypeEnabled = TRUE) {
self$.showParameterTypeEnabled <- .showParameterTypeEnabled
self$.parameterTypes <- list()
self$.catLines <- character()
self$.deprecatedFieldNames <- character()
},
.toString = function(startWithUpperCase = FALSE) {
s <- .formatCamelCase(.getClassName(self))
return(ifelse(startWithUpperCase, .firstCharacterToUpperCase(s), s))
},
.initParameterTypes = function() {
self$.parameterTypes <- list()
for (parameterName in self$.getVisibleFieldNames()) {
self$.parameterTypes[[parameterName]] <- C_PARAM_TYPE_UNKNOWN
}
},
.getParameterType = function(parameterName) {
if (is.null(parameterName) || length(parameterName) == 0 || is.na(parameterName)) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"'parameterName' must be a valid character with length > 0"
)
}
parameterType <- self$.parameterTypes[[parameterName]]
if (is.null(parameterType)) {
return(C_PARAM_TYPE_UNKNOWN)
}
return(parameterType[1])
},
.getParametersToShow = function() {
return(self$.getVisibleFieldNames())
},
.setParameterType = function(parameterName, parameterType) {
if (is.null(parameterName) || length(parameterName) == 0 || is.na(parameterName)) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"'parameterName' must be a valid character with length > 0"
)
}
parameterType <- parameterType[1]
if (!all(parameterType %in% c(
C_PARAM_USER_DEFINED, C_PARAM_DEFAULT_VALUE,
C_PARAM_GENERATED, C_PARAM_DERIVED, C_PARAM_NOT_APPLICABLE
))) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"'parameterType' ('", parameterType, "') is invalid"
)
}
self$.parameterTypes[[parameterName]] <- parameterType
invisible(parameterType)
},
isUserDefinedParameter = function(parameterName) {
return(self$.getParameterType(parameterName) == C_PARAM_USER_DEFINED)
},
isDefaultParameter = function(parameterName) {
return(self$.getParameterType(parameterName) == C_PARAM_DEFAULT_VALUE)
},
isGeneratedParameter = function(parameterName) {
return(self$.getParameterType(parameterName) == C_PARAM_GENERATED)
},
isDerivedParameter = function(parameterName) {
return(self$.getParameterType(parameterName) == C_PARAM_DERIVED)
},
isUndefinedParameter = function(parameterName) {
return(self$.getParameterType(parameterName) == C_PARAM_TYPE_UNKNOWN)
},
.getInputParameters = function() {
params <- self$.getParametersOfOneGroup(c(C_PARAM_USER_DEFINED, C_PARAM_DEFAULT_VALUE))
return(params)
},
.getUserDefinedParameters = function() {
return(self$.getParametersOfOneGroup(C_PARAM_USER_DEFINED))
},
.getDefaultParameters = function() {
return(self$.getParametersOfOneGroup(C_PARAM_DEFAULT_VALUE))
},
.getGeneratedParameters = function() {
return(self$.getParametersOfOneGroup(C_PARAM_GENERATED))
},
.getDerivedParameters = function() {
return(self$.getParametersOfOneGroup(C_PARAM_DERIVED))
},
.getUndefinedParameters = function() {
return(self$.getParametersOfOneGroup(C_PARAM_TYPE_UNKNOWN))
},
.getParameterValueIfUserDefinedOrDefault = function(parameterName) {
if (self$isUserDefinedParameter(parameterName) || self$isDefaultParameter(parameterName)) {
return(self[[parameterName]])
}
tryCatch({
parameterType <- .getClassName(self[[parameterName]])
}, error = function(e) {
parameterType <- "unknown"
})
if (parameterType == "numeric") {
return(NA_real_)
}
if (parameterType == "integer") {
return(NA_integer_)
}
if (parameterType == "character") {
return(NA_character_)
}
return(NA)
},
.getParametersOfOneGroup = function(parameterType) {
if (length(parameterType) == 1) {
parameterNames <- names(self$.parameterTypes[self$.parameterTypes == parameterType])
} else {
parameterNames <- names(self$.parameterTypes[which(self$.parameterTypes %in% parameterType)])
}
parametersToShow <- self$.getParametersToShow()
if (is.null(parametersToShow) || length(parametersToShow) == 0) {
return(parameterNames)
}
return(parametersToShow[parametersToShow %in% parameterNames])
},
.showParameterType = function(parameterName) {
if (!self$.showParameterTypeEnabled) {
return(" ")
}
return(paste0("[", self$.getParameterType(parameterName), "]"))
},
.showAllParameters = function(consoleOutputEnabled = TRUE) {
parametersToShow <- self$.getVisibleFieldNamesOrdered()
for (parameter in parametersToShow) {
self$.showParameter(parameter,
showParameterType = TRUE,
consoleOutputEnabled = consoleOutputEnabled
)
}
},
.getVisibleFieldNamesOrdered = function() {
visibleFieldNames <- self$.getVisibleFieldNames()
parametersToShowSorted <- self$.getParametersToShow()
if (is.null(parametersToShowSorted) || length(parametersToShowSorted) == 0) {
return(visibleFieldNames)
}
visibleFieldNames <- visibleFieldNames[!(visibleFieldNames %in% parametersToShowSorted)]
visibleFieldNames <- c(parametersToShowSorted, visibleFieldNames)
return(visibleFieldNames)
},
.show = function(..., consoleOutputEnabled = FALSE) {
showType <- .getOptionalArgument("showType", ...)
if (!is.null(showType) && showType == 2) {
self$.cat("Technical developer summary of the ", self$.toString(), " object (",
methods::classLabel(class(self)), "):\n\n",
sep = "", heading = 1,
consoleOutputEnabled = consoleOutputEnabled
)
self$.showAllParameters(consoleOutputEnabled = consoleOutputEnabled)
self$.showParameterTypeDescription(consoleOutputEnabled = consoleOutputEnabled)
} else {
stop(
C_EXCEPTION_TYPE_RUNTIME_ISSUE,
"method '.show()' is not implemented in class '", .getClassName(self), "'"
)
}
},
.catMarkdownText = function(...) {
self$.show(consoleOutputEnabled = FALSE, ...)
if (length(self$.catLines) == 0) {
return(invisible())
}
for (line in self$.catLines) {
cat(line)
}
},
.showParametersOfOneGroup = function(parameters, title,
orderByParameterName = TRUE, consoleOutputEnabled = TRUE) {
output <- ""
if (is.null(parameters) || length(parameters) == 0 || all(is.na(parameters))) {
if (!missing(title) && !is.null(title) && !is.na(title) && consoleOutputEnabled) {
output <- paste0(title, ": not available\n\n")
self$.cat(output, heading = 2, consoleOutputEnabled = consoleOutputEnabled)
}
invisible(output)
} else {
if (orderByParameterName) {
parameters <- sort(parameters)
}
if (!missing(title) && !is.null(title) && !is.na(title)) {
output <- paste0(title, ":\n")
self$.cat(output, heading = 2, consoleOutputEnabled = consoleOutputEnabled)
}
for (parameterName in parameters) {
output <- paste0(output, self$.showParameter(parameterName,
consoleOutputEnabled = consoleOutputEnabled
))
}
self$.cat("\n", consoleOutputEnabled = consoleOutputEnabled)
output <- paste0(output, "\n")
invisible(output)
}
},
.showParameter = function(parameterName, showParameterType = FALSE, consoleOutputEnabled = TRUE) {
tryCatch(
{
params <- .getParameterValueFormatted(obj = self, parameterName = parameterName)
if (is.null(params) || !is.list(params)) {
return(invisible(""))
}
if (!is.null(names(params)) && "paramValue" %in% names(params)) {
return(self$.showParameterSingle(
param = params,
parameterName = parameterName,
showParameterType = showParameterType,
consoleOutputEnabled = consoleOutputEnabled
))
}
output <- ""
for (i in 1:length(params)) {
param <- params[[i]]
category <- NULL
parts <- strsplit(param$paramName, "$", fixed = TRUE)[[1]]
if (length(parts) == 2) {
parameterName <- parts[1]
param$paramName <- parameterName
category <- parts[2]
categoryCaption <- .getParameterCaption(category, self)
if (is.null(categoryCaption)) {
categoryCaption <- paste0("%", category, "%")
}
category <- categoryCaption
}
outputPart <- self$.showParameterSingle(
param = param,
parameterName = parameterName,
category = category,
showParameterType = showParameterType,
consoleOutputEnabled = consoleOutputEnabled
)
if (nchar(output) > 0) {
output <- paste0(output, "\n", outputPart)
} else {
output <- outputPart
}
}
return(invisible(output))
},
error = function(e) {
if (consoleOutputEnabled) {
warning("Failed to show parameter '", parameterName, "': ", e$message)
}
}
)
},
.showParameterSingle = function(param,
parameterName, ...,
category = NULL,
showParameterType = FALSE,
consoleOutputEnabled = TRUE) {
if (is.null(param) || is.null(param$paramValue) || length(param$paramValue) == 0) {
return(invisible(""))
}
output <- ""
tryCatch(
{
if (param$type == "array" && length(dim(param$paramValue)) == 3) {
numberOfEntries <- dim(param$paramValue)[3]
numberOfRows <- dim(param$paramValue)[1]
if (numberOfEntries > 0 && numberOfRows > 0) {
index <- 1
for (i in 1:numberOfEntries) {
for (j in 1:numberOfRows) {
output <- paste0(output, self$.showParameterFormatted(
paramName = param$paramName,
paramValue = param$paramValue[j, , i],
paramValueFormatted = param$paramValueFormatted[[index]],
showParameterType = showParameterType,
category = i,
matrixRow = ifelse(numberOfRows == 1, NA_integer_, j),
consoleOutputEnabled = consoleOutputEnabled,
paramNameRaw = parameterName,
numberOfCategories = numberOfEntries
))
index <- index + 1
}
}
}
} else if (param$type %in% c("matrix", "array")) {
n <- length(param$paramValueFormatted)
if (n > 0) {
for (i in 1:n) {
paramValue <- param$paramValue
if (is.array(paramValue) &&
length(dim(paramValue)) == 3 &&
dim(paramValue)[3] == 1) {
paramValue <- paramValue[i, , 1]
} else if (dim(paramValue)[1] > 1 || dim(paramValue)[2] > 1) {
paramValue <- paramValue[i, ]
}
output <- paste0(output, self$.showParameterFormatted(
paramName = param$paramName,
paramValue = paramValue,
paramValueFormatted = param$paramValueFormatted[[i]],
showParameterType = showParameterType,
category = category,
matrixRow = ifelse(n == 1, NA_integer_, i),
consoleOutputEnabled = consoleOutputEnabled,
paramNameRaw = parameterName,
numberOfCategories = n
))
}
}
} else {
output <- self$.showParameterFormatted(
paramName = param$paramName,
paramValue = param$paramValue,
paramValueFormatted = param$paramValueFormatted,
showParameterType = showParameterType,
category = category,
consoleOutputEnabled = consoleOutputEnabled,
paramNameRaw = parameterName
)
}
},
error = function(e) {
if (consoleOutputEnabled) {
warning("Failed to show single parameter '", parameterName, "' (", param$type, "): ", e$message)
}
}
)
return(invisible(output))
},
.extractParameterNameAndValue = function(parameterName) {
tryCatch({
d <- regexpr("\\..+\\$", parameterName)
if (d[1] != 1) {
return(list(
parameterName = parameterName,
paramValue = base::get(parameterName, envir = self)
))
}
index <- attr(d, "match.length")
objectName <- substr(parameterName, 1, index - 1)
parameterName <- substr(parameterName, index + 1, nchar(parameterName))
obj <- base::get(objectName, envir = self)
paramValue <- base::get(parameterName, envir = obj)
#paramValue <- self[[objectName]][[parameterName]]
if (objectName == ".closedTestResults" && parameterName == "rejected") {
paramValueLogical <- as.logical(paramValue)
if (is.matrix(paramValue)) {
paramValueLogical <- matrix(paramValueLogical, ncol = ncol(paramValue))
}
paramValue <- paramValueLogical
}
return(list(parameterName = parameterName, paramValue = paramValue))
}, error = function(e) {
if (consoleOutputEnabled) {
warning("Failed to extract parameter name and value from ", sQuote(parameterName), ": ", e$message)
}
return(list(parameterName = parameterName, paramValue = ""))
})
},
.showUnknownParameters = function(consoleOutputEnabled = TRUE) {
params <- self$.getUndefinedParameters()
if (length(params) > 0) {
self$.showParametersOfOneGroup(params, "ISSUES (parameters with undefined type)",
consoleOutputEnabled = consoleOutputEnabled
)
}
},
.showParameterFormatted = function(paramName, paramValue, ..., paramValueFormatted = NA_character_,
showParameterType = FALSE, category = NULL, matrixRow = NA_integer_, consoleOutputEnabled = TRUE,
paramNameRaw = NA_character_, numberOfCategories = NA_integer_) {
if (!is.na(paramNameRaw)) {
paramCaption <- .getParameterCaption(paramNameRaw, self)
}
if (is.null(paramCaption)) {
paramCaption <- .getParameterCaption(paramName, self)
}
if (is.null(paramCaption)) {
paramCaption <- paste0("%", paramName, "%")
}
if (!is.null(category) && !is.na(category)) {
if (.isMultiArmSimulationResults(self) && paramName == "singleEventsPerArmAndStage") {
if (!inherits(self, "SimulationResultsEnrichmentSurvival") &&
!is.na(numberOfCategories) && numberOfCategories == category) {
category <- "control"
}
paramCaption <- paste0(paramCaption, " {", category, "}")
} else if (paramName == "effectList") {
paramCaption <- paste0(paramCaption, " [", category, "]")
} else if (.isEnrichmentSimulationResults(self)) {
categoryCaption <- .getCategoryCaptionEnrichment(self, paramName, category)
paramCaption <- paste0(paramCaption, " (", categoryCaption, ")")
} else {
paramCaption <- paste0(paramCaption, " (", category, ")")
}
if (!is.na(matrixRow)) {
if (paramName == "effectList") {
paramCaption <- paste0(paramCaption, " (", matrixRow, ")")
} else {
paramCaption <- paste0(paramCaption, " [", matrixRow, "]")
}
}
} else if (!is.na(matrixRow)) {
if (.isMultiArmAnalysisResults(self) && paramName %in%
c(
"conditionalErrorRate", "secondStagePValues",
"adjustedStageWisePValues", "overallAdjustedTestStatistics"
)) {
treatments <- self$.closedTestResults$.getHypothesisTreatmentArmVariants()[matrixRow]
paramCaption <- paste0(
"Treatment", ifelse(grepl(",", treatments), "s", ""), " ",
treatments, " vs. control"
)
} else if (.isEnrichmentAnalysisResults(self) || .isEnrichmentStageResults(self) ||
(inherits(self, "ClosedCombinationTestResults") && isTRUE(self$.enrichment))) {
if (paramName %in% c(
"indices", "conditionalErrorRate", "secondStagePValues",
"adjustedStageWisePValues", "overallAdjustedTestStatistics", "rejectedIntersections"
)) {
if (.isEnrichmentAnalysisResults(self)) {
populations <- self$.closedTestResults$.getHypothesisPopulationVariants()[matrixRow]
} else if (inherits(self, "ClosedCombinationTestResults")) {
populations <- self$.getHypothesisPopulationVariants()[matrixRow]
} else {
stop(
C_EXCEPTION_TYPE_RUNTIME_ISSUE, "only ClosedCombinationTestResults ",
"supports function .getHypothesisPopulationVariants() (object is ", .getClassName(self), ")"
)
}
paramCaption <- paste0(paramCaption, " ", populations)
} else {
if (!is.na(numberOfCategories) && numberOfCategories == matrixRow) {
paramCaption <- paste0(paramCaption, " F")
} else {
paramCaption <- paste0(paramCaption, " S", matrixRow)
}
}
} else if (.isMultiArmAnalysisResults(self) || grepl("StageResultsMultiArm", .getClassName(self)) ||
(inherits(self, "SimulationResults") && paramName == "effectMatrix") ||
(inherits(self, "ClosedCombinationTestResults") &&
paramName %in% c("rejected", "separatePValues"))) {
paramCaption <- paste0(paramCaption, " (", matrixRow, ")")
} else {
paramCaption <- paste0(paramCaption, " [", matrixRow, "]")
}
}
if (is.null(paramValueFormatted) || length(paramValueFormatted) == 0 ||
is.na(paramValueFormatted)) {
paramValueFormatted <- paramValue
}
if (is.list(paramValueFormatted)) {
paramValueFormatted <- .listToString(paramValueFormatted)
}
if (is.function(paramValue) || grepl("Function$", paramName)) {
paramValueFormatted <- ifelse(
self$.getParameterType(paramName) == C_PARAM_USER_DEFINED,
ifelse(.isCppCode(paramValueFormatted), "user defined (C++)", "user defined"),
"default"
)
}
prefix <- ifelse(showParameterType, self$.showParameterType(paramName), "")
variableNameFormatted <- .getFormattedVariableName(
name = paramCaption,
n = self$.getNChar(), prefix = prefix
)
output <- paste(variableNameFormatted, paramValueFormatted, "\n")
self$.cat(output, consoleOutputEnabled = consoleOutputEnabled)
invisible(output)
},
.getNChar = function() {
fieldNames <- self$.getVisibleFieldNames()
if (length(fieldNames) == 0) {
return(40)
}
fieldCaptions <- character()
for (parameterName in fieldNames) {
fieldCaptions <- c(fieldCaptions, .getParameterCaption(parameterName, self))
}
return(min(40, max(nchar(fieldCaptions))) + 4)
},
.showParameterTypeDescription = function(consoleOutputEnabled = consoleOutputEnabled) {
self$.cat("\n", consoleOutputEnabled = consoleOutputEnabled)
self$.cat("Legend:\n", heading = 2, consoleOutputEnabled = consoleOutputEnabled)
self$.cat(" ", C_PARAM_USER_DEFINED, ": user defined\n", consoleOutputEnabled = consoleOutputEnabled)
self$.cat(" ", C_PARAM_DERIVED, ": derived value\n", consoleOutputEnabled = consoleOutputEnabled)
self$.cat(" ", C_PARAM_DEFAULT_VALUE, ": default value\n", consoleOutputEnabled = consoleOutputEnabled)
self$.cat(" ", C_PARAM_GENERATED, ": generated/calculated value\n", consoleOutputEnabled = consoleOutputEnabled)
self$.cat(" ", C_PARAM_NOT_APPLICABLE, ": not applicable or hidden\n", consoleOutputEnabled = consoleOutputEnabled)
},
.printAsDataFrame = function(parameterNames, niceColumnNamesEnabled = FALSE,
includeAllParameters = FALSE, handleParameterNamesAsToBeExcluded = FALSE,
lineBreakEnabled = FALSE) {
if (.isTrialDesignPlan(self)) {
parameterNames <- NULL
}
dataFrame <- .getAsDataFrame(
parameterSet = self,
parameterNames = parameterNames,
niceColumnNamesEnabled = niceColumnNamesEnabled,
includeAllParameters = includeAllParameters,
handleParameterNamesAsToBeExcluded = handleParameterNamesAsToBeExcluded,
returnParametersAsCharacter = TRUE
)
result <- as.matrix(dataFrame)
if (.isTrialDesignPlan(self)) {
dimnames(result)[[1]] <- paste(" ", c(1:nrow(dataFrame)))
} else if (!is.null(dataFrame[["stages"]])) {
dimnames(result)[[1]] <- paste(" Stage", dataFrame$stages)
}
print(result, quote = FALSE, right = FALSE)
},
.getNumberOfRows = function(parameterNames) {
numberOfRows <- 1
for (parameterName in parameterNames) {
parameterValues <- self[[parameterName]]
if (is.vector(parameterValues) && length(parameterValues) > numberOfRows) {
numberOfRows <- length(parameterValues)
} else if (is.matrix(parameterValues) && (nrow(parameterValues) == 1 || ncol(parameterValues) == 1) &&
length(parameterValues) > numberOfRows) {
numberOfRows <- length(parameterValues)
}
}
return(numberOfRows)
},
.containsMultidimensionalParameters = function(parameterNames) {
for (parameterName in parameterNames) {
parameterValues <- self[[parameterName]]
if (!is.null(parameterValues) && is.matrix(parameterValues) &&
nrow(parameterValues) > 0 && ncol(parameterValues) > 0) {
return(TRUE)
}
}
return(FALSE)
},
.getMultidimensionalNumberOfStages = function(parameterNames) {
if (!is.null(self[[".design"]])) {
return(self$.design$kMax)
}
n <- 1
for (parameterName in parameterNames) {
parameterValues <- self[[parameterName]]
if (!is.null(parameterValues) && is.matrix(parameterValues) &&
ncol(parameterValues) > 0 && nrow(parameterValues) > n) {
n <- nrow(parameterValues)
}
}
return(n)
},
.getVariedParameter = function(parameterNames, numberOfVariants) {
# search for user defined parameters
for (parameterName in parameterNames) {
parameterValues <- self[[parameterName]]
if (!is.null(parameterValues) && !is.matrix(parameterValues) &&
length(parameterValues) == numberOfVariants &&
parameterName %in% C_VARIABLE_DESIGN_PLAN_PARAMETERS &&
self$.getParameterType(parameterName) == C_PARAM_USER_DEFINED) {
return(parameterName)
}
}
# search for default values
for (parameterName in parameterNames) {
parameterValues <- self[[parameterName]]
if (!is.null(parameterValues) && !is.matrix(parameterValues) &&
length(parameterValues) == numberOfVariants &&
parameterName %in% C_VARIABLE_DESIGN_PLAN_PARAMETERS &&
self$.getParameterType(parameterName) == C_PARAM_DEFAULT_VALUE) {
return(parameterName)
}
}
return(NULL)
},
.getDataFrameColumnCaption = function(parameterName, niceColumnNamesEnabled) {
if (length(parameterName) == 0 || parameterName == "") {
stop(C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT, "'parameterName' must be a valid parameter name")
}
if (!niceColumnNamesEnabled) {
return(parameterName)
}
tableColumnName <- .getParameterCaption(parameterName, self, tableOutputEnabled = TRUE)
return(ifelse(!is.null(tableColumnName), tableColumnName, parameterName))
},
.getUnidimensionalNumberOfStages = function(parameterNames) {
kMax <- self[["kMax"]]
if (is.null(kMax) && !is.null(self[[".design"]])) {
kMax <- self[[".design"]][["kMax"]]
}
if (!is.null(kMax) && length(kMax) == 1 && is.integer(kMax)) {
return(kMax)
}
n <- 1
for (parameterName in parameterNames) {
parameterValues <- self[[parameterName]]
if (!is.null(parameterValues) && !is.matrix(parameterValues) &&
length(parameterValues) > n) {
n <- length(parameterValues)
}
}
return(n)
},
.formatDataFrameParametersAsCharacter = function(dataFrame,
parameterName, parameterValues, parameterCaption) {
tryCatch(
{
formatFunctionName <- .getParameterFormatFunction(parameterName, self)
if (!is.null(formatFunctionName)) {
parameterValuesFormatted <- eval(call(formatFunctionName, parameterValues))
} else {
parameterValuesFormatted <- as.character(parameterValues)
}
if (parameterName == "sided") {
parameterValuesFormatted <- ifelse(parameterValues == 1,
"one-sided", "two-sided"
)
}
if (!is.null(dataFrame[[parameterCaption]])) {
parameterValuesFormatted[is.na(dataFrame[[parameterCaption]])] <- ""
}
parameterValuesFormatted[is.na(parameterValuesFormatted)] <- ""
parameterValuesFormatted[parameterValuesFormatted == "NA"] <- ""
if (is.null(dataFrame)) {
dataFrame <- data.frame(x = parameterValuesFormatted)
names(dataFrame) <- parameterCaption
} else {
dataFrame[[parameterCaption]] <- parameterValuesFormatted
}
},
error = function(e) {
.logError(paste0(
"Error in '.getAsDataFrame'. Failed to show parameter '%s' ",
"(class '%s'): %s"
), parameterName, .getClassName(self), e)
}
)
},
#
# Returns a sub-list.
#
# @param x A list from which you would like to get a sub-list.
# @param listEntryNames A vector of names which specify the entries of the sub-list to return.
#
.getSubListByNames = function(x, listEntryNames) {
"Returns a sub-list."
if (!is.list(x) && !inherits(x, "Dictionary")) {
stop(C_EXCEPTION_TYPE_RUNTIME_ISSUE, "'x' must be a list or Dictionary (is ", .getClassName(x), ")")
}
if (!is.character(listEntryNames)) {
stop(C_EXCEPTION_TYPE_RUNTIME_ISSUE, "'listEntryNames' must be a character vector")
}
if (inherits(x, "Dictionary")) {
return(getDictionarySubset(x, listEntryNames))
}
return(x[which(names(x) %in% listEntryNames)])
},
.isMultiHypothesesObject = function() {
return(.isEnrichmentAnalysisResults(self) || .isEnrichmentStageResults(self) ||
.isMultiArmAnalysisResults(self) || .isMultiArmStageResults(self))
},
.isEnrichmentObject = function() {
return(.isEnrichmentAnalysisResults(self) || .isEnrichmentStageResults(self))
}
)
)
.getMultidimensionalNumberOfVariants <- function(parameterSet, parameterNames) {
if (!is.null(parameterSet[["effectList"]])) {
effectMatrixName <- .getSimulationEnrichmentEffectMatrixName(parameterSet)
return(nrow(parameterSet$effectList[[effectMatrixName]]))
}
parameterNames <- parameterNames[!(parameterNames %in% c(
"accrualTime", "accrualIntensity",
"plannedSubjects", "plannedEvents",
"minNumberOfSubjectsPerStage", "maxNumberOfSubjectsPerStage",
"minNumberOfEventsPerStage", "maxNumberOfEventsPerStage",
"piecewiseSurvivalTime", "lambda2", "adaptations",
"adjustedStageWisePValues", "overallAdjustedTestStatistics"
))]
if (!is.null(parameterSet[[".piecewiseSurvivalTime"]]) &&
parameterSet$.piecewiseSurvivalTime$piecewiseSurvivalEnabled) {
parameterNames <- parameterNames[!(parameterNames %in% c("lambda1"))]
}
n <- 1
for (parameterName in parameterNames) {
parameterValues <- parameterSet[[parameterName]]
if (!is.null(parameterValues) && (is.matrix(parameterValues) || !is.array(parameterValues))) {
if (is.matrix(parameterValues)) {
if (parameterSet$.isMultiHypothesesObject()) {
if (nrow(parameterValues) > n && ncol(parameterValues) > 0) {
n <- nrow(parameterValues)
}
} else if (nrow(parameterValues) > 0 && ncol(parameterValues) > n) {
n <- ncol(parameterValues)
}
} else if (length(parameterValues) > n &&
!parameterSet$.isMultiHypothesesObject()) {
n <- length(parameterValues)
}
}
}
return(n)
}
.getDataFrameColumnValues <- function(parameterSet,
parameterName,
numberOfVariants,
numberOfStages,
includeAllParameters,
mandatoryParameterNames) {
if (parameterSet$.getParameterType(parameterName) == C_PARAM_TYPE_UNKNOWN &&
parameterName != "futilityStop") {
return(NULL)
}
if (!includeAllParameters &&
parameterSet$.getParameterType(parameterName) == C_PARAM_NOT_APPLICABLE &&
!(parameterName %in% mandatoryParameterNames)) {
return(NULL)
}
parameterValues <- parameterSet[[parameterName]]
if (is.null(parameterValues) || length(parameterValues) == 0) {
return(NULL)
}
if (is.function(parameterValues)) {
return(NULL)
}
if (is.array(parameterValues) && !is.matrix(parameterValues)) {
return(NULL)
}
if (parameterName %in% c("adjustedStageWisePValues", "overallAdjustedTestStatistics")) {
return(NULL)
}
if (!is.matrix(parameterValues)) {
if (length(parameterValues) == 1) {
return(rep(parameterValues, numberOfVariants * numberOfStages))
}
if (parameterSet$.isMultiHypothesesObject()) {
if (length(parameterValues) == numberOfStages) {
return(as.vector(sapply(FUN = rep, X = parameterValues, times = numberOfVariants)))
}
}
if (length(parameterValues) == numberOfVariants) {
return(rep(parameterValues, numberOfStages))
}
if (length(parameterValues) == numberOfStages &&
parameterName %in% c(
"plannedEvents", "plannedSubjects",
"minNumberOfEventsPerStage", "maxNumberOfEventsPerStage",
"minNumberOfSubjectsPerStage", "maxNumberOfSubjectsPerStage",
"allocationRatioPlanned"