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class_summary.R
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class_summary.R
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## |
## | *Summary classes and functions*
## |
## | 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: 7958 $
## | Last changed: $Date: 2024-05-30 09:56:27 +0200 (Do, 30 Mai 2024) $
## | Last changed by: $Author: pahlke $
## |
#' @include f_core_utilities.R
#' @include f_core_assertions.R
NULL
SummaryItem <- R6::R6Class("SummaryItem",
public = list(
title = NULL,
values = NULL,
legendEntry = NULL,
initialize = function(title = NA_character_, values = NA_character_, legendEntry = NULL, ...) {
self$title <- title
self$values <- values
self$legendEntry <- legendEntry
if (!is.null(self$legendEntry) && length(self$legendEntry) > 0) {
if (is.null(names(self$legendEntry))) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
sQuote("legendEntry"), " must be a named list"
)
}
for (l in self$legendEntry) {
if (length(l) == 0) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
sQuote("legendEntry"), " must be not empty"
)
}
}
}
},
show = function() {
cat(self$title, "=", self$values, "\n")
},
toList = function() {
result <- list()
result[[self$title]] <- self$values
}
)
)
#'
#' @title
#' Summary Factory Plotting
#'
#' @param x The summary factory object.
#' @param y Not available for this kind of plot (is only defined
#' to be compatible to the generic plot function).
#' @param showSummary Show the summary before creating the
#' plot output, default is \code{FALSE}.
#' @inheritParams param_three_dots_plot
#'
#' @description
#' Plots a summary factory.
#'
#' @details
#' Generic function to plot all kinds of summary factories.
#'
#' @template return_object_ggplot
#'
#' @export
#'
plot.SummaryFactory <- function(x, y, ..., showSummary = FALSE) {
fCall <- match.call(expand.dots = FALSE)
if (isTRUE(showSummary) || .isSummaryPipe(fCall)) {
markdown <- .getOptionalArgument("markdown", ..., optionalArgumentDefaultValue = NA)
if (is.na(markdown)) {
markdown <- .isMarkdownEnabled()
}
if (markdown) {
x$.catMarkdownText()
} else {
x$show()
}
}
plot(x = x$object, y = y, ...)
}
#'
#' @title
#' Print Summary Factory in Markdown Code Chunks
#'
#' @description
#' The function `knit_print.SummaryFactory` is the default
#' printing function for rpact summary objects in knitr.
#' The chunk option `render` uses this function by default.
#' To fall back to the normal printing behavior set the
#' chunk option `render = normal_print`.
#' For more information see \code{\link[knitr]{knit_print}}.
#'
#' @param x A \code{SummaryFactory}.
#' @param ... Other arguments (see \code{\link[knitr]{knit_print}}).
#'
#' @details
#' Generic function to print a summary object in Markdown.
#' Use \code{options("rpact.print.heading.base.number" = "NUMBER")}
#' (where \code{NUMBER} is an integer value >= -1) to
#' specify the heading level. The default is
#' \code{options("rpact.print.heading.base.number" = "0")}, i.e., the
#' top headings start with \code{##} in Markdown.
#' \code{options("rpact.print.heading.base.number" = "-1")} means
#' that all headings will be written bold but are not
#' explicit defined as header.
#'
#' @export
#'
knit_print.SummaryFactory <- function(x, ...) {
result <- paste0(utils::capture.output(x$.catMarkdownText()), collapse = "\n")
if (isTRUE(base::attr(x$object, "printObject"))) {
sep <- base::attr(x$object, "printObjectSeparator")
if (is.null(sep) || !is.character(sep)) {
sep <- "\n-----\n\n"
}
result <- paste0(
result, sep,
paste0(utils::capture.output(x$object$.catMarkdownText()), collapse = "\n")
)
}
if (isTRUE(x[["markdown"]])) {
sep <- "\n-----\n\n"
result <- paste0(sep, result)
}
return(knitr::asis_output(result))
}
#'
#' @title
#' Summary Factory Printing
#'
#' @param x The summary factory object.
#' @param markdown If \code{TRUE}, the object \code{x}
#' will be printed using markdown syntax;
#' normal representation will be used otherwise (default is \code{FALSE})
#' @param sep The separator line between the summary and the print output.
#' @inheritParams param_three_dots_plot
#'
#' @description
#' Prints the result object stored inside a summary factory.
#'
#' @details
#' Generic function to print all kinds of summary factories.
#'
#' @export
#'
print.SummaryFactory <- function(x, ...,
markdown = NA,
sep = "\n-----\n\n") {
if (is.na(markdown)) {
markdown <- .isMarkdownEnabled()
}
if (markdown || isTRUE(x[["markdown"]])) {
result <- paste0(utils::capture.output(x$.catMarkdownText()), collapse = "\n")
cat(sep)
cat(trimws(result), "\n")
return(invisible())
}
x$show()
}
#' @name SummaryFactory
#'
#' @title
#' Summary Factory
#'
#' @description
#' Basic class for summaries
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SummaryFactory <- R6::R6Class("SummaryFactory",
inherit = ParameterSet,
public = list(
object = NULL,
title = NULL,
header = NULL,
summaryItems = NULL,
intervalFormat = NULL,
justify = NULL,
output = NULL,
markdown = NULL,
initialize = function(...,
object = NULL,
intervalFormat = "[%s; %s]",
output = "all",
markdown = FALSE) {
super$initialize(...)
self$object <- object
self$intervalFormat <- intervalFormat
self$output <- output
self$markdown <- markdown
self$summaryItems <- list()
self$justify <- getOption("rpact.summary.justify", "right")
},
show = function(showType = 1, digits = NA_integer_) {
self$.show(showType = showType, digits = digits, consoleOutputEnabled = TRUE)
},
.show = function(showType = 1, digits = NA_integer_, ..., consoleOutputEnabled = TRUE) {
if (self$output %in% c("all", "title")) {
if (is.null(self$title) || length(self$title) == 0) {
self$title <- .createSummaryTitleObject(self$object)
}
if (!is.null(self$title) && length(self$title) == 1 && trimws(self$title) != "") {
self$.cat(self$title, "\n\n",
heading = 1,
consoleOutputEnabled = consoleOutputEnabled
)
}
}
if (self$output %in% c("all", "overview")) {
if (is.null(self$header) || length(self$header) == 0) {
self$header <- .createSummaryHeaderObject(self$object, self, digits)
}
if (!is.null(self$header) && length(self$header) == 1 && trimws(self$header) != "") {
self$.cat(self$header, "\n\n",
consoleOutputEnabled = consoleOutputEnabled
)
}
}
if (!(self$output %in% c("all", "body"))) {
return(invisible())
}
legendEntries <- c()
legendEntriesUnique <- c()
summaryItemNames <- c()
for (summaryItem in self$summaryItems) {
if (!is.null(summaryItem$title) && length(summaryItem$title) == 1 && !is.na(summaryItem$title)) {
summaryItemNames <- c(summaryItemNames, summaryItem$title)
}
if (length(summaryItem$legendEntry) > 0) {
a <- sort(names(summaryItem$legendEntry))
for (aa in a) {
if (!(aa %in% legendEntriesUnique)) {
legendEntriesUnique <- c(legendEntriesUnique, aa)
b <- summaryItem$legendEntry[[aa]]
legendEntries <- c(legendEntries, paste0(" ", aa, ": ", b))
}
}
}
}
summaryItemNames <- paste0(format(summaryItemNames), " ")
na <- ifelse(.isDataset(self$object), "NA", NA_character_)
tableColumns <- 0
maxValueWidth <- 1
if (length(self$summaryItems) > 0) {
for (i in 1:length(self$summaryItems)) {
validValues <- na.omit(self$summaryItems[[i]]$values)
if (length(validValues) > 0) {
w <- max(nchar(validValues))
maxValueWidth <- max(maxValueWidth, w)
tableColumns <- max(tableColumns, 1 + length(validValues))
}
}
spaceString <- paste0(rep(" ", maxValueWidth + 1), collapse = "")
for (i in 1:length(self$summaryItems)) {
itemTitle <- self$summaryItems[[i]]$title
if (!is.null(itemTitle) && length(itemTitle) == 1 && !is.na(itemTitle)) {
summaryItemName <- summaryItemNames[i]
values <- self$summaryItems[[i]]$values
values <- trimws(values)
indices <- !grepl("(\\])$", values)
values[indices] <- paste0(values[indices], " ")
values <- format(c(spaceString, values), justify = self$justify)[2:(length(values) + 1)]
self$.cat(summaryItemName, values, "\n",
tableColumns = tableColumns,
consoleOutputEnabled = consoleOutputEnabled, na = na
)
if (!consoleOutputEnabled && trimws(summaryItemName) == "Stage") {
self$.cat(rep("----- ", tableColumns), "\n",
tableColumns = tableColumns,
consoleOutputEnabled = consoleOutputEnabled, na = na
)
}
}
}
}
if (length(legendEntries) > 0) {
self$.cat("\n", consoleOutputEnabled = consoleOutputEnabled)
self$.cat("Legend:\n", consoleOutputEnabled = consoleOutputEnabled)
if (!consoleOutputEnabled) {
self$.cat("\n", consoleOutputEnabled = consoleOutputEnabled)
}
for (legendEntry in legendEntries) {
self$.cat(legendEntry, "\n", consoleOutputEnabled = consoleOutputEnabled)
}
self$.cat("\n", consoleOutputEnabled = consoleOutputEnabled)
}
},
addItem = function(title, values, legendEntry = list()) {
if (!is.character(values)) {
values <- as.character(values)
}
tryCatch(
{
self$addSummaryItem(SummaryItem$new(title = title, values = values, legendEntry = legendEntry))
},
error = function(e) {
stop(
C_EXCEPTION_TYPE_RUNTIME_ISSUE, "failed to add summary item '", title,
"' = ", .arrayToString(values), " (class: ", .getClassName(values), "): ", e$message
)
}
)
},
addSummaryItem = function(summaryItem) {
if (!inherits(summaryItem, "SummaryItem")) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"'summaryItem' must be an instance of class ",
"'SummaryItem' (was '", .getClassName(summaryItem), "')"
)
}
self$summaryItems <- c(self$summaryItems, summaryItem)
},
.getFormattedParameterValue = function(valuesToShow, valuesToShow2) {
naText <- getOption("rpact.summary.na", "")
if (length(valuesToShow) == length(valuesToShow2) && !all(is.na(valuesToShow2))) {
for (variantIndex in 1:length(valuesToShow)) {
value1 <- as.character(valuesToShow[variantIndex])
value2 <- as.character(valuesToShow2[variantIndex])
if (grepl("^ *NA *$", value1)) {
value1 <- naText
}
if (grepl("^ *NA *$", value2)) {
value2 <- naText
}
if (trimws(value1) == "" && trimws(value2) == "") {
valuesToShow[variantIndex] <- naText
} else {
valuesToShow[variantIndex] <- sprintf(self$intervalFormat, value1, value2)
}
}
} else {
valuesToShow[is.na(valuesToShow) | trimws(valuesToShow) == "NA"] <- naText
}
return(valuesToShow)
},
addParameter = function(parameterSet, ...,
parameterName = NULL, values = NULL, parameterCaption,
roundDigits = NA_integer_, ceilingEnabled = FALSE, cumsumEnabled = FALSE,
twoSided = FALSE, transpose = FALSE, smoothedZeroFormat = FALSE,
parameterCaptionSingle = parameterCaption, legendEntry = list(),
enforceFirstCase = FALSE, formatRepeatedPValues = FALSE,
validateParameterType = TRUE) {
if (!is.null(parameterName) && length(parameterName) == 1 &&
inherits(parameterSet, "ParameterSet") &&
parameterSet$.getParameterType(parameterName) == C_PARAM_NOT_APPLICABLE) {
if (.getLogicalEnvironmentVariable("RPACT_DEVELOPMENT_MODE") && validateParameterType) {
warning(
"Failed to add parameter ", .arrayToString(parameterName), " (",
.arrayToString(values), ") stored in ",
.getClassName(parameterSet), " because the ",
"parameter has type C_PARAM_NOT_APPLICABLE"
)
}
return(invisible())
}
parameterName1 <- parameterName[1]
if (!is.null(parameterName1) && is.character(parameterName1) && is.null(values)) {
values <- parameterSet[[parameterName1]]
if (is.null(values)) {
stop(
C_EXCEPTION_TYPE_RUNTIME_ISSUE, .getClassName(parameterSet),
" does not contain a field '", parameterName1, "'"
)
}
}
parameterName2 <- NA_character_
values2 <- NA_real_
if (!is.null(parameterName) && length(parameterName) > 1) {
parameterName2 <- parameterName[2]
values2 <- parameterSet[[parameterName2]]
parameterName <- parameterName[1]
if (is.null(values2)) {
stop(
C_EXCEPTION_TYPE_RUNTIME_ISSUE, .getClassName(parameterSet),
" does not contain a field '", parameterName2, "'"
)
}
}
if (is.null(values) && is.null(parameterName1)) {
stop(C_EXCEPTION_TYPE_RUNTIME_ISSUE, "'parameterName' or 'values' must be defined")
}
if (transpose) {
if (!is.matrix(values)) {
values <- as.matrix(values)
} else {
values <- t(values)
}
}
if (is.list(parameterSet) && is.matrix(values)) {
parameterSet <- parameterSet[["parameterSet"]]
if (is.null(parameterSet)) {
stop(C_EXCEPTION_TYPE_RUNTIME_ISSUE, "'parameterSet' must be added to list")
}
}
parameterNames <- ""
numberOfVariants <- 1
numberOfStages <- ifelse(is.matrix(values), ncol(values), length(values))
if (inherits(parameterSet, "ParameterSet")) {
parameterNames <- parameterSet$.getVisibleFieldNamesOrdered()
numberOfVariants <- .getMultidimensionalNumberOfVariants(parameterSet, parameterNames)
numberOfStages <- parameterSet$.getMultidimensionalNumberOfStages(parameterNames)
}
stages <- parameterSet[["stages"]]
if (is.null(stages) && !is.null(parameterSet[[".stageResults"]])) {
stages <- parameterSet[[".stageResults"]][["stages"]]
}
if (is.null(stages) && inherits(parameterSet, "ClosedCombinationTestResults")) {
stages <- parameterSet[[".design"]][["stages"]]
}
if (!is.null(stages) && length(stages) > 0) {
numberOfStages <- max(na.omit(stages))
if (is.matrix(values) && nrow(values) > 0) {
numberOfVariants <- nrow(values)
}
if (is.matrix(values) && ncol(values) > 0) {
numberOfStages <- ncol(values)
}
}
if (!is.null(parameterSet[[".piecewiseSurvivalTime"]]) &&
isTRUE(parameterSet[[".piecewiseSurvivalTime"]]$delayedResponseEnabled)) {
numberOfVariants <- 1
}
if (twoSided) {
values <- 2 * values
}
caseCondition <- list(
and1 = enforceFirstCase,
and2 = inherits(parameterSet, "Dataset"),
and3 = list(
or1 = list(
and1 = !transpose,
and2 = numberOfVariants == 1
),
or2 = list(
and1 = !is.matrix(values),
and2 = (!transpose && ncol(values) == 1),
and3 = (transpose && nrow(values) == 1)
),
or3 = list(
and1 = .isTrialDesign(parameterSet),
and2 = (numberOfStages > 1 && numberOfStages == length(values)),
and3 = length(values) != numberOfVariants,
and4 = length(values) == 1,
and5 = parameterName %in% c(
"futilityBoundsEffectScale",
"futilityBoundsEffectScaleLower",
"futilityBoundsEffectScaleUpper",
"futilityPerStage",
"earlyStop"
)
)
)
)
if (.isConditionTrue(caseCondition, "or", showDebugMessages = FALSE)) {
valuesToShow <- .getSummaryValuesFormatted(
parameterSet, parameterName1, values,
roundDigits = roundDigits,
ceilingEnabled = ceilingEnabled, cumsumEnabled = cumsumEnabled,
smoothedZeroFormat = smoothedZeroFormat,
formatRepeatedPValues = formatRepeatedPValues
)
if (parameterName1 %in% c("piControl", "overallPiControl", "overallPooledStDevs")) {
valuesToShow <- self$.getInnerValues(valuesToShow, transpose = TRUE)
} else {
valuesToShow <- self$.getInnerValues(valuesToShow, transpose = transpose)
}
valuesToShow2 <- NA_real_
if (!all(is.na(values2))) {
valuesToShow2 <- .getSummaryValuesFormatted(parameterSet,
parameterName1, values2,
roundDigits = roundDigits,
ceilingEnabled = ceilingEnabled, cumsumEnabled = cumsumEnabled,
smoothedZeroFormat = smoothedZeroFormat,
formatRepeatedPValues = formatRepeatedPValues
)
valuesToShow2 <- self$.getInnerValues(valuesToShow2, transpose = transpose)
}
valuesToShow <- self$.getFormattedParameterValue(valuesToShow, valuesToShow2)
self$addItem(parameterCaptionSingle, valuesToShow, legendEntry)
} else {
if (!inherits(parameterSet, "ParameterSet")) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"for varied values 'parameterSet' must be an instance of ",
"class 'ParameterSet' (was '", .getClassName(parameterSet), "')"
)
}
transposed <- !transpose && grepl("MultiArm|Enrichment", .getClassName(parameterSet)) &&
(!is.matrix(values) || ncol(values) > 1)
userDefinedEffectMatrix <- FALSE
if (grepl("MultiArm|Enrichment", .getClassName(parameterSet)) ||
inherits(parameterSet, "AnalysisResultsConditionalDunnett") ||
inherits(parameterSet, "ClosedCombinationTestResults") ||
inherits(parameterSet, "ConditionalPowerResults")) {
if (grepl("SimulationResults(MultiArm|Enrichment)", .getClassName(parameterSet)) &&
parameterName %in% c(
"rejectAtLeastOne",
"earlyStop",
"futilityPerStage",
"successPerStage",
"expectedNumberOfSubjects",
"expectedNumberOfEvents",
"singleEventsPerArmAndStage",
"singleEventsPerSubsetAndStage",
"numberOfActiveArms",
"numberOfPopulations",
"conditionalPowerAchieved"
)) {
transposed <- TRUE
userDefinedEffectMatrix <-
parameterSet$.getParameterType("effectMatrix") == C_PARAM_USER_DEFINED
if (userDefinedEffectMatrix) {
legendEntry[["[j]"]] <- "effect matrix row j (situation to consider)"
}
if (grepl("Survival", .getClassName(parameterSet)) &&
!grepl("Enrichment", .getClassName(parameterSet))) {
legendEntry[["(i)"]] <- "results of treatment arm i vs. control arm"
}
if (grepl("SimulationResultsEnrichment", .getClassName(parameterSet))) {
variedParameterName <- .getSummaryVariedParameterNameEnrichment(parameterSet)
variedParameterValues <- parameterSet$effectList[[variedParameterName]]
if (variedParameterName == "piTreatments") {
variedParameterCaption <- "pi(treatment)"
} else {
variedParameterCaption <- .getParameterCaption(variedParameterName)
if (is.matrix(variedParameterValues) && ncol(variedParameterValues) == 1) {
variedParameterCaption <- sub("s$", "", variedParameterCaption)
}
}
if (is.matrix(variedParameterValues)) {
numberOfVariants <- nrow(variedParameterValues)
} else {
numberOfVariants <- length(variedParameterValues)
}
} else {
variedParameterName <- .getVariedParameterSimulationMultiArm(parameterSet)
variedParameterValues <- parameterSet[[variedParameterName]]
variedParameterCaption <- .getParameterCaption(variedParameterName)
numberOfVariants <- length(variedParameterValues)
}
variedParameterCaption <- tolower(variedParameterCaption)
} else if (self$.isEnrichmentObject(parameterSet)) {
transposed <- TRUE
variedParameterCaption <- "populations"
if (parameterName1 %in% c(
"indices",
"conditionalErrorRate",
"secondStagePValues",
"adjustedStageWisePValues",
"overallAdjustedTestStatistics",
"rejectedIntersections"
)) {
if (.isEnrichmentAnalysisResults(parameterSet)) {
variedParameterValues <- parameterSet$.closedTestResults$.getHypothesisPopulationVariants()
} else {
variedParameterValues <- parameterSet$.getHypothesisPopulationVariants()
}
} else {
variedParameterValues <- c(paste0("S", 1:(numberOfVariants - 1)), "F")
}
numberOfVariants <- length(variedParameterValues)
legendEntry[["S[i]"]] <- "population i"
legendEntry[["F"]] <- "full population"
} else if (!inherits(parameterSet, "ClosedCombinationTestResults") ||
parameterName %in% c("rejected", "separatePValues")) {
if (inherits(parameterSet, "AnalysisResultsConditionalDunnett") &&
(!is.matrix(values) || ncol(values) > 1)) {
transposed <- TRUE
}
if (inherits(parameterSet, "ClosedCombinationTestResults") &&
parameterSet$.getParameterType("adjustedStageWisePValues") != "g" &&
parameterName == "separatePValues") {
transposed <- TRUE
}
if (inherits(parameterSet, "ClosedCombinationTestResults") &&
parameterName %in% c("rejected")) {
transposed <- TRUE
}
if (inherits(parameterSet, "ConditionalPowerResults") &&
parameterName %in% c("conditionalPower", "values")) {
transposed <- TRUE
}
variedParameterCaption <- "arm"
variedParameterValues <- 1:numberOfVariants
legendEntry[["(i)"]] <- "results of treatment arm i vs. control arm"
} else {
transposed <- TRUE
variedParameterCaption <- "arms"
variedParameterValues <- parameterSet$.getHypothesisTreatmentArmVariants()
numberOfVariants <- length(variedParameterValues)
legendEntry[["(i, j, ...)"]] <- "comparison of treatment arms 'i, j, ...' vs. control arm"
}
} else {
if (inherits(parameterSet, "Dataset")) {
variedParameter <- "groups"
} else if (inherits(parameterSet, "PerformanceScore")) {
variedParameter <- ".alternative"
} else {
variedParameter <- parameterSet$.getVariedParameter(parameterNames, numberOfVariants)
}
if (is.null(variedParameter) || length(variedParameter) == 0 || variedParameter == "") {
if (.getLogicalEnvironmentVariable("RPACT_DEVELOPMENT_MODE")) {
warning(
"Failed to get varied parameter from ", .getClassName(parameterSet),
" (", length(parameterNames), " parameter names; numberOfVariants: ", numberOfVariants, ")"
)
}
return(invisible())
}
variedParameterCaption <- parameterSet$.getDataFrameColumnCaption(
variedParameter,
niceColumnNamesEnabled = TRUE
)
variedParameterCaption <- tolower(variedParameterCaption)
if (variedParameterCaption == "alternative" || variedParameterCaption == ".alternative") {
legendEntry[["alt."]] <- "alternative"
variedParameterCaption <- "alt."
} else if (variedParameterCaption == "hazard ratio") {
legendEntry[["HR"]] <- "hazard ratio"
variedParameterCaption <- "HR"
} else if (grepl("\\(1\\)$", variedParameterCaption)) {
groups <- parameterSet[["groups"]]
if (!is.null(groups) && length(groups) == 1 && groups == 1) {
variedParameterCaption <- sub(" \\(1\\)$", "", variedParameterCaption)
}
}
variedParameterValues <- round(parameterSet[[variedParameter]], 3)
}
for (variantIndex in 1:numberOfVariants) {
colValues <- self$.getColumnValues(parameterName, values, variantIndex, transposed)
colValues <- .getSummaryValuesFormatted(parameterSet, parameterName1,
colValues,
roundDigits = roundDigits,
ceilingEnabled = ceilingEnabled, cumsumEnabled = cumsumEnabled,
smoothedZeroFormat = smoothedZeroFormat,
formatRepeatedPValues = formatRepeatedPValues
)
colValues2 <- NA_real_
if (!all(is.na(values2))) {
colValues2 <- self$.getColumnValues(parameterName, values2, variantIndex, transposed)
colValues2 <- .getSummaryValuesFormatted(parameterSet, parameterName2, colValues2,
roundDigits = roundDigits, ceilingEnabled = ceilingEnabled,
cumsumEnabled = cumsumEnabled,
smoothedZeroFormat = smoothedZeroFormat,
formatRepeatedPValues = formatRepeatedPValues
)
}
colValues <- self$.getFormattedParameterValue(valuesToShow = colValues, valuesToShow2 = colValues2)
if (numberOfVariants == 1) {
self$addItem(parameterCaption, colValues, legendEntry)
} else if (self$.isEnrichmentObject(parameterSet)) {
self$addItem(paste0(
parameterCaption, " ",
variedParameterValues[variantIndex]
), colValues, legendEntry)
} else if (
(grepl("MultiArm|Enrichment", .getClassName(parameterSet)) &&
!grepl("Simulation", .getClassName(parameterSet))) ||
inherits(parameterSet, "AnalysisResultsConditionalDunnett") ||
inherits(parameterSet, "ClosedCombinationTestResults") ||
inherits(parameterSet, "ConditionalPowerResults")) {
spacePrefix <- ifelse(parameterCaption %in% c("pi", "lambda", "median"), "", " ")
self$addItem(paste0(
parameterCaption, spacePrefix,
"(", variedParameterValues[variantIndex], ")"
), colValues, legendEntry)
} else if (userDefinedEffectMatrix) {
self$addItem(paste0(parameterCaption, " [", variantIndex, "]"), colValues, legendEntry)
} else {
if (is.matrix(variedParameterValues) && ncol(variedParameterValues) > 1) {
variedParameterValuesFormatted <-
.arrayToString(variedParameterValues[variantIndex, ], vectorLookAndFeelEnabled = TRUE)
} else {
variedParameterValuesFormatted <- variedParameterValues[variantIndex]
}
self$addItem(
paste0(
parameterCaption, ", ",
variedParameterCaption, " = ", variedParameterValuesFormatted
),
colValues, legendEntry
)
}
}
}
},
.isEnrichmentObject = function(parameterSet) {
return(
.isEnrichmentAnalysisResults(parameterSet) ||
.isEnrichmentStageResults(parameterSet) ||
.isEnrichmentConditionalPowerResults(parameterSet) ||
(inherits(parameterSet, "ClosedCombinationTestResults") &&
isTRUE(parameterSet$.enrichment))
)
},
.getInnerValues = function(values, transpose = FALSE) {
if (!is.matrix(values)) {
return(values)
}
if (nrow(values) == 1 && ncol(values) == 1) {
return(values[1, 1])
}
if (transpose) {
return(values[1, ])
}
return(values[, 1])
},
.getColumnValues = function(parameterName, values, variantIndex, transposed = FALSE) {
tryCatch(
{
if (transposed) {
if (!is.matrix(values)) {
return(values)
}
if (nrow(values) == 0) {
return("")
}
if (nrow(values) == 1 && ncol(values) == 1) {
colValues <- values[1, 1]
} else if (nrow(values) == 1) {
colValues <- values[1, variantIndex]
} else if (ncol(values) == 1) {
colValues <- values[variantIndex, 1]
} else {
colValues <- values[variantIndex, ]
}
return(colValues)
}
if (length(values) <= 1 && !is.matrix(values)) {
colValues <- values
} else if (is.matrix(values)) {
if (length(values) == 0 || nrow(values) == 0 || ncol(values) == 0) {
return("")
}
if (nrow(values) == 1 && ncol(values) == 1) {
colValues <- values[1, 1]
} else if (ncol(values) == 1) {
colValues <- values[variantIndex, 1]
} else if (nrow(values) == 1) {
colValues <- values[1, variantIndex]
} else {
if (ncol(values) == 0) {
return("")
}
colValues <- values[, variantIndex]
}
} else {
colValues <- values[variantIndex]
}
return(colValues)
},
error = function(e) {
stop(
".getColumnValues(", dQuote(parameterName), "): ", e$message,
"; .getClassName(values) = ", .getClassName(values),
"; dim(values) = ", .arrayToString(dim(values), vectorLookAndFeelEnabled = TRUE),
"; variantIndex = ", variantIndex,
"; transposed = ", transposed
)
}
)
}
)
)
.formatSummaryValues <- function(values, digits, smoothedZeroFormat = FALSE, formatRepeatedPValues = FALSE) {
if (is.na(digits)) {
digits <- 3
}
if (digits < 1) {
formattedValue <- as.character(values)
formattedValue[is.na(formattedValue) | trimws(formattedValue) == "NA"] <- getOption("rpact.summary.na", "")
return(formattedValue)
}
if (sum(is.na(values)) == length(values)) {
formattedValue <- rep(getOption("rpact.summary.na", ""), length(values))
return(formattedValue)
}
threshold <- 10^-digits
text <- "<0."
if (digits > 1) {
for (i in 1:(digits - 1)) {
text <- paste0(text, "0")
}
}
text <- paste0(text, "1")
if (smoothedZeroFormat) {
values[abs(values) < 1e-15] <- 0
}
indices <- (!is.na(values) & values > 1e-10 & abs(values) < threshold)
values[!is.na(values) & !indices] <- round(values[!is.na(values) & !indices], digits)
if (sum(indices) > 0) {
values[indices] <- threshold
formattedValue <- .getFormattedValue(values, digits = digits, nsmall = digits, scientific = FALSE)
formattedValue[indices] <- text
} else {
formattedValue <- .getFormattedValue(values, digits = digits, nsmall = digits, scientific = FALSE)
formattedValue <- format(formattedValue, scientific = FALSE)
}
if (formatRepeatedPValues) {
formattedValue[!is.na(formattedValue) &
nchar(gsub("\\D", "", (formattedValue))) > 0 & formattedValue > 0.4999] <- ">0.5"
}
if (as.logical(getOption("rpact.summary.trim.zeroes", TRUE))) {
zeroes <- grepl("^0\\.0*$", formattedValue)
if (sum(zeroes) > 0) {
formattedValue[zeroes] <- "0"
}
}
formattedValue[is.na(formattedValue) | trimws(formattedValue) == "NA"] <- getOption("rpact.summary.na", "")
return(formattedValue)
}
.getSummaryValuesFormatted <- function(fieldSet, parameterName, values,
roundDigits = NA_integer_, ceilingEnabled = FALSE, cumsumEnabled = FALSE,
smoothedZeroFormat = FALSE, formatRepeatedPValues = FALSE) {
if (!is.numeric(values)) {
return(values)
}
if (cumsumEnabled) {
values <- cumsum(values)
}
if (ceilingEnabled) {
values <- ceiling(values)
} else {
tryCatch(
{
formatFunctionName <- NULL
if (!is.null(parameterName) && length(parameterName) == 1 && !is.na(parameterName)) {
if (parameterName == "futilityBounds") {
values[!is.na(values) & values <= -6] <- -Inf
} else if (parameterName %in% c(
"criticalValues",
"decisionCriticalValue", "overallAdjustedTestStatistics"
)) {
design <- fieldSet
if (!.isTrialDesign(design)) {
design <- fieldSet[[".design"]]
}
if (!is.null(design) && .isTrialDesignFisher(design)) {
roundDigits <- 0
}
}
if (!is.na(roundDigits) && roundDigits == 0) {
if (inherits(fieldSet, "Dataset") &&
grepl("samplesize|event", tolower(parameterName))) {
} else {
formatFunctionName <- .getParameterFormatFunction(parameterName, fieldSet)
}
}
}
if (!is.null(formatFunctionName)) {
values <- eval(call(formatFunctionName, values))
} else {
values <- .formatSummaryValues(values,
digits = roundDigits,
smoothedZeroFormat = smoothedZeroFormat,
formatRepeatedPValues = formatRepeatedPValues
)
}
},
error = function(e) {
stop(
C_EXCEPTION_TYPE_RUNTIME_ISSUE,
"failed to show parameter '", parameterName, "': ", e$message
)
}
)
}
return(format(values))
}
.createSummaryTitleObject <- function(object) {
design <- NULL
designPlan <- NULL
if (inherits(object, "TrialDesignCharacteristics")) {
design <- object$.design
} else if (.isTrialDesignPlan(object) || inherits(object, "SimulationResults")) {
design <- object$.design
designPlan <- object
} else if (inherits(object, "AnalysisResults")) {
return(.createSummaryTitleAnalysisResults(object$.design, object))
} else if (.isTrialDesign(object)) {
design <- object
}
if (!is.null(design)) {
return(.createSummaryTitleDesign(design, designPlan))
}
return("")
}
.createSummaryTitleAnalysisResults <- function(design, analysisResults) {
kMax <- design$kMax
title <- ""
if (kMax == 1) {
title <- paste0(title, "Fixed sample analysis results")
} else {
title <- paste0(title, "Sequential analysis results with a maximum of ", kMax, " looks")
}
if (!is.null(analysisResults)) {
if (.isMultiArmAnalysisResults(analysisResults)) {
title <- "Multi-arm analysis results for a "
} else if (.isEnrichmentAnalysisResults(analysisResults)) {
title <- "Enrichment analysis results for a "
} else {
title <- "Analysis results for a "
}
if (grepl("Means", .getClassName(analysisResults$.dataInput))) {
title <- paste0(title, "continuous endpoint")
} else if (grepl("Rates", .getClassName(analysisResults$.dataInput))) {
title <- paste0(title, "binary endpoint")
} else if (grepl("Survival", .getClassName(analysisResults$.dataInput))) {
title <- paste0(title, "survival endpoint")
}