Nothing
R/class_simulation_results.R
In rpact: Confirmatory Adaptive Clinical Trial Design and Analysis
Defines functions
print.SimulationResults
names.SimulationResults
Documented in
names.SimulationResults
print.SimulationResults
## |
## | *Simulation result 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: 7672 $
## | Last changed: $Date: 2024-02-27 10:42:41 +0100 (Di, 27 Feb 2024) $
## | Last changed by: $Author: pahlke $
## |
#' @include f_core_utilities.R
NULL
#'
#' @title
#' Names of a Simulation Results Object
#'
#' @description
#' Function to get the names of a \code{\link{SimulationResults}} object.
#'
#' @param x A \code{\link{SimulationResults}} object created by \code{getSimulationResults[MultiArm/Enrichment][Means/Rates/Survival]}.
#'
#' @details
#' Returns the names of a simulation results that can be accessed by the user.
#'
#' @template return_names
#'
#' @export
#'
#' @keywords internal
#'
names.SimulationResults <- function(x) {
namesToShow <- c(".design", ".data", ".rawData")
if (inherits(x, "SimulationResultsSurvival")) {
namesToShow <- c(namesToShow, ".piecewiseSurvivalTime", ".accrualTime")
}
namesToShow <- c(namesToShow, x$.getVisibleFieldNames())
return(namesToShow)
}
#'
#' @name SimulationResults
#'
#' @title
#' Class for Simulation Results
#'
#' @description
#' A class for simulation results.
#'
#' @template field_seed
#' @template field_iterations
#'
#' @details
#' \code{SimulationResults} is the basic class for
#' \itemize{
#' \item \code{\link{SimulationResultsMeans}},
#' \item \code{\link{SimulationResultsRates}},
#' \item \code{\link{SimulationResultsSurvival}},
#' \item \code{\link{SimulationResultsMultiArmMeans}},
#' \item \code{\link{SimulationResultsMultiArmRates}},
#' \item \code{\link{SimulationResultsMultiArmSurvival}},
#' \item \code{\link{SimulationResultsEnrichmentMeans}},
#' \item \code{\link{SimulationResultsEnrichmentRates}}, and
#' \item \code{\link{SimulationResultsEnrichmentSurvival}}.
#' }
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#' @include f_simulation_utilities.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResults <- setRefClass("SimulationResults",
contains = "ParameterSet",
fields = list(
.plotSettings = "PlotSettings",
.design = "TrialDesign",
.data = "data.frame",
.rawData = "data.frame",
.showStatistics = "logical",
maxNumberOfIterations = "integer",
seed = "numeric",
allocationRatioPlanned = "numeric",
conditionalPower = "numeric",
iterations = "matrix",
futilityPerStage = "matrix",
futilityStop = "numeric"
),
methods = list(
initialize = function(design, ..., showStatistics = FALSE) {
callSuper(.design = design, .showStatistics = showStatistics, ...)
.plotSettings <<- PlotSettings()
},
getPlotSettings = function() {
return(.plotSettings)
},
setShowStatistics = function(showStatistics) {
.assertIsSingleLogical(showStatistics, "showStatistics")
.showStatistics <<- showStatistics
},
show = function(showType = 1, digits = NA_integer_, showStatistics = FALSE) {
.show(
showType = showType, digits = digits, showStatistics = showStatistics,
consoleOutputEnabled = TRUE
)
},
.show = function(..., showType = 1, digits = NA_integer_,
showStatistics = FALSE, consoleOutputEnabled = TRUE, performanceScore = NULL) {
"Method for automatically printing simulation result objects"
.resetCat()
if (showType == 3) {
.createSummary(.self, digits = digits)$.show(
showType = 1,
digits = digits, consoleOutputEnabled = consoleOutputEnabled
)
} else if (showType == 2) {
callSuper(showType = showType, digits = digits, consoleOutputEnabled = consoleOutputEnabled)
} else {
if (is.null(showStatistics) || length(showStatistics) != 1) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"'showStatistics' (", .arrayToString(showStatistics),
") must be a single logical or character"
)
}
if (!is.character(showStatistics) || showStatistics != "exclusive") {
.cat(.toString(startWithUpperCase = TRUE), ":\n\n",
heading = 1,
consoleOutputEnabled = consoleOutputEnabled
)
.showParametersOfOneGroup(.getDesignParametersToShow(.self), "Design parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
userDefinedParameters <- .getUserDefinedParameters()
if (inherits(.self, "SimulationResultsSurvival") &&
.self$.piecewiseSurvivalTime$delayedResponseEnabled) {
userDefinedParameters <- c(
userDefinedParameters,
".piecewiseSurvivalTime$delayedResponseEnabled"
)
}
.showParametersOfOneGroup(userDefinedParameters, "User defined parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
derivedParameters <- .getDerivedParameters()
if (length(derivedParameters) > 0) {
.showParametersOfOneGroup(derivedParameters, "Derived from user defined parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
}
.showParametersOfOneGroup(.getDefaultParameters(), "Default parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
.showParametersOfOneGroup(.getGeneratedParameters(), "Results",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
.showUnknownParameters(consoleOutputEnabled = consoleOutputEnabled)
}
## statistics of simulated data
if (isTRUE(showStatistics) || .showStatistics ||
(is.character(showStatistics) && showStatistics == "exclusive")) {
.cat("Simulated data:\n", heading = 2, consoleOutputEnabled = consoleOutputEnabled)
params <- c()
if (inherits(.self, "SimulationResultsMeans")) {
params <- c(
"effectMeasure",
"numberOfSubjects",
"testStatistic"
)
} else if (inherits(.self, "SimulationResultsRates")) {
params <- c(
"effectMeasure",
"numberOfSubjects",
"testStatistic"
)
} else if (inherits(.self, "SimulationResultsSurvival")) {
params <- c(
"effectMeasure",
"analysisTime",
"numberOfSubjects",
"eventsPerStage1",
"eventsPerStage2",
"cumulativeEventsPerStage",
"testStatistic",
"logRankStatistic",
"hazardRatioEstimateLR"
)
} else if (inherits(.self, "SimulationResultsMultiArmMeans") ||
inherits(.self, "SimulationResultsMultiArmRates")) {
params <- c(
"effectMeasure",
"subjectsActiveArm",
"testStatistic",
"conditionalCriticalValue",
"rejectPerStage",
"successStop",
"futilityPerStage"
)
} else if (inherits(.self, "SimulationResultsEnrichmentMeans") ||
inherits(.self, "SimulationResultsEnrichmentRates")) {
params <- c(
"effectMeasure",
"subjectsPopulation",
"testStatistic",
"conditionalCriticalValue",
"rejectPerStage",
"successStop",
"futilityPerStage"
)
} else if (inherits(.self, "SimulationResultsMultiArmSurvival") ||
inherits(.self, "SimulationResultsEnrichmentSurvival")) {
params <- c(
"effectMeasure",
"numberOfEvents",
"singleEventsPerArmAndStage",
"singleEventsPerSubsetAndStage",
"testStatistic",
"conditionalCriticalValue",
"rejectPerStage",
"successStop",
"futilityPerStage"
)
}
if (!is.null(.self[["conditionalPowerAchieved"]]) &&
!all(is.na(conditionalPowerAchieved)) &&
any(!is.na(conditionalPowerAchieved)) &&
any(na.omit(conditionalPowerAchieved) != 0)) {
params <- c(params, "conditionalPowerAchieved")
}
stages <- sort(unique(.self$.data$stageNumber))
variedParameterName1 <- .getVariedParameterName(1)
variedParameterName2 <- .getVariedParameterName(2)
parameterValues1 <- .getVariedParameterValues(variedParameterName1)
parameterValues2 <- .getVariedParameterValues(variedParameterName2)
for (parameterName in params) {
paramCaption <- .getParameterCaption(parameterName, .self)
if (is.null(paramCaption)) {
paramCaption <- paste0("%", parameterName, "%")
}
for (parameterValue1 in parameterValues1) {
for (parameterValue2 in parameterValues2) {
for (stage in stages) {
if (length(parameterValues1) > 1) {
.catStatisticsLine(
stage = stage,
parameterName = parameterName,
paramCaption = paramCaption,
parameterValue1 = parameterValue1,
variedParameterName1 = variedParameterName1,
parameterValue2 = parameterValue2,
variedParameterName2 = variedParameterName2,
consoleOutputEnabled = consoleOutputEnabled
)
} else {
.catStatisticsLine(
stage = stage,
parameterName = parameterName,
paramCaption = paramCaption,
parameterValue1 = parameterValue2,
variedParameterName1 = variedParameterName2,
consoleOutputEnabled = consoleOutputEnabled
)
}
}
}
if (parameterName == "subjectsActiveArm" && variedParameterName2 == "armNumber") {
parameterName2 <- "subjectsControlArm"
paramCaption2 <- .getParameterCaption(parameterName2, .self)
if (is.null(paramCaption2)) {
paramCaption2 <- paste0("%", parameterName2, "%")
}
for (stage in stages) {
.catStatisticsLine(
stage = stage,
parameterName = parameterName2,
paramCaption = paramCaption2,
parameterValue1 = parameterValue1,
variedParameterName1 = variedParameterName1,
parameterValue2 = unique(parameterValues2),
variedParameterName2 = variedParameterName2,
consoleOutputEnabled = consoleOutputEnabled
)
}
}
}
}
.cat("\n", consoleOutputEnabled = consoleOutputEnabled)
}
twoGroupsEnabled <- !inherits(.self, "SimulationResultsMeans")
multiArmSurvivalEnabled <- inherits(.self, "SimulationResultsMultiArmSurvival")
enrichmentEnabled <- grepl("SimulationResultsEnrichment", .getClassName(.self))
if (!is.null(performanceScore)) {
performanceScore$.showParametersOfOneGroup(
performanceScore$.getGeneratedParameters(), "Performance",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
performanceScore$.showUnknownParameters(consoleOutputEnabled = consoleOutputEnabled)
}
if (.design$kMax > 1 || twoGroupsEnabled || multiArmSurvivalEnabled) {
.cat("Legend:\n", heading = 2, consoleOutputEnabled = consoleOutputEnabled)
if (multiArmSurvivalEnabled) {
.cat(" (i): values of treatment arm i compared to control\n", consoleOutputEnabled = consoleOutputEnabled)
.cat(" {j}: values of treatment arm j\n", consoleOutputEnabled = consoleOutputEnabled)
} else if (enrichmentEnabled) {
matrixName <- .getSimulationEnrichmentEffectMatrixName(.self)
if (nrow(.self$effectList[[matrixName]]) > 1) {
.cat(" (i): results of situation i\n", consoleOutputEnabled = consoleOutputEnabled)
}
} else if (twoGroupsEnabled) {
.cat(" (i): values of treatment arm i\n", consoleOutputEnabled = consoleOutputEnabled)
}
if (.design$kMax > 1) {
.cat(" [k]: values at stage k\n", consoleOutputEnabled = consoleOutputEnabled)
}
if (enrichmentEnabled) {
if (length(.self$effectList$subGroups) > 1) {
.cat(paste0(" S[i]: population i\n"), consoleOutputEnabled = consoleOutputEnabled)
}
.cat(paste0(" F: full population\n"), consoleOutputEnabled = consoleOutputEnabled)
if (length(.self$effectList$subGroups) > 1) {
.cat(paste0(" R: remaining population\n"), consoleOutputEnabled = consoleOutputEnabled)
}
}
.cat("\n", consoleOutputEnabled = consoleOutputEnabled)
}
}
},
.getVariedParameterName = function(number = 1) {
if (number == 2) {
if (!inherits(.self, "SimulationResultsMeans") &&
!inherits(.self, "SimulationResultsRates") &&
!inherits(.self, "SimulationResultsSurvival") &&
grepl("MultiArm", .getClassName(.self))) {
return("armNumber")
}
return(NA_character_)
}
variedParameterName1 <- NA_character_
if (inherits(.self, "SimulationResultsMeans")) {
variedParameterName1 <- "alternative"
} else if (inherits(.self, "SimulationResultsRates") || inherits(.self, "SimulationResultsSurvival")) {
variedParameterName1 <- "pi1"
} else if (grepl("MultiArm", .getClassName(.self))) {
if (inherits(.self, "SimulationResultsMultiArmMeans")) {
variedParameterName1 <- "muMax"
} else if (inherits(.self, "SimulationResultsMultiArmRates")) {
variedParameterName1 <- "piMax"
} else if (inherits(.self, "SimulationResultsMultiArmSurvival")) {
variedParameterName1 <- "omegaMax"
}
}
return(variedParameterName1)
},
.getVariedParameterValues = function(variedParameterName) {
if (is.na(variedParameterName)) {
return(NA_real_)
}
parameterValues <- .self$.data[[variedParameterName]]
if (is.null(parameterValues)) {
return(NA_real_)
}
parameterValues <- unique(parameterValues)
if (length(parameterValues) > 1 && !any(is.na(parameterValues))) {
parameterValues <- sort(parameterValues)
}
return(parameterValues)
},
.getVariedParameterValueString = function(variedParameterName, parameterValue) {
if (variedParameterName %in% c("armNumber")) {
return(paste0(" (", parameterValue[1], ")"))
}
variedParameterName <- sub("Max$", "_max", variedParameterName)
return(paste0(", ", variedParameterName, " = ", round(parameterValue[1], 4)))
},
.catStatisticsLine = function(..., stage, parameterName, paramCaption,
parameterValue1, variedParameterName1, parameterValue2 = NA_real_,
variedParameterName2 = NA_character_, consoleOutputEnabled = TRUE) {
if (stage == 1 && parameterName == "conditionalPowerAchieved") {
return(invisible())
}
postfix <- ""
if (!is.na(parameterValue1)) {
if (!all(is.na(parameterValue2))) {
postfix <- paste0(postfix, .getVariedParameterValueString(
variedParameterName1, parameterValue1
))
if (parameterName != "subjectsControlArm") {
postfix <- paste0(postfix, .getVariedParameterValueString(
variedParameterName2, parameterValue2
))
}
paramValue <- .self$.data[[parameterName]][
.self$.data$stageNumber == stage &
.self$.data[[variedParameterName1]] == parameterValue1 &
.self$.data[[variedParameterName2]] %in% parameterValue2
]
} else {
postfix <- paste0(postfix, .getVariedParameterValueString(
variedParameterName1, parameterValue1
))
paramValue <- .self$.data[[parameterName]][
.self$.data$stageNumber == stage &
.self$.data[[variedParameterName1]] == parameterValue1
]
}
} else {
paramValue <- .self$.data[[parameterName]][
.self$.data$stageNumber == stage
]
}
if (.design$kMax > 1) {
postfix <- paste0(postfix, " [", stage, "]")
}
if (!consoleOutputEnabled) {
paramCaption <- paste0("*", paramCaption, "*")
}
variableNameFormatted <- .getFormattedVariableName(
name = paramCaption,
n = .getNChar(), prefix = "", postfix = postfix
)
if (!is.null(paramValue)) {
paramValue <- stats::na.omit(paramValue)
if (length(paramValue) > 0 && is.numeric(paramValue)) {
paramValueFormatted <- paste0(
"median [range]: ", round(stats::median(paramValue), 3),
" [", paste(round(base::range(paramValue), 3), collapse = " - "), "]; ",
"mean +/-sd: ", round(base::mean(paramValue), 3), " +/-", round(stats::sd(paramValue), 3)
)
} else {
paramValueFormatted <- "median [range]: NA [NA - NA]; mean +/sd: NA +/-NA"
}
output <- paste(variableNameFormatted, paramValueFormatted, "\n")
if (!grepl(": median \\[range\\]: NA \\[NA - NA\\]", output)) {
.cat(output, consoleOutputEnabled = consoleOutputEnabled)
}
}
},
.toString = function(startWithUpperCase = FALSE) {
s <- "simulation of"
if (grepl("MultiArm", .getClassName(.self)) && !is.null(.self[["activeArms"]]) && .self$activeArms > 1) {
s <- paste(s, "multi-arm")
}
if (grepl("Enrichment", .getClassName(.self)) && !is.null(.self[["populations"]]) && .self$populations > 1) {
s <- paste(s, "enrichment")
}
if (inherits(.self, "SimulationResultsBaseMeans")) {
s <- paste(s, "means")
} else if (inherits(.self, "SimulationResultsBaseRates")) {
s <- paste(s, "rates")
} else if (inherits(.self, "SimulationResultsBaseSurvival")) {
s <- paste(s, "survival data")
} else if (inherits(.self, "SimulationResultsBaseCountData")) {
s <- paste(s, "count data")
} else {
s <- paste(s, "UNDEFINED")
}
if (.design$kMax > 1) {
if (.isTrialDesignGroupSequential(.design)) {
s <- paste(s, "(group sequential design)")
} else if (.isTrialDesignInverseNormal(.design)) {
s <- paste(s, "(inverse normal combination test design)")
} else if (.isTrialDesignFisher(.design)) {
s <- paste(s, "(Fisher's combination test design)")
} else if (.isTrialDesignConditionalDunnett(.design)) {
s <- paste(s, "(conditional Dunnett design)")
}
} else {
s <- paste(s, "(fixed sample size design)")
}
return(ifelse(startWithUpperCase, .firstCharacterToUpperCase(s), s))
},
.getParametersToShow = function() {
parametersToShow <- .getVisibleFieldNames()
y <- c(
"singleEventsPerStage",
"cumulativeEventsPerStage",
"iterations",
"overallReject", # base
"rejectAtLeastOne",
"rejectPerStage",
"rejectedArmsPerStage",
"rejectedPopulationsPerStage"
)
if (.design$kMax > 2) {
y <- c(y, "futilityStop")
}
y <- c(
y,
"futilityPerStage",
"earlyStop", # base
"successPerStage",
"selectedArms",
"selectedPopulations",
"numberOfActiveArms",
"numberOfPopulations",
"expectedNumberOfSubjects",
"expectedNumberOfEvents",
"sampleSizes",
"singleEventsPerArmAndStage",
"singleEventsPerSubsetAndStage",
"conditionalPowerAchieved" # base
)
parametersToShow <- c(parametersToShow[!(parametersToShow %in% y)], y[y %in% parametersToShow])
return(parametersToShow)
},
.isSampleSizeObject = function() {
return(FALSE)
},
getRawDataResults = function(maxNumberOfIterations = NA_integer_) {
return(.getSimulationParametersFromRawData(
data = .self$.data,
variantName = .getVariedParameterName(),
maxNumberOfIterations = maxNumberOfIterations
))
}
)
)
SimulationResultsBaseMeans <- setRefClass("SimulationResultsBaseMeans",
contains = "SimulationResults",
fields = list(
stDev = "numeric",
plannedSubjects = "numeric",
minNumberOfSubjectsPerStage = "numeric",
maxNumberOfSubjectsPerStage = "numeric",
thetaH1 = "numeric",
stDevH1 = "numeric",
calcSubjectsFunction = "ANY",
expectedNumberOfSubjects = "numeric"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
generatedParams <- c(
"iterations",
"expectedNumberOfSubjects",
"sampleSizes",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsMeans
#'
#' @title
#' Class for Simulation Results Means
#'
#' @description
#' A class for simulation results means.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_stDev
#' @template field_plannedSubjects
#' @template field_minNumberOfSubjectsPerStage
#' @template field_maxNumberOfSubjectsPerStage
#' @template field_thetaH1
#' @template field_stDevH1
#' @template field_calcSubjectsFunction
#' @template field_expectedNumberOfSubjects
#' @template field_meanRatio
#' @template field_thetaH0
#' @template field_normalApproximation
#' @template field_alternative
#' @template field_groups
#' @template field_directionUpper
#' @template field_effect
#' @template field_earlyStop
#' @template field_sampleSizes
#' @template field_overallReject
#' @template field_rejectPerStage
#' @template field_conditionalPowerAchieved
#'
#' @details
#' Use \code{\link[=getSimulationMeans]{getSimulationMeans()}} to create an object of this type.
#'
#' \code{SimulationResultsMeans} is the basic class for
#' \itemize{
#' \item \code{\link{SimulationResultsMeans}},
#' \item \code{\link{SimulationResultsMultiArmMeans}}, and
#' \item \code{\link{SimulationResultsEnrichmentMeans}}.
#' }
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsMeans <- setRefClass("SimulationResultsMeans",
contains = "SimulationResultsBaseMeans",
fields = list(
meanRatio = "logical",
thetaH0 = "numeric",
normalApproximation = "logical",
alternative = "numeric",
groups = "integer",
directionUpper = "logical",
effect = "numeric",
earlyStop = "numeric",
sampleSizes = "matrix",
overallReject = "numeric", # = rejectedArmsPerStage in multi-arm
rejectPerStage = "matrix",
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
}
)
)
#'
#' @name SimulationResultsMultiArmMeans
#'
#' @title
#' Class for Simulation Results Multi-Arm Means
#'
#' @description
#' A class for simulation results means in multi-arm designs.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_stDev
#' @template field_plannedSubjects
#' @template field_minNumberOfSubjectsPerStage
#' @template field_maxNumberOfSubjectsPerStage
#' @template field_thetaH1
#' @template field_stDevH1
#' @template field_calcSubjectsFunction
#' @template field_expectedNumberOfSubjects
#' @template field_activeArms
#' @template field_effectMatrix
#' @template field_typeOfShape
#' @template field_muMaxVector
#' @template field_gED50
#' @template field_slope
#' @template field_intersectionTest
#' @template field_adaptations
#' @template field_typeOfSelection
#' @template field_effectMeasure
#' @template field_successCriterion
#' @template field_epsilonValue
#' @template field_rValue
#' @template field_threshold
#' @template field_selectArmsFunction
#' @template field_earlyStop
#' @template field_selectedArms
#' @template field_numberOfActiveArms
#' @template field_rejectAtLeastOne
#' @template field_rejectedArmsPerStage
#' @template field_successPerStage
#' @template field_sampleSizes
#' @template field_conditionalPowerAchieved
#'
#' @details
#' Use \code{\link[=getSimulationMultiArmMeans]{getSimulationMultiArmMeans()}} to create an object of this type.
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsMultiArmMeans <- setRefClass("SimulationResultsMultiArmMeans",
contains = "SimulationResultsBaseMeans",
fields = list(
activeArms = "integer",
effectMatrix = "matrix",
typeOfShape = "character",
muMaxVector = "numeric",
gED50 = "numeric",
slope = "numeric",
intersectionTest = "character",
adaptations = "logical",
typeOfSelection = "character",
effectMeasure = "character",
successCriterion = "character",
epsilonValue = "numeric",
rValue = "numeric",
threshold = "numeric",
selectArmsFunction = "function",
earlyStop = "matrix",
selectedArms = "array",
numberOfActiveArms = "matrix",
rejectAtLeastOne = "numeric",
rejectedArmsPerStage = "array",
successPerStage = "matrix",
sampleSizes = "array",
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedArms",
"numberOfActiveArms",
"rejectedArmsPerStage",
"successPerStage"
)) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
SimulationResultsBaseRates <- setRefClass("SimulationResultsBaseRates",
contains = "SimulationResults",
fields = list(
directionUpper = "logical",
plannedSubjects = "numeric",
minNumberOfSubjectsPerStage = "numeric",
maxNumberOfSubjectsPerStage = "numeric",
calcSubjectsFunction = "ANY",
expectedNumberOfSubjects = "numeric"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
generatedParams <- c(
"iterations",
"expectedNumberOfSubjects",
"sampleSizes",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsRates
#'
#' @title
#' Class for Simulation Results Rates
#'
#' @description
#' A class for simulation results rates.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_directionUpper
#' @template field_plannedSubjects
#' @template field_maxNumberOfSubjects
#' @template field_calcSubjectsFunction
#' @template field_expectedNumberOfSubjects
#' @template field_riskRatio
#' @template field_thetaH0
#' @template field_normalApproximation
#' @template field_pi1
#' @template field_pi2
#' @template field_groups
#' @template field_pi1H1
#' @template field_pi2H1
#' @template field_effect
#' @template field_earlyStop
#' @template field_sampleSizes
#' @template field_overallReject
#' @template field_rejectPerStage
#' @template field_conditionalPowerAchieved
#'
#'
#' @details
#' Use \code{\link[=getSimulationRates]{getSimulationRates()}} to create an object of this type.
#'
#' \code{SimulationResultsRates} is the basic class for
#' \itemize{
#' \item \code{\link{SimulationResultsRates}},
#' \item \code{\link{SimulationResultsMultiArmRates}}, and
#' \item \code{\link{SimulationResultsEnrichmentRates}}.
#' }
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsRates <- setRefClass("SimulationResultsRates",
contains = "SimulationResultsBaseRates",
fields = list(
riskRatio = "logical",
thetaH0 = "numeric",
normalApproximation = "logical",
pi1 = "numeric",
pi2 = "numeric",
groups = "integer",
directionUpper = "logical",
pi1H1 = "numeric",
pi2H1 = "numeric",
effect = "numeric",
earlyStop = "numeric",
sampleSizes = "matrix",
overallReject = "numeric",
rejectPerStage = "matrix",
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
generatedParams <- c(
"effect",
"iterations",
"sampleSizes",
"eventsNotAchieved",
"expectedNumberOfSubjects",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop",
"analysisTime",
"studyDuration"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsMultiArmRates
#'
#' @title
#' Class for Simulation Results Multi-Arm Rates
#'
#' @description
#' A class for simulation results rates in multi-arm designs.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_directionUpper
#' @template field_plannedSubjects
#' @template field_maxNumberOfSubjects
#' @template field_calcSubjectsFunction
#' @template field_expectedNumberOfSubjects
#' @template field_activeArms
#' @template field_effectMatrix
#' @template field_typeOfShape
#' @template field_piMaxVector
#' @template field_piControl
#' @template field_piH1
#' @template field_piControlH1
#' @template field_gED50
#' @template field_slope
#' @template field_intersectionTest
#' @template field_adaptations
#' @template field_typeOfSelection
#' @template field_effectMeasure
#' @template field_successCriterion
#' @template field_epsilonValue
#' @template field_rValue
#' @template field_threshold
#' @template field_selectArmsFunction
#' @template field_earlyStop
#' @template field_selectedArms
#' @template field_numberOfActiveArms
#' @template field_rejectAtLeastOne
#' @template field_rejectedArmsPerStage
#' @template field_successPerStage
#' @template field_sampleSizes
#' @template field_conditionalPowerAchieved
#'
#'
#' @details
#' Use \code{\link[=getSimulationMultiArmRates]{getSimulationMultiArmRates()}} to create an object of this type.
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsMultiArmRates <- setRefClass("SimulationResultsMultiArmRates",
contains = "SimulationResultsBaseRates",
fields = list(
activeArms = "integer",
effectMatrix = "matrix",
typeOfShape = "character",
piMaxVector = "numeric",
piControl = "numeric",
piTreatmentsH1 = "numeric",
piControlH1 = "numeric",
gED50 = "numeric",
slope = "numeric",
intersectionTest = "character",
adaptations = "logical",
typeOfSelection = "character",
effectMeasure = "character",
successCriterion = "character",
epsilonValue = "numeric",
rValue = "numeric",
threshold = "numeric",
selectArmsFunction = "function",
earlyStop = "matrix",
selectedArms = "array",
numberOfActiveArms = "matrix",
rejectAtLeastOne = "numeric",
rejectedArmsPerStage = "array",
successPerStage = "matrix",
sampleSizes = "array",
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedArms",
"numberOfActiveArms",
"rejectedArmsPerStage",
"successPerStage"
)) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
SimulationResultsBaseSurvival <- setRefClass("SimulationResultsBaseSurvival",
contains = "SimulationResults",
fields = list(
directionUpper = "logical",
plannedEvents = "numeric",
minNumberOfEventsPerStage = "numeric",
maxNumberOfEventsPerStage = "numeric",
thetaH1 = "numeric",
calcEventsFunction = "ANY",
expectedNumberOfEvents = "numeric"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
generatedParams <- c(
"iterations",
"expectedNumberOfEvents",
"cumulativeEventsPerStage",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsSurvival
#'
#' @title
#' Class for Simulation Results Survival
#'
#' @description
#' A class for simulation results survival.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_directionUpper
#' @template field_plannedEvents
#' @template field_minNumberOfEventsPerStage
#' @template field_maxNumberOfEventsPerStage
#' @template field_thetaH1
#' @template field_calcEventsFunction
#' @template field_expectedNumberOfEvents
#' @template field_pi1_survival
#' @template field_pi2_survival
#' @template field_median1
#' @template field_median2
#' @template field_maxNumberOfSubjects
#' @template field_accrualTime
#' @template field_accrualIntensity
#' @template field_dropoutRate1
#' @template field_dropoutRate2
#' @template field_dropoutTime
#' @template field_eventTime
#' @template field_thetaH0
#' @template field_allocation1
#' @template field_allocation2
#' @template field_kappa
#' @template field_piecewiseSurvivalTime
#' @template field_lambda1
#' @template field_lambda2
#' @template field_earlyStop
#' @template field_hazardRatio
#' @template field_studyDuration
#' @template field_eventsNotAchieved
#' @template field_numberOfSubjects
#' @template field_numberOfSubjects1
#' @template field_numberOfSubjects2
#' @template field_singleEventsPerStage
#' @template field_cumulativeEventsPerStage
#' @template field_expectedNumberOfSubjects
#' @template field_rejectPerStage
#' @template field_overallReject
#' @template field_conditionalPowerAchieved
#'
#' @details
#' Use \code{\link[=getSimulationSurvival]{getSimulationSurvival()}} to create an object of this type.
#'
#' \code{SimulationResultsSurvival} is the basic class for
#' \itemize{
#' \item \code{\link{SimulationResultsSurvival}},
#' \item \code{\link{SimulationResultsMultiArmSurvival}}, and
#' \item \code{\link{SimulationResultsEnrichmentSurvival}}.
#' }
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsSurvival <- setRefClass("SimulationResultsSurvival",
contains = "SimulationResultsBaseSurvival",
fields = list(
.piecewiseSurvivalTime = "PiecewiseSurvivalTime",
.accrualTime = "AccrualTime",
pi1 = "numeric",
pi2 = "numeric",
median1 = "numeric",
median2 = "numeric",
maxNumberOfSubjects = "numeric",
accrualTime = "numeric",
accrualIntensity = "numeric",
dropoutRate1 = "numeric",
dropoutRate2 = "numeric",
dropoutTime = "numeric",
eventTime = "numeric",
thetaH0 = "numeric",
allocation1 = "numeric",
allocation2 = "numeric",
kappa = "numeric",
piecewiseSurvivalTime = "numeric",
lambda1 = "numeric",
lambda2 = "numeric",
earlyStop = "numeric",
hazardRatio = "numeric",
analysisTime = "matrix",
studyDuration = "numeric",
eventsNotAchieved = "matrix",
numberOfSubjects = "matrix",
numberOfSubjects1 = "matrix",
numberOfSubjects2 = "matrix",
eventsPerStage = "matrix", # deprecated
overallEventsPerStage = "matrix", # deprecated
singleEventsPerStage = "matrix",
cumulativeEventsPerStage = "matrix",
expectedNumberOfSubjects = "numeric",
rejectPerStage = "matrix",
overallReject = "numeric",
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
generatedParams <- c(
"hazardRatio",
"iterations",
"expectedNumberOfEvents",
"eventsNotAchieved",
"numberOfSubjects",
"expectedNumberOfSubjects",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop",
"analysisTime",
"studyDuration",
"allocationRatioPlanned"
)
if (inherits(.self, "SimulationResultsMultiArmSurvival")) {
generatedParams <- c(generatedParams,
"cumulativeEventsPerStage", "singleEventsPerArmAndStage")
} else {
generatedParams <- c(generatedParams, "singleEventsPerSubsetAndStage")
}
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
.setParameterType("numberOfSubjects1", C_PARAM_NOT_APPLICABLE)
.setParameterType("numberOfSubjects2", C_PARAM_NOT_APPLICABLE)
.setParameterType("median1", C_PARAM_NOT_APPLICABLE)
.setParameterType("median2", C_PARAM_NOT_APPLICABLE)
.setParameterType("eventsPerStage", C_PARAM_NOT_APPLICABLE)
.setParameterType("overallEventsPerStage", C_PARAM_NOT_APPLICABLE)
}
)
)
#'
#' @name SimulationResultsMultiArmSurvival
#'
#' @title
#' Class for Simulation Results Multi-Arm Survival
#'
#' @description
#' A class for simulation results survival in multi-arm designs.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_directionUpper
#' @template field_plannedEvents
#' @template field_minNumberOfEventsPerStage
#' @template field_maxNumberOfEventsPerStage
#' @template field_expectedNumberOfEvents
#' @template field_activeArms
#' @template field_effectMatrix
#' @template field_typeOfShape
#' @template field_omegaMaxVector
#' @template field_gED50
#' @template field_slope
#' @template field_intersectionTest
#' @template field_adaptations
#' @template field_epsilonValue
#' @template field_rValue
#' @template field_threshold
#' @template field_selectArmsFunction
#' @template field_correlationComputation
#' @template field_earlyStop
#' @template field_selectedArms
#' @template field_numberOfActiveArms
#' @template field_rejectAtLeastOne
#' @template field_rejectedArmsPerStage
#' @template field_successPerStage
#' @template field_eventsPerStage
#' @template field_singleNumberOfEventsPerStage
#' @template field_singleEventsPerArmAndStage
#' @template field_singleEventsPerStage
#' @template field_cumulativeEventsPerStage
#' @template field_conditionalPowerAchieved
#'
#' @details
#' Use \code{\link[=getSimulationMultiArmSurvival]{getSimulationMultiArmSurvival()}} to create an object of this type.
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsMultiArmSurvival <- setRefClass("SimulationResultsMultiArmSurvival",
contains = "SimulationResultsBaseSurvival",
fields = list(
activeArms = "integer",
effectMatrix = "matrix",
typeOfShape = "character",
omegaMaxVector = "numeric",
gED50 = "numeric",
slope = "numeric",
intersectionTest = "character",
adaptations = "logical",
typeOfSelection = "character",
effectMeasure = "character",
successCriterion = "character",
epsilonValue = "numeric",
rValue = "numeric",
threshold = "numeric",
selectArmsFunction = "function",
correlationComputation = "character",
earlyStop = "matrix",
selectedArms = "array",
numberOfActiveArms = "matrix",
rejectAtLeastOne = "numeric",
rejectedArmsPerStage = "array",
successPerStage = "matrix",
eventsPerStage = "array", # deprecated
singleEventsPerStage = "array",
cumulativeEventsPerStage = "array",
singleEventsPerArmAndStage = "array",
singleNumberOfEventsPerStage = "array", # deprecated
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedArms",
"numberOfActiveArms",
"rejectedArmsPerStage",
"successPerStage"
)) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsEnrichmentMeans
#'
#' @title
#' Class for Simulation Results Enrichment Means
#'
#' @description
#' A class for simulation results means in enrichment designs.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_stDev
#' @template field_plannedSubjects
#' @template field_minNumberOfSubjectsPerStage
#' @template field_maxNumberOfSubjectsPerStage
#' @template field_thetaH1
#' @template field_stDevH1
#' @template field_calcSubjectsFunction
#' @template field_expectedNumberOfSubjects
#' @template field_populations
#' @template field_effectList
#' @template field_intersectionTest
#' @template field_stratifiedAnalysis
#' @template field_adaptations
#' @template field_typeOfSelection
#' @template field_effectMeasure
#' @template field_successCriterion
#' @template field_epsilonValue
#' @template field_rValue
#' @template field_threshold
#' @template field_selectPopulationsFunction
#' @template field_earlyStop
#' @template field_selectedPopulations
#' @template field_numberOfPopulations
#' @template field_rejectAtLeastOne
#' @template field_rejectedPopulationsPerStage
#' @template field_successPerStage
#' @template field_sampleSizes
#' @template field_conditionalPowerAchieved
#'
#' @details
#' Use \code{\link[=getSimulationEnrichmentMeans]{getSimulationEnrichmentMeans()}} to create an object of this type.
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#' @include class_simulation_results.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsEnrichmentMeans <- setRefClass("SimulationResultsEnrichmentMeans",
contains = "SimulationResultsBaseMeans",
fields = list(
populations = "integer",
effectList = "list",
intersectionTest = "character",
stratifiedAnalysis = "logical",
adaptations = "logical",
typeOfSelection = "character",
effectMeasure = "character",
successCriterion = "character",
epsilonValue = "numeric",
rValue = "numeric",
threshold = "numeric",
selectPopulationsFunction = "function",
earlyStop = "matrix",
selectedPopulations = "array",
numberOfPopulations = "matrix",
rejectAtLeastOne = "numeric",
rejectedPopulationsPerStage = "array",
successPerStage = "matrix",
sampleSizes = "array",
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedPopulations",
"numberOfPopulations",
"rejectedPopulationsPerStage",
"successPerStage"
)) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsEnrichmentRates
#'
#' @title
#' Class for Simulation Results Enrichment Rates
#'
#' @description
#' A class for simulation results rates in enrichment designs.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_directionUpper
#' @template field_plannedSubjects
#' @template field_minNumberOfSubjectsPerStage
#' @template field_maxNumberOfSubjectsPerStage
#' @template field_calcSubjectsFunction
#' @template field_expectedNumberOfSubjects
#' @template field_populations
#' @template field_effectList
#' @template field_intersectionTest
#' @template field_stratifiedAnalysis
#' @template field_adaptations
#' @template field_piTreatmentH1
#' @template field_piControlH1
#' @template field_typeOfSelection
#' @template field_effectMeasure
#' @template field_successCriterion
#' @template field_epsilonValue
#' @template field_rValue
#' @template field_threshold
#' @template field_selectPopulationsFunction
#' @template field_earlyStop
#' @template field_selectedPopulations
#' @template field_numberOfPopulations
#' @template field_rejectAtLeastOne
#' @template field_rejectedPopulationsPerStage
#' @template field_successPerStage
#' @template field_sampleSizes
#' @template field_conditionalPowerAchieved
#'
#' @details
#' Use \code{\link[=getSimulationEnrichmentRates]{getSimulationEnrichmentRates()}} to create an object of this type.
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#' @include class_simulation_results.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsEnrichmentRates <- setRefClass("SimulationResultsEnrichmentRates",
contains = "SimulationResultsBaseRates",
fields = list(
populations = "integer",
effectList = "list",
intersectionTest = "character",
stratifiedAnalysis = "logical",
adaptations = "logical",
piTreatmentH1 = "numeric",
piControlH1 = "numeric",
typeOfSelection = "character",
effectMeasure = "character",
successCriterion = "character",
epsilonValue = "numeric",
rValue = "numeric",
threshold = "numeric",
selectPopulationsFunction = "function",
earlyStop = "matrix",
selectedPopulations = "array",
numberOfPopulations = "matrix",
rejectAtLeastOne = "numeric",
rejectedPopulationsPerStage = "array",
successPerStage = "matrix",
sampleSizes = "array",
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedPopulations",
"numberOfPopulations",
"rejectedPopulationsPerStage",
"successPerStage"
)) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsEnrichmentSurvival
#'
#' @title
#' Class for Simulation Results Enrichment Survival
#'
#' @description
#' A class for simulation results survival in enrichment designs.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_directionUpper
#' @template field_plannedSubjects
#' @template field_minNumberOfSubjectsPerStage
#' @template field_maxNumberOfSubjectsPerStage
#' @template field_thetaH1_survival
#' @template field_calcEventsFunction
#' @template field_expectedNumberOfEvents
#' @template field_populations
#' @template field_effectList
#' @template field_intersectionTest
#' @template field_stratifiedAnalysis
#' @template field_adaptations
#' @template field_typeOfSelection
#' @template field_effectMeasure
#' @template field_successCriterion
#' @template field_epsilonValue
#' @template field_rValue
#' @template field_threshold
#' @template field_selectPopulationsFunction
#' @template field_correlationComputation
#' @template field_earlyStop
#' @template field_selectedPopulations
#' @template field_numberOfPopulations
#' @template field_rejectAtLeastOne
#' @template field_rejectedPopulationsPerStage
#' @template field_successPerStage
#' @template field_eventsPerStage
#' @template field_singleNumberOfEventsPerStage
#' @template field_singleEventsPerSubsetAndStage
#' @template field_conditionalPowerAchieved
#'
#' @details
#' Use \code{\link[=getSimulationEnrichmentSurvival]{getSimulationEnrichmentSurvival()}} to create an object of this type.
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#' @include class_simulation_results.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsEnrichmentSurvival <- setRefClass("SimulationResultsEnrichmentSurvival",
contains = "SimulationResultsBaseSurvival",
fields = list(
populations = "integer",
effectList = "list",
intersectionTest = "character",
stratifiedAnalysis = "logical",
adaptations = "logical",
typeOfSelection = "character",
effectMeasure = "character",
successCriterion = "character",
epsilonValue = "numeric",
rValue = "numeric",
threshold = "numeric",
selectPopulationsFunction = "function",
correlationComputation = "character",
earlyStop = "matrix",
selectedPopulations = "array",
numberOfPopulations = "matrix",
rejectAtLeastOne = "numeric",
rejectedPopulationsPerStage = "array",
successPerStage = "matrix",
eventsPerStage = "array", # deprecated
singleEventsPerSubsetAndStage = "array",
singleNumberOfEventsPerStage = "array", # deprecated
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedPopulations",
"numberOfPopulations",
"rejectedPopulationsPerStage",
"successPerStage"
)) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @title
#' Print Simulation Results
#'
#' @description
#' \code{print} prints its \code{SimulationResults} argument and returns it invisibly (via \code{invisible(x)}).
#'
#' @param x The \code{\link{SimulationResults}} object to print.
#' @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})
#' @inheritParams param_three_dots
#'
#' @details
#' Prints the parameters and results of an \code{SimulationResults} object.
#'
#' @export
#'
#' @keywords internal
#'
print.SimulationResults <- function(x, ..., showStatistics = FALSE, markdown = FALSE) {
if (markdown) {
x$.catMarkdownText(showStatistics = showStatistics)
return(invisible(x))
}
x$show(showStatistics = showStatistics)
invisible(x)
}
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Defines functions print.SimulationResults names.SimulationResults
Documented in names.SimulationResults print.SimulationResults
## |
## | *Simulation result 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: 7672 $
## | Last changed: $Date: 2024-02-27 10:42:41 +0100 (Di, 27 Feb 2024) $
## | Last changed by: $Author: pahlke $
## |
#' @include f_core_utilities.R
NULL
#'
#' @title
#' Names of a Simulation Results Object
#'
#' @description
#' Function to get the names of a \code{\link{SimulationResults}} object.
#'
#' @param x A \code{\link{SimulationResults}} object created by \code{getSimulationResults[MultiArm/Enrichment][Means/Rates/Survival]}.
#'
#' @details
#' Returns the names of a simulation results that can be accessed by the user.
#'
#' @template return_names
#'
#' @export
#'
#' @keywords internal
#'
names.SimulationResults <- function(x) {
namesToShow <- c(".design", ".data", ".rawData")
if (inherits(x, "SimulationResultsSurvival")) {
namesToShow <- c(namesToShow, ".piecewiseSurvivalTime", ".accrualTime")
}
namesToShow <- c(namesToShow, x$.getVisibleFieldNames())
return(namesToShow)
}
#'
#' @name SimulationResults
#'
#' @title
#' Class for Simulation Results
#'
#' @description
#' A class for simulation results.
#'
#' @template field_seed
#' @template field_iterations
#'
#' @details
#' \code{SimulationResults} is the basic class for
#' \itemize{
#' \item \code{\link{SimulationResultsMeans}},
#' \item \code{\link{SimulationResultsRates}},
#' \item \code{\link{SimulationResultsSurvival}},
#' \item \code{\link{SimulationResultsMultiArmMeans}},
#' \item \code{\link{SimulationResultsMultiArmRates}},
#' \item \code{\link{SimulationResultsMultiArmSurvival}},
#' \item \code{\link{SimulationResultsEnrichmentMeans}},
#' \item \code{\link{SimulationResultsEnrichmentRates}}, and
#' \item \code{\link{SimulationResultsEnrichmentSurvival}}.
#' }
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#' @include f_simulation_utilities.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResults <- setRefClass("SimulationResults",
contains = "ParameterSet",
fields = list(
.plotSettings = "PlotSettings",
.design = "TrialDesign",
.data = "data.frame",
.rawData = "data.frame",
.showStatistics = "logical",
maxNumberOfIterations = "integer",
seed = "numeric",
allocationRatioPlanned = "numeric",
conditionalPower = "numeric",
iterations = "matrix",
futilityPerStage = "matrix",
futilityStop = "numeric"
),
methods = list(
initialize = function(design, ..., showStatistics = FALSE) {
callSuper(.design = design, .showStatistics = showStatistics, ...)
.plotSettings <<- PlotSettings()
},
getPlotSettings = function() {
return(.plotSettings)
},
setShowStatistics = function(showStatistics) {
.assertIsSingleLogical(showStatistics, "showStatistics")
.showStatistics <<- showStatistics
},
show = function(showType = 1, digits = NA_integer_, showStatistics = FALSE) {
.show(
showType = showType, digits = digits, showStatistics = showStatistics,
consoleOutputEnabled = TRUE
)
},
.show = function(..., showType = 1, digits = NA_integer_,
showStatistics = FALSE, consoleOutputEnabled = TRUE, performanceScore = NULL) {
"Method for automatically printing simulation result objects"
.resetCat()
if (showType == 3) {
.createSummary(.self, digits = digits)$.show(
showType = 1,
digits = digits, consoleOutputEnabled = consoleOutputEnabled
)
} else if (showType == 2) {
callSuper(showType = showType, digits = digits, consoleOutputEnabled = consoleOutputEnabled)
} else {
if (is.null(showStatistics) || length(showStatistics) != 1) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"'showStatistics' (", .arrayToString(showStatistics),
") must be a single logical or character"
)
}
if (!is.character(showStatistics) || showStatistics != "exclusive") {
.cat(.toString(startWithUpperCase = TRUE), ":\n\n",
heading = 1,
consoleOutputEnabled = consoleOutputEnabled
)
.showParametersOfOneGroup(.getDesignParametersToShow(.self), "Design parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
userDefinedParameters <- .getUserDefinedParameters()
if (inherits(.self, "SimulationResultsSurvival") &&
.self$.piecewiseSurvivalTime$delayedResponseEnabled) {
userDefinedParameters <- c(
userDefinedParameters,
".piecewiseSurvivalTime$delayedResponseEnabled"
)
}
.showParametersOfOneGroup(userDefinedParameters, "User defined parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
derivedParameters <- .getDerivedParameters()
if (length(derivedParameters) > 0) {
.showParametersOfOneGroup(derivedParameters, "Derived from user defined parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
}
.showParametersOfOneGroup(.getDefaultParameters(), "Default parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
.showParametersOfOneGroup(.getGeneratedParameters(), "Results",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
.showUnknownParameters(consoleOutputEnabled = consoleOutputEnabled)
}
## statistics of simulated data
if (isTRUE(showStatistics) || .showStatistics ||
(is.character(showStatistics) && showStatistics == "exclusive")) {
.cat("Simulated data:\n", heading = 2, consoleOutputEnabled = consoleOutputEnabled)
params <- c()
if (inherits(.self, "SimulationResultsMeans")) {
params <- c(
"effectMeasure",
"numberOfSubjects",
"testStatistic"
)
} else if (inherits(.self, "SimulationResultsRates")) {
params <- c(
"effectMeasure",
"numberOfSubjects",
"testStatistic"
)
} else if (inherits(.self, "SimulationResultsSurvival")) {
params <- c(
"effectMeasure",
"analysisTime",
"numberOfSubjects",
"eventsPerStage1",
"eventsPerStage2",
"cumulativeEventsPerStage",
"testStatistic",
"logRankStatistic",
"hazardRatioEstimateLR"
)
} else if (inherits(.self, "SimulationResultsMultiArmMeans") ||
inherits(.self, "SimulationResultsMultiArmRates")) {
params <- c(
"effectMeasure",
"subjectsActiveArm",
"testStatistic",
"conditionalCriticalValue",
"rejectPerStage",
"successStop",
"futilityPerStage"
)
} else if (inherits(.self, "SimulationResultsEnrichmentMeans") ||
inherits(.self, "SimulationResultsEnrichmentRates")) {
params <- c(
"effectMeasure",
"subjectsPopulation",
"testStatistic",
"conditionalCriticalValue",
"rejectPerStage",
"successStop",
"futilityPerStage"
)
} else if (inherits(.self, "SimulationResultsMultiArmSurvival") ||
inherits(.self, "SimulationResultsEnrichmentSurvival")) {
params <- c(
"effectMeasure",
"numberOfEvents",
"singleEventsPerArmAndStage",
"singleEventsPerSubsetAndStage",
"testStatistic",
"conditionalCriticalValue",
"rejectPerStage",
"successStop",
"futilityPerStage"
)
}
if (!is.null(.self[["conditionalPowerAchieved"]]) &&
!all(is.na(conditionalPowerAchieved)) &&
any(!is.na(conditionalPowerAchieved)) &&
any(na.omit(conditionalPowerAchieved) != 0)) {
params <- c(params, "conditionalPowerAchieved")
}
stages <- sort(unique(.self$.data$stageNumber))
variedParameterName1 <- .getVariedParameterName(1)
variedParameterName2 <- .getVariedParameterName(2)
parameterValues1 <- .getVariedParameterValues(variedParameterName1)
parameterValues2 <- .getVariedParameterValues(variedParameterName2)
for (parameterName in params) {
paramCaption <- .getParameterCaption(parameterName, .self)
if (is.null(paramCaption)) {
paramCaption <- paste0("%", parameterName, "%")
}
for (parameterValue1 in parameterValues1) {
for (parameterValue2 in parameterValues2) {
for (stage in stages) {
if (length(parameterValues1) > 1) {
.catStatisticsLine(
stage = stage,
parameterName = parameterName,
paramCaption = paramCaption,
parameterValue1 = parameterValue1,
variedParameterName1 = variedParameterName1,
parameterValue2 = parameterValue2,
variedParameterName2 = variedParameterName2,
consoleOutputEnabled = consoleOutputEnabled
)
} else {
.catStatisticsLine(
stage = stage,
parameterName = parameterName,
paramCaption = paramCaption,
parameterValue1 = parameterValue2,
variedParameterName1 = variedParameterName2,
consoleOutputEnabled = consoleOutputEnabled
)
}
}
}
if (parameterName == "subjectsActiveArm" && variedParameterName2 == "armNumber") {
parameterName2 <- "subjectsControlArm"
paramCaption2 <- .getParameterCaption(parameterName2, .self)
if (is.null(paramCaption2)) {
paramCaption2 <- paste0("%", parameterName2, "%")
}
for (stage in stages) {
.catStatisticsLine(
stage = stage,
parameterName = parameterName2,
paramCaption = paramCaption2,
parameterValue1 = parameterValue1,
variedParameterName1 = variedParameterName1,
parameterValue2 = unique(parameterValues2),
variedParameterName2 = variedParameterName2,
consoleOutputEnabled = consoleOutputEnabled
)
}
}
}
}
.cat("\n", consoleOutputEnabled = consoleOutputEnabled)
}
twoGroupsEnabled <- !inherits(.self, "SimulationResultsMeans")
multiArmSurvivalEnabled <- inherits(.self, "SimulationResultsMultiArmSurvival")
enrichmentEnabled <- grepl("SimulationResultsEnrichment", .getClassName(.self))
if (!is.null(performanceScore)) {
performanceScore$.showParametersOfOneGroup(
performanceScore$.getGeneratedParameters(), "Performance",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
performanceScore$.showUnknownParameters(consoleOutputEnabled = consoleOutputEnabled)
}
if (.design$kMax > 1 || twoGroupsEnabled || multiArmSurvivalEnabled) {
.cat("Legend:\n", heading = 2, consoleOutputEnabled = consoleOutputEnabled)
if (multiArmSurvivalEnabled) {
.cat(" (i): values of treatment arm i compared to control\n", consoleOutputEnabled = consoleOutputEnabled)
.cat(" {j}: values of treatment arm j\n", consoleOutputEnabled = consoleOutputEnabled)
} else if (enrichmentEnabled) {
matrixName <- .getSimulationEnrichmentEffectMatrixName(.self)
if (nrow(.self$effectList[[matrixName]]) > 1) {
.cat(" (i): results of situation i\n", consoleOutputEnabled = consoleOutputEnabled)
}
} else if (twoGroupsEnabled) {
.cat(" (i): values of treatment arm i\n", consoleOutputEnabled = consoleOutputEnabled)
}
if (.design$kMax > 1) {
.cat(" [k]: values at stage k\n", consoleOutputEnabled = consoleOutputEnabled)
}
if (enrichmentEnabled) {
if (length(.self$effectList$subGroups) > 1) {
.cat(paste0(" S[i]: population i\n"), consoleOutputEnabled = consoleOutputEnabled)
}
.cat(paste0(" F: full population\n"), consoleOutputEnabled = consoleOutputEnabled)
if (length(.self$effectList$subGroups) > 1) {
.cat(paste0(" R: remaining population\n"), consoleOutputEnabled = consoleOutputEnabled)
}
}
.cat("\n", consoleOutputEnabled = consoleOutputEnabled)
}
}
},
.getVariedParameterName = function(number = 1) {
if (number == 2) {
if (!inherits(.self, "SimulationResultsMeans") &&
!inherits(.self, "SimulationResultsRates") &&
!inherits(.self, "SimulationResultsSurvival") &&
grepl("MultiArm", .getClassName(.self))) {
return("armNumber")
}
return(NA_character_)
}
variedParameterName1 <- NA_character_
if (inherits(.self, "SimulationResultsMeans")) {
variedParameterName1 <- "alternative"
} else if (inherits(.self, "SimulationResultsRates") || inherits(.self, "SimulationResultsSurvival")) {
variedParameterName1 <- "pi1"
} else if (grepl("MultiArm", .getClassName(.self))) {
if (inherits(.self, "SimulationResultsMultiArmMeans")) {
variedParameterName1 <- "muMax"
} else if (inherits(.self, "SimulationResultsMultiArmRates")) {
variedParameterName1 <- "piMax"
} else if (inherits(.self, "SimulationResultsMultiArmSurvival")) {
variedParameterName1 <- "omegaMax"
}
}
return(variedParameterName1)
},
.getVariedParameterValues = function(variedParameterName) {
if (is.na(variedParameterName)) {
return(NA_real_)
}
parameterValues <- .self$.data[[variedParameterName]]
if (is.null(parameterValues)) {
return(NA_real_)
}
parameterValues <- unique(parameterValues)
if (length(parameterValues) > 1 && !any(is.na(parameterValues))) {
parameterValues <- sort(parameterValues)
}
return(parameterValues)
},
.getVariedParameterValueString = function(variedParameterName, parameterValue) {
if (variedParameterName %in% c("armNumber")) {
return(paste0(" (", parameterValue[1], ")"))
}
variedParameterName <- sub("Max$", "_max", variedParameterName)
return(paste0(", ", variedParameterName, " = ", round(parameterValue[1], 4)))
},
.catStatisticsLine = function(..., stage, parameterName, paramCaption,
parameterValue1, variedParameterName1, parameterValue2 = NA_real_,
variedParameterName2 = NA_character_, consoleOutputEnabled = TRUE) {
if (stage == 1 && parameterName == "conditionalPowerAchieved") {
return(invisible())
}
postfix <- ""
if (!is.na(parameterValue1)) {
if (!all(is.na(parameterValue2))) {
postfix <- paste0(postfix, .getVariedParameterValueString(
variedParameterName1, parameterValue1
))
if (parameterName != "subjectsControlArm") {
postfix <- paste0(postfix, .getVariedParameterValueString(
variedParameterName2, parameterValue2
))
}
paramValue <- .self$.data[[parameterName]][
.self$.data$stageNumber == stage &
.self$.data[[variedParameterName1]] == parameterValue1 &
.self$.data[[variedParameterName2]] %in% parameterValue2
]
} else {
postfix <- paste0(postfix, .getVariedParameterValueString(
variedParameterName1, parameterValue1
))
paramValue <- .self$.data[[parameterName]][
.self$.data$stageNumber == stage &
.self$.data[[variedParameterName1]] == parameterValue1
]
}
} else {
paramValue <- .self$.data[[parameterName]][
.self$.data$stageNumber == stage
]
}
if (.design$kMax > 1) {
postfix <- paste0(postfix, " [", stage, "]")
}
if (!consoleOutputEnabled) {
paramCaption <- paste0("*", paramCaption, "*")
}
variableNameFormatted <- .getFormattedVariableName(
name = paramCaption,
n = .getNChar(), prefix = "", postfix = postfix
)
if (!is.null(paramValue)) {
paramValue <- stats::na.omit(paramValue)
if (length(paramValue) > 0 && is.numeric(paramValue)) {
paramValueFormatted <- paste0(
"median [range]: ", round(stats::median(paramValue), 3),
" [", paste(round(base::range(paramValue), 3), collapse = " - "), "]; ",
"mean +/-sd: ", round(base::mean(paramValue), 3), " +/-", round(stats::sd(paramValue), 3)
)
} else {
paramValueFormatted <- "median [range]: NA [NA - NA]; mean +/sd: NA +/-NA"
}
output <- paste(variableNameFormatted, paramValueFormatted, "\n")
if (!grepl(": median \\[range\\]: NA \\[NA - NA\\]", output)) {
.cat(output, consoleOutputEnabled = consoleOutputEnabled)
}
}
},
.toString = function(startWithUpperCase = FALSE) {
s <- "simulation of"
if (grepl("MultiArm", .getClassName(.self)) && !is.null(.self[["activeArms"]]) && .self$activeArms > 1) {
s <- paste(s, "multi-arm")
}
if (grepl("Enrichment", .getClassName(.self)) && !is.null(.self[["populations"]]) && .self$populations > 1) {
s <- paste(s, "enrichment")
}
if (inherits(.self, "SimulationResultsBaseMeans")) {
s <- paste(s, "means")
} else if (inherits(.self, "SimulationResultsBaseRates")) {
s <- paste(s, "rates")
} else if (inherits(.self, "SimulationResultsBaseSurvival")) {
s <- paste(s, "survival data")
} else if (inherits(.self, "SimulationResultsBaseCountData")) {
s <- paste(s, "count data")
} else {
s <- paste(s, "UNDEFINED")
}
if (.design$kMax > 1) {
if (.isTrialDesignGroupSequential(.design)) {
s <- paste(s, "(group sequential design)")
} else if (.isTrialDesignInverseNormal(.design)) {
s <- paste(s, "(inverse normal combination test design)")
} else if (.isTrialDesignFisher(.design)) {
s <- paste(s, "(Fisher's combination test design)")
} else if (.isTrialDesignConditionalDunnett(.design)) {
s <- paste(s, "(conditional Dunnett design)")
}
} else {
s <- paste(s, "(fixed sample size design)")
}
return(ifelse(startWithUpperCase, .firstCharacterToUpperCase(s), s))
},
.getParametersToShow = function() {
parametersToShow <- .getVisibleFieldNames()
y <- c(
"singleEventsPerStage",
"cumulativeEventsPerStage",
"iterations",
"overallReject", # base
"rejectAtLeastOne",
"rejectPerStage",
"rejectedArmsPerStage",
"rejectedPopulationsPerStage"
)
if (.design$kMax > 2) {
y <- c(y, "futilityStop")
}
y <- c(
y,
"futilityPerStage",
"earlyStop", # base
"successPerStage",
"selectedArms",
"selectedPopulations",
"numberOfActiveArms",
"numberOfPopulations",
"expectedNumberOfSubjects",
"expectedNumberOfEvents",
"sampleSizes",
"singleEventsPerArmAndStage",
"singleEventsPerSubsetAndStage",
"conditionalPowerAchieved" # base
)
parametersToShow <- c(parametersToShow[!(parametersToShow %in% y)], y[y %in% parametersToShow])
return(parametersToShow)
},
.isSampleSizeObject = function() {
return(FALSE)
},
getRawDataResults = function(maxNumberOfIterations = NA_integer_) {
return(.getSimulationParametersFromRawData(
data = .self$.data,
variantName = .getVariedParameterName(),
maxNumberOfIterations = maxNumberOfIterations
))
}
)
)
SimulationResultsBaseMeans <- setRefClass("SimulationResultsBaseMeans",
contains = "SimulationResults",
fields = list(
stDev = "numeric",
plannedSubjects = "numeric",
minNumberOfSubjectsPerStage = "numeric",
maxNumberOfSubjectsPerStage = "numeric",
thetaH1 = "numeric",
stDevH1 = "numeric",
calcSubjectsFunction = "ANY",
expectedNumberOfSubjects = "numeric"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
generatedParams <- c(
"iterations",
"expectedNumberOfSubjects",
"sampleSizes",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsMeans
#'
#' @title
#' Class for Simulation Results Means
#'
#' @description
#' A class for simulation results means.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_stDev
#' @template field_plannedSubjects
#' @template field_minNumberOfSubjectsPerStage
#' @template field_maxNumberOfSubjectsPerStage
#' @template field_thetaH1
#' @template field_stDevH1
#' @template field_calcSubjectsFunction
#' @template field_expectedNumberOfSubjects
#' @template field_meanRatio
#' @template field_thetaH0
#' @template field_normalApproximation
#' @template field_alternative
#' @template field_groups
#' @template field_directionUpper
#' @template field_effect
#' @template field_earlyStop
#' @template field_sampleSizes
#' @template field_overallReject
#' @template field_rejectPerStage
#' @template field_conditionalPowerAchieved
#'
#' @details
#' Use \code{\link[=getSimulationMeans]{getSimulationMeans()}} to create an object of this type.
#'
#' \code{SimulationResultsMeans} is the basic class for
#' \itemize{
#' \item \code{\link{SimulationResultsMeans}},
#' \item \code{\link{SimulationResultsMultiArmMeans}}, and
#' \item \code{\link{SimulationResultsEnrichmentMeans}}.
#' }
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsMeans <- setRefClass("SimulationResultsMeans",
contains = "SimulationResultsBaseMeans",
fields = list(
meanRatio = "logical",
thetaH0 = "numeric",
normalApproximation = "logical",
alternative = "numeric",
groups = "integer",
directionUpper = "logical",
effect = "numeric",
earlyStop = "numeric",
sampleSizes = "matrix",
overallReject = "numeric", # = rejectedArmsPerStage in multi-arm
rejectPerStage = "matrix",
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
}
)
)
#'
#' @name SimulationResultsMultiArmMeans
#'
#' @title
#' Class for Simulation Results Multi-Arm Means
#'
#' @description
#' A class for simulation results means in multi-arm designs.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_stDev
#' @template field_plannedSubjects
#' @template field_minNumberOfSubjectsPerStage
#' @template field_maxNumberOfSubjectsPerStage
#' @template field_thetaH1
#' @template field_stDevH1
#' @template field_calcSubjectsFunction
#' @template field_expectedNumberOfSubjects
#' @template field_activeArms
#' @template field_effectMatrix
#' @template field_typeOfShape
#' @template field_muMaxVector
#' @template field_gED50
#' @template field_slope
#' @template field_intersectionTest
#' @template field_adaptations
#' @template field_typeOfSelection
#' @template field_effectMeasure
#' @template field_successCriterion
#' @template field_epsilonValue
#' @template field_rValue
#' @template field_threshold
#' @template field_selectArmsFunction
#' @template field_earlyStop
#' @template field_selectedArms
#' @template field_numberOfActiveArms
#' @template field_rejectAtLeastOne
#' @template field_rejectedArmsPerStage
#' @template field_successPerStage
#' @template field_sampleSizes
#' @template field_conditionalPowerAchieved
#'
#' @details
#' Use \code{\link[=getSimulationMultiArmMeans]{getSimulationMultiArmMeans()}} to create an object of this type.
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsMultiArmMeans <- setRefClass("SimulationResultsMultiArmMeans",
contains = "SimulationResultsBaseMeans",
fields = list(
activeArms = "integer",
effectMatrix = "matrix",
typeOfShape = "character",
muMaxVector = "numeric",
gED50 = "numeric",
slope = "numeric",
intersectionTest = "character",
adaptations = "logical",
typeOfSelection = "character",
effectMeasure = "character",
successCriterion = "character",
epsilonValue = "numeric",
rValue = "numeric",
threshold = "numeric",
selectArmsFunction = "function",
earlyStop = "matrix",
selectedArms = "array",
numberOfActiveArms = "matrix",
rejectAtLeastOne = "numeric",
rejectedArmsPerStage = "array",
successPerStage = "matrix",
sampleSizes = "array",
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedArms",
"numberOfActiveArms",
"rejectedArmsPerStage",
"successPerStage"
)) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
SimulationResultsBaseRates <- setRefClass("SimulationResultsBaseRates",
contains = "SimulationResults",
fields = list(
directionUpper = "logical",
plannedSubjects = "numeric",
minNumberOfSubjectsPerStage = "numeric",
maxNumberOfSubjectsPerStage = "numeric",
calcSubjectsFunction = "ANY",
expectedNumberOfSubjects = "numeric"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
generatedParams <- c(
"iterations",
"expectedNumberOfSubjects",
"sampleSizes",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsRates
#'
#' @title
#' Class for Simulation Results Rates
#'
#' @description
#' A class for simulation results rates.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_directionUpper
#' @template field_plannedSubjects
#' @template field_maxNumberOfSubjects
#' @template field_calcSubjectsFunction
#' @template field_expectedNumberOfSubjects
#' @template field_riskRatio
#' @template field_thetaH0
#' @template field_normalApproximation
#' @template field_pi1
#' @template field_pi2
#' @template field_groups
#' @template field_pi1H1
#' @template field_pi2H1
#' @template field_effect
#' @template field_earlyStop
#' @template field_sampleSizes
#' @template field_overallReject
#' @template field_rejectPerStage
#' @template field_conditionalPowerAchieved
#'
#'
#' @details
#' Use \code{\link[=getSimulationRates]{getSimulationRates()}} to create an object of this type.
#'
#' \code{SimulationResultsRates} is the basic class for
#' \itemize{
#' \item \code{\link{SimulationResultsRates}},
#' \item \code{\link{SimulationResultsMultiArmRates}}, and
#' \item \code{\link{SimulationResultsEnrichmentRates}}.
#' }
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsRates <- setRefClass("SimulationResultsRates",
contains = "SimulationResultsBaseRates",
fields = list(
riskRatio = "logical",
thetaH0 = "numeric",
normalApproximation = "logical",
pi1 = "numeric",
pi2 = "numeric",
groups = "integer",
directionUpper = "logical",
pi1H1 = "numeric",
pi2H1 = "numeric",
effect = "numeric",
earlyStop = "numeric",
sampleSizes = "matrix",
overallReject = "numeric",
rejectPerStage = "matrix",
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
generatedParams <- c(
"effect",
"iterations",
"sampleSizes",
"eventsNotAchieved",
"expectedNumberOfSubjects",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop",
"analysisTime",
"studyDuration"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsMultiArmRates
#'
#' @title
#' Class for Simulation Results Multi-Arm Rates
#'
#' @description
#' A class for simulation results rates in multi-arm designs.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_directionUpper
#' @template field_plannedSubjects
#' @template field_maxNumberOfSubjects
#' @template field_calcSubjectsFunction
#' @template field_expectedNumberOfSubjects
#' @template field_activeArms
#' @template field_effectMatrix
#' @template field_typeOfShape
#' @template field_piMaxVector
#' @template field_piControl
#' @template field_piH1
#' @template field_piControlH1
#' @template field_gED50
#' @template field_slope
#' @template field_intersectionTest
#' @template field_adaptations
#' @template field_typeOfSelection
#' @template field_effectMeasure
#' @template field_successCriterion
#' @template field_epsilonValue
#' @template field_rValue
#' @template field_threshold
#' @template field_selectArmsFunction
#' @template field_earlyStop
#' @template field_selectedArms
#' @template field_numberOfActiveArms
#' @template field_rejectAtLeastOne
#' @template field_rejectedArmsPerStage
#' @template field_successPerStage
#' @template field_sampleSizes
#' @template field_conditionalPowerAchieved
#'
#'
#' @details
#' Use \code{\link[=getSimulationMultiArmRates]{getSimulationMultiArmRates()}} to create an object of this type.
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsMultiArmRates <- setRefClass("SimulationResultsMultiArmRates",
contains = "SimulationResultsBaseRates",
fields = list(
activeArms = "integer",
effectMatrix = "matrix",
typeOfShape = "character",
piMaxVector = "numeric",
piControl = "numeric",
piTreatmentsH1 = "numeric",
piControlH1 = "numeric",
gED50 = "numeric",
slope = "numeric",
intersectionTest = "character",
adaptations = "logical",
typeOfSelection = "character",
effectMeasure = "character",
successCriterion = "character",
epsilonValue = "numeric",
rValue = "numeric",
threshold = "numeric",
selectArmsFunction = "function",
earlyStop = "matrix",
selectedArms = "array",
numberOfActiveArms = "matrix",
rejectAtLeastOne = "numeric",
rejectedArmsPerStage = "array",
successPerStage = "matrix",
sampleSizes = "array",
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedArms",
"numberOfActiveArms",
"rejectedArmsPerStage",
"successPerStage"
)) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
SimulationResultsBaseSurvival <- setRefClass("SimulationResultsBaseSurvival",
contains = "SimulationResults",
fields = list(
directionUpper = "logical",
plannedEvents = "numeric",
minNumberOfEventsPerStage = "numeric",
maxNumberOfEventsPerStage = "numeric",
thetaH1 = "numeric",
calcEventsFunction = "ANY",
expectedNumberOfEvents = "numeric"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
generatedParams <- c(
"iterations",
"expectedNumberOfEvents",
"cumulativeEventsPerStage",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsSurvival
#'
#' @title
#' Class for Simulation Results Survival
#'
#' @description
#' A class for simulation results survival.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_directionUpper
#' @template field_plannedEvents
#' @template field_minNumberOfEventsPerStage
#' @template field_maxNumberOfEventsPerStage
#' @template field_thetaH1
#' @template field_calcEventsFunction
#' @template field_expectedNumberOfEvents
#' @template field_pi1_survival
#' @template field_pi2_survival
#' @template field_median1
#' @template field_median2
#' @template field_maxNumberOfSubjects
#' @template field_accrualTime
#' @template field_accrualIntensity
#' @template field_dropoutRate1
#' @template field_dropoutRate2
#' @template field_dropoutTime
#' @template field_eventTime
#' @template field_thetaH0
#' @template field_allocation1
#' @template field_allocation2
#' @template field_kappa
#' @template field_piecewiseSurvivalTime
#' @template field_lambda1
#' @template field_lambda2
#' @template field_earlyStop
#' @template field_hazardRatio
#' @template field_studyDuration
#' @template field_eventsNotAchieved
#' @template field_numberOfSubjects
#' @template field_numberOfSubjects1
#' @template field_numberOfSubjects2
#' @template field_singleEventsPerStage
#' @template field_cumulativeEventsPerStage
#' @template field_expectedNumberOfSubjects
#' @template field_rejectPerStage
#' @template field_overallReject
#' @template field_conditionalPowerAchieved
#'
#' @details
#' Use \code{\link[=getSimulationSurvival]{getSimulationSurvival()}} to create an object of this type.
#'
#' \code{SimulationResultsSurvival} is the basic class for
#' \itemize{
#' \item \code{\link{SimulationResultsSurvival}},
#' \item \code{\link{SimulationResultsMultiArmSurvival}}, and
#' \item \code{\link{SimulationResultsEnrichmentSurvival}}.
#' }
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsSurvival <- setRefClass("SimulationResultsSurvival",
contains = "SimulationResultsBaseSurvival",
fields = list(
.piecewiseSurvivalTime = "PiecewiseSurvivalTime",
.accrualTime = "AccrualTime",
pi1 = "numeric",
pi2 = "numeric",
median1 = "numeric",
median2 = "numeric",
maxNumberOfSubjects = "numeric",
accrualTime = "numeric",
accrualIntensity = "numeric",
dropoutRate1 = "numeric",
dropoutRate2 = "numeric",
dropoutTime = "numeric",
eventTime = "numeric",
thetaH0 = "numeric",
allocation1 = "numeric",
allocation2 = "numeric",
kappa = "numeric",
piecewiseSurvivalTime = "numeric",
lambda1 = "numeric",
lambda2 = "numeric",
earlyStop = "numeric",
hazardRatio = "numeric",
analysisTime = "matrix",
studyDuration = "numeric",
eventsNotAchieved = "matrix",
numberOfSubjects = "matrix",
numberOfSubjects1 = "matrix",
numberOfSubjects2 = "matrix",
eventsPerStage = "matrix", # deprecated
overallEventsPerStage = "matrix", # deprecated
singleEventsPerStage = "matrix",
cumulativeEventsPerStage = "matrix",
expectedNumberOfSubjects = "numeric",
rejectPerStage = "matrix",
overallReject = "numeric",
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
generatedParams <- c(
"hazardRatio",
"iterations",
"expectedNumberOfEvents",
"eventsNotAchieved",
"numberOfSubjects",
"expectedNumberOfSubjects",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop",
"analysisTime",
"studyDuration",
"allocationRatioPlanned"
)
if (inherits(.self, "SimulationResultsMultiArmSurvival")) {
generatedParams <- c(generatedParams,
"cumulativeEventsPerStage", "singleEventsPerArmAndStage")
} else {
generatedParams <- c(generatedParams, "singleEventsPerSubsetAndStage")
}
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
.setParameterType("numberOfSubjects1", C_PARAM_NOT_APPLICABLE)
.setParameterType("numberOfSubjects2", C_PARAM_NOT_APPLICABLE)
.setParameterType("median1", C_PARAM_NOT_APPLICABLE)
.setParameterType("median2", C_PARAM_NOT_APPLICABLE)
.setParameterType("eventsPerStage", C_PARAM_NOT_APPLICABLE)
.setParameterType("overallEventsPerStage", C_PARAM_NOT_APPLICABLE)
}
)
)
#'
#' @name SimulationResultsMultiArmSurvival
#'
#' @title
#' Class for Simulation Results Multi-Arm Survival
#'
#' @description
#' A class for simulation results survival in multi-arm designs.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_directionUpper
#' @template field_plannedEvents
#' @template field_minNumberOfEventsPerStage
#' @template field_maxNumberOfEventsPerStage
#' @template field_expectedNumberOfEvents
#' @template field_activeArms
#' @template field_effectMatrix
#' @template field_typeOfShape
#' @template field_omegaMaxVector
#' @template field_gED50
#' @template field_slope
#' @template field_intersectionTest
#' @template field_adaptations
#' @template field_epsilonValue
#' @template field_rValue
#' @template field_threshold
#' @template field_selectArmsFunction
#' @template field_correlationComputation
#' @template field_earlyStop
#' @template field_selectedArms
#' @template field_numberOfActiveArms
#' @template field_rejectAtLeastOne
#' @template field_rejectedArmsPerStage
#' @template field_successPerStage
#' @template field_eventsPerStage
#' @template field_singleNumberOfEventsPerStage
#' @template field_singleEventsPerArmAndStage
#' @template field_singleEventsPerStage
#' @template field_cumulativeEventsPerStage
#' @template field_conditionalPowerAchieved
#'
#' @details
#' Use \code{\link[=getSimulationMultiArmSurvival]{getSimulationMultiArmSurvival()}} to create an object of this type.
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsMultiArmSurvival <- setRefClass("SimulationResultsMultiArmSurvival",
contains = "SimulationResultsBaseSurvival",
fields = list(
activeArms = "integer",
effectMatrix = "matrix",
typeOfShape = "character",
omegaMaxVector = "numeric",
gED50 = "numeric",
slope = "numeric",
intersectionTest = "character",
adaptations = "logical",
typeOfSelection = "character",
effectMeasure = "character",
successCriterion = "character",
epsilonValue = "numeric",
rValue = "numeric",
threshold = "numeric",
selectArmsFunction = "function",
correlationComputation = "character",
earlyStop = "matrix",
selectedArms = "array",
numberOfActiveArms = "matrix",
rejectAtLeastOne = "numeric",
rejectedArmsPerStage = "array",
successPerStage = "matrix",
eventsPerStage = "array", # deprecated
singleEventsPerStage = "array",
cumulativeEventsPerStage = "array",
singleEventsPerArmAndStage = "array",
singleNumberOfEventsPerStage = "array", # deprecated
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedArms",
"numberOfActiveArms",
"rejectedArmsPerStage",
"successPerStage"
)) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsEnrichmentMeans
#'
#' @title
#' Class for Simulation Results Enrichment Means
#'
#' @description
#' A class for simulation results means in enrichment designs.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_stDev
#' @template field_plannedSubjects
#' @template field_minNumberOfSubjectsPerStage
#' @template field_maxNumberOfSubjectsPerStage
#' @template field_thetaH1
#' @template field_stDevH1
#' @template field_calcSubjectsFunction
#' @template field_expectedNumberOfSubjects
#' @template field_populations
#' @template field_effectList
#' @template field_intersectionTest
#' @template field_stratifiedAnalysis
#' @template field_adaptations
#' @template field_typeOfSelection
#' @template field_effectMeasure
#' @template field_successCriterion
#' @template field_epsilonValue
#' @template field_rValue
#' @template field_threshold
#' @template field_selectPopulationsFunction
#' @template field_earlyStop
#' @template field_selectedPopulations
#' @template field_numberOfPopulations
#' @template field_rejectAtLeastOne
#' @template field_rejectedPopulationsPerStage
#' @template field_successPerStage
#' @template field_sampleSizes
#' @template field_conditionalPowerAchieved
#'
#' @details
#' Use \code{\link[=getSimulationEnrichmentMeans]{getSimulationEnrichmentMeans()}} to create an object of this type.
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#' @include class_simulation_results.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsEnrichmentMeans <- setRefClass("SimulationResultsEnrichmentMeans",
contains = "SimulationResultsBaseMeans",
fields = list(
populations = "integer",
effectList = "list",
intersectionTest = "character",
stratifiedAnalysis = "logical",
adaptations = "logical",
typeOfSelection = "character",
effectMeasure = "character",
successCriterion = "character",
epsilonValue = "numeric",
rValue = "numeric",
threshold = "numeric",
selectPopulationsFunction = "function",
earlyStop = "matrix",
selectedPopulations = "array",
numberOfPopulations = "matrix",
rejectAtLeastOne = "numeric",
rejectedPopulationsPerStage = "array",
successPerStage = "matrix",
sampleSizes = "array",
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedPopulations",
"numberOfPopulations",
"rejectedPopulationsPerStage",
"successPerStage"
)) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsEnrichmentRates
#'
#' @title
#' Class for Simulation Results Enrichment Rates
#'
#' @description
#' A class for simulation results rates in enrichment designs.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_directionUpper
#' @template field_plannedSubjects
#' @template field_minNumberOfSubjectsPerStage
#' @template field_maxNumberOfSubjectsPerStage
#' @template field_calcSubjectsFunction
#' @template field_expectedNumberOfSubjects
#' @template field_populations
#' @template field_effectList
#' @template field_intersectionTest
#' @template field_stratifiedAnalysis
#' @template field_adaptations
#' @template field_piTreatmentH1
#' @template field_piControlH1
#' @template field_typeOfSelection
#' @template field_effectMeasure
#' @template field_successCriterion
#' @template field_epsilonValue
#' @template field_rValue
#' @template field_threshold
#' @template field_selectPopulationsFunction
#' @template field_earlyStop
#' @template field_selectedPopulations
#' @template field_numberOfPopulations
#' @template field_rejectAtLeastOne
#' @template field_rejectedPopulationsPerStage
#' @template field_successPerStage
#' @template field_sampleSizes
#' @template field_conditionalPowerAchieved
#'
#' @details
#' Use \code{\link[=getSimulationEnrichmentRates]{getSimulationEnrichmentRates()}} to create an object of this type.
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#' @include class_simulation_results.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsEnrichmentRates <- setRefClass("SimulationResultsEnrichmentRates",
contains = "SimulationResultsBaseRates",
fields = list(
populations = "integer",
effectList = "list",
intersectionTest = "character",
stratifiedAnalysis = "logical",
adaptations = "logical",
piTreatmentH1 = "numeric",
piControlH1 = "numeric",
typeOfSelection = "character",
effectMeasure = "character",
successCriterion = "character",
epsilonValue = "numeric",
rValue = "numeric",
threshold = "numeric",
selectPopulationsFunction = "function",
earlyStop = "matrix",
selectedPopulations = "array",
numberOfPopulations = "matrix",
rejectAtLeastOne = "numeric",
rejectedPopulationsPerStage = "array",
successPerStage = "matrix",
sampleSizes = "array",
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedPopulations",
"numberOfPopulations",
"rejectedPopulationsPerStage",
"successPerStage"
)) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsEnrichmentSurvival
#'
#' @title
#' Class for Simulation Results Enrichment Survival
#'
#' @description
#' A class for simulation results survival in enrichment designs.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_futilityStop
#' @template field_directionUpper
#' @template field_plannedSubjects
#' @template field_minNumberOfSubjectsPerStage
#' @template field_maxNumberOfSubjectsPerStage
#' @template field_thetaH1_survival
#' @template field_calcEventsFunction
#' @template field_expectedNumberOfEvents
#' @template field_populations
#' @template field_effectList
#' @template field_intersectionTest
#' @template field_stratifiedAnalysis
#' @template field_adaptations
#' @template field_typeOfSelection
#' @template field_effectMeasure
#' @template field_successCriterion
#' @template field_epsilonValue
#' @template field_rValue
#' @template field_threshold
#' @template field_selectPopulationsFunction
#' @template field_correlationComputation
#' @template field_earlyStop
#' @template field_selectedPopulations
#' @template field_numberOfPopulations
#' @template field_rejectAtLeastOne
#' @template field_rejectedPopulationsPerStage
#' @template field_successPerStage
#' @template field_eventsPerStage
#' @template field_singleNumberOfEventsPerStage
#' @template field_singleEventsPerSubsetAndStage
#' @template field_conditionalPowerAchieved
#'
#' @details
#' Use \code{\link[=getSimulationEnrichmentSurvival]{getSimulationEnrichmentSurvival()}} to create an object of this type.
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#' @include class_simulation_results.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsEnrichmentSurvival <- setRefClass("SimulationResultsEnrichmentSurvival",
contains = "SimulationResultsBaseSurvival",
fields = list(
populations = "integer",
effectList = "list",
intersectionTest = "character",
stratifiedAnalysis = "logical",
adaptations = "logical",
typeOfSelection = "character",
effectMeasure = "character",
successCriterion = "character",
epsilonValue = "numeric",
rValue = "numeric",
threshold = "numeric",
selectPopulationsFunction = "function",
correlationComputation = "character",
earlyStop = "matrix",
selectedPopulations = "array",
numberOfPopulations = "matrix",
rejectAtLeastOne = "numeric",
rejectedPopulationsPerStage = "array",
successPerStage = "matrix",
eventsPerStage = "array", # deprecated
singleEventsPerSubsetAndStage = "array",
singleNumberOfEventsPerStage = "array", # deprecated
conditionalPowerAchieved = "matrix"
),
methods = list(
initialize = function(design, ...) {
callSuper(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedPopulations",
"numberOfPopulations",
"rejectedPopulationsPerStage",
"successPerStage"
)) {
.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @title
#' Print Simulation Results
#'
#' @description
#' \code{print} prints its \code{SimulationResults} argument and returns it invisibly (via \code{invisible(x)}).
#'
#' @param x The \code{\link{SimulationResults}} object to print.
#' @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})
#' @inheritParams param_three_dots
#'
#' @details
#' Prints the parameters and results of an \code{SimulationResults} object.
#'
#' @export
#'
#' @keywords internal
#'
print.SimulationResults <- function(x, ..., showStatistics = FALSE, markdown = FALSE) {
if (markdown) {
x$.catMarkdownText(showStatistics = showStatistics)
return(invisible(x))
}
x$show(showStatistics = showStatistics)
invisible(x)
}
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