Nothing
R/class_simulation_results.R
In rpact: Confirmatory Adaptive Clinical Trial Design and Analysis
Defines functions
names.SimulationResults
Documented in
names.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: 8474 $
## | Last changed: $Date: 2025-01-14 14:32:53 +0100 (Di, 14 Jan 2025) $
## | 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$.getVisibleFieldNames())
return(namesToShow)
}
#'
#' @name SimulationResults
#'
#' @title
#' Class for Simulation Results
#'
#' @description
#' A class for simulation results.
#'
#' @template field_seed
#' @template field_iterations
#'
#' @details
#' \code{SimulationResults} is the basic class for
#' \itemize{
#' \item \code{\link{SimulationResultsMeans}},
#' \item \code{\link{SimulationResultsRates}},
#' \item \code{\link{SimulationResultsSurvival}},
#' \item \code{\link{SimulationResultsCountData}},
#' \item \code{\link{SimulationResultsMultiArmMeans}},
#' \item \code{\link{SimulationResultsMultiArmRates}},
#' \item \code{\link{SimulationResultsMultiArmSurvival}},
#' \item \code{\link{SimulationResultsEnrichmentMeans}},
#' \item \code{\link{SimulationResultsEnrichmentRates}}, and
#' \item \code{\link{SimulationResultsEnrichmentSurvival}}.
#' }
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#' @include f_simulation_utilities.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResults <- R6::R6Class("SimulationResults",
inherit = ParameterSet,
public = list(
.plotSettings = NULL,
.design = NULL,
.data = NULL,
.rawData = NULL,
.showStatistics = NULL,
maxNumberOfIterations = NULL,
seed = NULL,
allocationRatioPlanned = numeric(),
conditionalPower = NULL,
iterations = NULL,
futilityPerStage = NULL,
futilityStop = NULL,
initialize = function(design, ..., showStatistics = FALSE) {
super$initialize(...)
self$.design <- design
self$.showStatistics <- showStatistics
self$.plotSettings <- PlotSettings$new()
},
getPlotSettings = function() {
return(self$.plotSettings)
},
setShowStatistics = function(showStatistics) {
.assertIsSingleLogical(showStatistics, "showStatistics")
self$.showStatistics <- showStatistics
},
show = function(showType = 1, digits = NA_integer_, showStatistics = FALSE) {
self$.show(
showType = showType, digits = digits, showStatistics = showStatistics,
consoleOutputEnabled = TRUE
)
},
.show = function(..., showType = 1, digits = NA_integer_,
showStatistics = FALSE, consoleOutputEnabled = TRUE, performanceScore = NULL) {
"Method for automatically printing simulation result objects"
self$.resetCat()
if (showType == 3) {
.createSummary(self, digits = digits)$.show(
showType = 1,
digits = digits, consoleOutputEnabled = consoleOutputEnabled
)
} else if (showType == 2) {
super$.show(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",
call. = FALSE
)
}
if (!is.character(showStatistics) || showStatistics != "exclusive") {
self$.cat(self$.toString(startWithUpperCase = TRUE), ":\n\n",
heading = 1,
consoleOutputEnabled = consoleOutputEnabled
)
self$.showParametersOfOneGroup(.getDesignParametersToShow(self), "Design parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
userDefinedParameters <- self$.getUserDefinedParameters()
if (inherits(self, "SimulationResultsSurvival") &&
self$.piecewiseSurvivalTime$delayedResponseEnabled) {
userDefinedParameters <- c(
userDefinedParameters,
".piecewiseSurvivalTime$delayedResponseEnabled"
)
}
self$.showParametersOfOneGroup(userDefinedParameters, "User defined parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
derivedParameters <- self$.getDerivedParameters()
if (length(derivedParameters) > 0) {
self$.showParametersOfOneGroup(derivedParameters, "Derived from user defined parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
}
self$.showParametersOfOneGroup(self$.getDefaultParameters(), "Default parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
self$.showParametersOfOneGroup(self$.getGeneratedParameters(), "Results",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
self$.showUnknownParameters(consoleOutputEnabled = consoleOutputEnabled)
}
## statistics of simulated data
if (isTRUE(showStatistics) || self$.showStatistics ||
(is.character(showStatistics) && showStatistics == "exclusive")) {
self$.cat("Simulated data:\n", heading = 2, consoleOutputEnabled = consoleOutputEnabled)
params <- c()
if (inherits(self, "SimulationResultsMeans")) {
params <- c(
"effectMeasure",
"numberOfSubjects",
"testStatistic"
)
} else if (inherits(self, "SimulationResultsRates")) {
params <- c(
"effectMeasure",
"numberOfSubjects",
"testStatistic"
)
} else if (inherits(self, "SimulationResultsSurvival")) {
params <- c(
"effectMeasure",
"analysisTime",
"numberOfSubjects",
"eventsPerStage1",
"eventsPerStage2",
"cumulativeEventsPerStage",
"testStatistic",
"logRankStatistic",
"hazardRatioEstimateLR"
)
} else if (inherits(self, "SimulationResultsMultiArmMeans") ||
inherits(self, "SimulationResultsMultiArmRates")) {
params <- c(
"effectMeasure",
"subjectsActiveArm",
"testStatistic",
"conditionalCriticalValue",
"rejectPerStage",
"successStop",
"futilityPerStage"
)
} else if (inherits(self, "SimulationResultsEnrichmentMeans") ||
inherits(self, "SimulationResultsEnrichmentRates")) {
params <- c(
"effectMeasure",
"subjectsPopulation",
"testStatistic",
"conditionalCriticalValue",
"rejectPerStage",
"successStop",
"futilityPerStage"
)
} else if (inherits(self, "SimulationResultsMultiArmSurvival") ||
inherits(self, "SimulationResultsEnrichmentSurvival")) {
params <- c(
"effectMeasure",
"numberOfEvents",
"singleEventsPerArmAndStage",
"singleEventsPerSubsetAndStage",
"testStatistic",
"conditionalCriticalValue",
"rejectPerStage",
"successStop",
"futilityPerStage"
)
}
if (!is.null(self[["conditionalPowerAchieved"]]) &&
!all(is.na(self$conditionalPowerAchieved)) &&
any(!is.na(self$conditionalPowerAchieved)) &&
any(na.omit(self$conditionalPowerAchieved) != 0)) {
params <- c(params, "conditionalPowerAchieved")
}
stages <- sort(unique(self$.data$stageNumber))
variedParameterName1 <- self$.getVariedParameterName(1)
variedParameterName2 <- self$.getVariedParameterName(2)
parameterValues1 <- self$.getVariedParameterValues(variedParameterName1)
parameterValues2 <- self$.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) {
self$.catStatisticsLine(
stage = stage,
parameterName = parameterName,
paramCaption = paramCaption,
parameterValue1 = parameterValue1,
variedParameterName1 = variedParameterName1,
parameterValue2 = parameterValue2,
variedParameterName2 = variedParameterName2,
consoleOutputEnabled = consoleOutputEnabled
)
} else {
self$.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) {
self$.catStatisticsLine(
stage = stage,
parameterName = parameterName2,
paramCaption = paramCaption2,
parameterValue1 = parameterValue1,
variedParameterName1 = variedParameterName1,
parameterValue2 = unique(parameterValues2),
variedParameterName2 = variedParameterName2,
consoleOutputEnabled = consoleOutputEnabled
)
}
}
}
}
self$.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$.showUnknownParameters(
consoleOutputEnabled = consoleOutputEnabled
)
}
if (self$.design$kMax > 1 || twoGroupsEnabled || multiArmSurvivalEnabled) {
self$.cat("Legend:\n",
heading = 2,
consoleOutputEnabled = consoleOutputEnabled
)
if (multiArmSurvivalEnabled) {
self$.cat(" (i): values of treatment arm i compared to control\n",
consoleOutputEnabled = consoleOutputEnabled
)
self$.cat(" {j}: values of treatment arm j\n",
consoleOutputEnabled = consoleOutputEnabled
)
} else if (enrichmentEnabled) {
matrixName <- .getSimulationEnrichmentEffectMatrixName(self)
if (nrow(self$effectList[[matrixName]]) > 1) {
self$.cat(" (i): results of situation i\n",
consoleOutputEnabled = consoleOutputEnabled
)
}
} else if (twoGroupsEnabled) {
self$.cat(" (i): values of treatment arm i\n",
consoleOutputEnabled = consoleOutputEnabled
)
}
if (self$.design$kMax > 1) {
self$.cat(" [k]: values at stage k\n",
consoleOutputEnabled = consoleOutputEnabled
)
}
if (enrichmentEnabled) {
if (length(self$effectList$subGroups) > 1) {
self$.cat(paste0(" S[i]: population i\n"),
consoleOutputEnabled = consoleOutputEnabled
)
}
self$.cat(paste0(" F: full population\n"),
consoleOutputEnabled = consoleOutputEnabled
)
if (length(self$effectList$subGroups) > 1) {
self$.cat(paste0(" R: remaining population\n"),
consoleOutputEnabled = consoleOutputEnabled
)
}
}
self$.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, self$.getVariedParameterValueString(
variedParameterName1, parameterValue1
))
if (parameterName != "subjectsControlArm") {
postfix <- paste0(postfix, self$.getVariedParameterValueString(
variedParameterName2, parameterValue2
))
}
paramValue <- self$.data[[parameterName]][
self$.data$stageNumber == stage &
self$.data[[variedParameterName1]] == parameterValue1 &
self$.data[[variedParameterName2]] %in% parameterValue2
]
} else {
postfix <- paste0(postfix, self$.getVariedParameterValueString(
variedParameterName1, parameterValue1
))
paramValue <- self$.data[[parameterName]][
self$.data$stageNumber == stage &
self$.data[[variedParameterName1]] == parameterValue1
]
}
} else {
paramValue <- self$.data[[parameterName]][
self$.data$stageNumber == stage
]
}
if (self$.design$kMax > 1) {
postfix <- paste0(postfix, " [", stage, "]")
}
if (!consoleOutputEnabled) {
paramCaption <- paste0("*", paramCaption, "*")
}
variableNameFormatted <- .getFormattedVariableName(
name = paramCaption,
n = self$.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), "; ",
"n = ", length(paramValue)
)
} else {
paramValueFormatted <- "median [range]: NA [NA - NA]; mean +/sd: NA +/-NA"
}
output <- paste(variableNameFormatted, paramValueFormatted, "\n")
if (!grepl(": median \\[range\\]: NA \\[NA - NA\\]", output)) {
self$.cat(output, consoleOutputEnabled = consoleOutputEnabled)
}
}
},
.toString = function(startWithUpperCase = FALSE) {
s <- "simulation of"
if (grepl("MultiArm", .getClassName(self)) &&
!is.null(self[["activeArms"]]) && self$activeArms > 1) {
s <- paste(s, "multi-arm")
}
if (grepl("Enrichment", .getClassName(self)) &&
!is.null(self[["populations"]]) && self$populations > 1) {
s <- paste(s, "enrichment")
}
if (inherits(self, "SimulationResultsBaseMeans")) {
s <- paste(s, "means")
} else if (inherits(self, "SimulationResultsBaseRates")) {
s <- paste(s, "rates")
} else if (inherits(self, "SimulationResultsBaseSurvival")) {
s <- paste(s, "survival data")
} else if (inherits(self, "SimulationResultsCountData")) {
s <- paste(s, "count data")
} else {
s <- paste(s, "UNDEFINED")
}
if (self$.design$kMax > 1) {
if (.isTrialDesignGroupSequential(self$.design)) {
s <- paste(s, "(group sequential design)")
} else if (.isTrialDesignInverseNormal(self$.design)) {
s <- paste(s, "(inverse normal combination test design)")
} else if (.isTrialDesignFisher(self$.design)) {
s <- paste(s, "(Fisher's combination test design)")
} else if (.isTrialDesignConditionalDunnett(self$.design)) {
s <- paste(s, "(conditional Dunnett design)")
}
} else {
s <- paste(s, "(fixed sample size design)")
}
return(ifelse(startWithUpperCase, .firstCharacterToUpperCase(s), s))
},
.getParametersToShow = function() {
parametersToShow <- self$.getVisibleFieldNames()
y <- c(
"singleEventsPerStage",
"cumulativeEventsPerStage",
"iterations",
"overallReject", # base
"rejectAtLeastOne",
"rejectPerStage",
"rejectedArmsPerStage",
"rejectedPopulationsPerStage"
)
if (self$.design$kMax > 2) {
y <- c(y, "futilityStop")
}
y <- c(
y,
"futilityPerStage",
"earlyStop", # base
"successPerStage",
"selectedArms",
"selectedPopulations",
"numberOfActiveArms",
"numberOfPopulations",
"expectedNumberOfSubjects",
"expectedNumberOfEvents",
"numberOfSubjects",
"numberOfSubjects1",
"numberOfSubjects2",
"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$.data,
variantName = self$.getVariedParameterName(),
maxNumberOfIterations = maxNumberOfIterations
))
}
)
)
SimulationResultsBaseMeans <- R6::R6Class("SimulationResultsBaseMeans",
inherit = SimulationResults,
public = list(
stDev = NULL,
plannedSubjects = NULL,
minNumberOfSubjectsPerStage = NULL,
maxNumberOfSubjectsPerStage = NULL,
thetaH1 = NULL,
stDevH1 = NULL,
calcSubjectsFunction = NULL,
expectedNumberOfSubjects = NULL,
initialize = function(design, ...) {
super$initialize(design = design, ...)
generatedParams <- c(
"iterations",
"expectedNumberOfSubjects",
"sampleSizes",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
self$.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 <- R6::R6Class("SimulationResultsMeans",
inherit = SimulationResultsBaseMeans,
public = list(
meanRatio = NULL,
thetaH0 = NULL,
normalApproximation = NULL,
alternative = NULL,
groups = NULL,
directionUpper = NULL,
effect = NULL,
earlyStop = NULL,
sampleSizes = NULL,
overallReject = NULL, # = rejectedArmsPerStage in multi-arm
rejectPerStage = NULL,
conditionalPowerAchieved = NULL,
initialize = function(design, ...) {
super$initialize(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 <- R6::R6Class("SimulationResultsMultiArmMeans",
inherit = SimulationResultsBaseMeans,
public = list(
activeArms = NULL,
effectMatrix = NULL,
typeOfShape = NULL,
muMaxVector = NULL,
gED50 = NULL,
slope = NULL,
doseLevels = NULL,
intersectionTest = NULL,
adaptations = NULL,
typeOfSelection = NULL,
effectMeasure = NULL,
successCriterion = NULL,
epsilonValue = NULL,
rValue = NULL,
threshold = NULL,
selectArmsFunction = NULL,
earlyStop = NULL,
selectedArms = NULL,
numberOfActiveArms = NULL,
rejectAtLeastOne = NULL,
rejectedArmsPerStage = NULL,
successPerStage = NULL,
sampleSizes = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedArms",
"numberOfActiveArms",
"rejectedArmsPerStage",
"successPerStage"
)) {
self$.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
SimulationResultsBaseRates <- R6::R6Class("SimulationResultsBaseRates",
inherit = SimulationResults,
public = list(
directionUpper = NULL,
plannedSubjects = NULL,
minNumberOfSubjectsPerStage = NULL,
maxNumberOfSubjectsPerStage = NULL,
calcSubjectsFunction = NULL,
expectedNumberOfSubjects = NULL,
initialize = function(design, ...) {
super$initialize(design = design, ...)
generatedParams <- c(
"iterations",
"expectedNumberOfSubjects",
"sampleSizes",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
self$.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 <- R6::R6Class("SimulationResultsRates",
inherit = SimulationResultsBaseRates,
public = list(
riskRatio = NULL,
thetaH0 = NULL,
normalApproximation = NULL,
pi1 = NULL,
pi2 = NULL,
groups = NULL,
# directionUpper = NULL,
pi1H1 = NULL,
pi2H1 = NULL,
effect = NULL,
earlyStop = NULL,
sampleSizes = NULL,
expectedNumberOfSubjects = NULL,
overallReject = NULL,
rejectPerStage = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(design = design, ...)
generatedParams <- c(
"effect",
"iterations",
"sampleSizes",
"eventsNotAchieved",
"expectedNumberOfSubjects",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop",
"analysisTime",
"studyDuration"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
self$.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 <- R6::R6Class("SimulationResultsMultiArmRates",
inherit = SimulationResultsBaseRates,
public = list(
activeArms = NULL,
effectMatrix = NULL,
typeOfShape = NULL,
piMaxVector = NULL,
piControl = NULL,
piTreatmentsH1 = NULL,
piControlH1 = NULL,
gED50 = NULL,
slope = NULL,
doseLevels = NULL,
intersectionTest = NULL,
adaptations = NULL,
typeOfSelection = NULL,
effectMeasure = NULL,
successCriterion = NULL,
epsilonValue = NULL,
rValue = NULL,
threshold = NULL,
selectArmsFunction = NULL,
earlyStop = NULL,
selectedArms = NULL,
numberOfActiveArms = NULL,
rejectAtLeastOne = NULL,
rejectedArmsPerStage = NULL,
successPerStage = NULL,
sampleSizes = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedArms",
"numberOfActiveArms",
"rejectedArmsPerStage",
"successPerStage"
)) {
self$.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
SimulationResultsBaseSurvival <- R6::R6Class("SimulationResultsBaseSurvival",
inherit = SimulationResults,
public = list(
directionUpper = NULL,
plannedEvents = NULL,
minNumberOfEventsPerStage = NULL,
maxNumberOfEventsPerStage = NULL,
thetaH1 = NULL,
calcEventsFunction = NULL,
expectedNumberOfEvents = NULL,
initialize = function(design, ...) {
super$initialize(design = design, ...)
generatedParams <- c(
"iterations",
"expectedNumberOfEvents",
"cumulativeEventsPerStage",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
self$.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 <- R6::R6Class("SimulationResultsSurvival",
inherit = SimulationResultsBaseSurvival,
public = list(
.piecewiseSurvivalTime = NULL,
.accrualTime = NULL,
pi1 = NULL,
pi2 = NULL,
median1 = NULL,
median2 = NULL,
maxNumberOfSubjects = NULL,
accrualTime = NULL,
accrualIntensity = NULL,
dropoutRate1 = NULL,
dropoutRate2 = NULL,
dropoutTime = NULL,
eventTime = NULL,
thetaH0 = NULL,
allocation1 = NULL,
allocation2 = NULL,
kappa = NULL,
piecewiseSurvivalTime = NULL,
lambda1 = NULL,
lambda2 = NULL,
earlyStop = NULL,
hazardRatio = NULL,
analysisTime = NULL,
studyDuration = NULL,
eventsNotAchieved = NULL,
numberOfSubjects = NULL,
numberOfSubjects1 = NULL,
numberOfSubjects2 = NULL,
eventsPerStage = NULL,
overallEventsPerStage = NULL,
singleEventsPerStage = NULL,
cumulativeEventsPerStage = NULL,
expectedNumberOfSubjects = NULL,
rejectPerStage = NULL,
overallReject = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(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$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
self$.setParameterType(generatedParam, C_PARAM_GENERATED)
}
self$.setParameterType("numberOfSubjects1", C_PARAM_NOT_APPLICABLE)
self$.setParameterType("numberOfSubjects2", C_PARAM_NOT_APPLICABLE)
self$.setParameterType("median1", C_PARAM_NOT_APPLICABLE)
self$.setParameterType("median2", C_PARAM_NOT_APPLICABLE)
self$.setParameterType("eventsPerStage", C_PARAM_NOT_APPLICABLE)
self$.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 <- R6::R6Class("SimulationResultsMultiArmSurvival",
inherit = SimulationResultsBaseSurvival,
public = list(
activeArms = NULL,
effectMatrix = NULL,
typeOfShape = NULL,
omegaMaxVector = NULL,
gED50 = NULL,
slope = NULL,
doseLevels = NULL,
intersectionTest = NULL,
adaptations = NULL,
typeOfSelection = NULL,
effectMeasure = NULL,
successCriterion = NULL,
epsilonValue = NULL,
rValue = NULL,
threshold = NULL,
selectArmsFunction = NULL,
correlationComputation = NULL,
earlyStop = NULL,
selectedArms = NULL,
numberOfActiveArms = NULL,
rejectAtLeastOne = NULL,
rejectedArmsPerStage = NULL,
successPerStage = NULL,
eventsPerStage = NULL,
singleEventsPerStage = NULL,
cumulativeEventsPerStage = NULL,
singleEventsPerArmAndStage = NULL,
singleNumberOfEventsPerStage = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedArms",
"numberOfActiveArms",
"rejectedArmsPerStage",
"successPerStage"
)) {
self$.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 <- R6::R6Class("SimulationResultsEnrichmentMeans",
inherit = SimulationResultsBaseMeans,
public = list(
populations = NULL,
effectList = NULL,
intersectionTest = NULL,
stratifiedAnalysis = NULL,
adaptations = NULL,
typeOfSelection = NULL,
effectMeasure = NULL,
successCriterion = NULL,
epsilonValue = NULL,
rValue = NULL,
threshold = NULL,
selectPopulationsFunction = NULL,
earlyStop = NULL,
selectedPopulations = NULL,
numberOfPopulations = NULL,
rejectAtLeastOne = NULL,
rejectedPopulationsPerStage = NULL,
successPerStage = NULL,
sampleSizes = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedPopulations",
"numberOfPopulations",
"rejectedPopulationsPerStage",
"successPerStage"
)) {
self$.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 <- R6::R6Class("SimulationResultsEnrichmentRates",
inherit = SimulationResultsBaseRates,
public = list(
populations = NULL,
effectList = NULL,
intersectionTest = NULL,
stratifiedAnalysis = NULL,
adaptations = NULL,
piTreatmentH1 = NULL,
piControlH1 = NULL,
typeOfSelection = NULL,
effectMeasure = NULL,
successCriterion = NULL,
epsilonValue = NULL,
rValue = NULL,
threshold = NULL,
selectPopulationsFunction = NULL,
earlyStop = NULL,
selectedPopulations = NULL,
numberOfPopulations = NULL,
rejectAtLeastOne = NULL,
rejectedPopulationsPerStage = NULL,
successPerStage = NULL,
sampleSizes = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedPopulations",
"numberOfPopulations",
"rejectedPopulationsPerStage",
"successPerStage"
)) {
self$.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 <- R6::R6Class("SimulationResultsEnrichmentSurvival",
inherit = SimulationResultsBaseSurvival,
public = list(
populations = NULL,
effectList = NULL,
intersectionTest = NULL,
stratifiedAnalysis = NULL,
adaptations = NULL,
typeOfSelection = NULL,
effectMeasure = NULL,
successCriterion = NULL,
epsilonValue = NULL,
rValue = NULL,
threshold = NULL,
selectPopulationsFunction = NULL,
correlationComputation = NULL,
earlyStop = NULL,
selectedPopulations = NULL,
numberOfPopulations = NULL,
rejectAtLeastOne = NULL,
rejectedPopulationsPerStage = NULL,
successPerStage = NULL,
eventsPerStage = NULL,
singleEventsPerSubsetAndStage = NULL,
singleNumberOfEventsPerStage = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedPopulations",
"numberOfPopulations",
"rejectedPopulationsPerStage",
"successPerStage"
)) {
self$.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsCountData
#'
#' @title
#' Class for Simulation Results Count Data
#'
#' @description
#' A class for simulation results count data.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_thetaH0
#' @template field_accrualTime
#' @template field_accrualIntensity
#' @template field_groups
#' @template field_directionUpper
#' @template field_earlyStop
#' @template field_sampleSizes
#' @template field_expectedNumberOfSubjects
#' @template field_overallReject
#' @template field_rejectPerStage
#'
#' @details
#' Use \code{\link[=getSimulationCounts]{getSimulationCounts()}}
#' 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 f_simulation_base_counts.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsCountData <- R6::R6Class("SimulationResultsCountData",
inherit = SimulationResults,
public = list(
maxNumberOfSubjects = NULL,
plannedCalendarTime = NULL,
directionUpper = NULL,
lambda1 = NULL,
lambda2 = NULL,
lambda = NULL,
theta = NULL,
thetaH0 = NULL,
overdispersion = NULL,
fixedExposureTime = NULL,
accrualTime = NULL,
accrualIntensity = NULL,
followUpTime = NULL,
groups = NULL,
expectedNumberOfSubjects = NULL,
numberOfSubjects = NULL,
numberOfSubjects1 = NULL,
numberOfSubjects2 = NULL,
iterations = NULL,
futilityStop = NULL,
futilityPerStage = NULL,
rejectPerStage = NULL,
earlyStop = NULL,
overallReject = NULL,
calcSubjectsFunction = NULL,
initialize = function(design, ...) {
super$initialize(design = design, ...)
self$groups <- 2L
self$.setParameterType("conditionalPower", C_PARAM_NOT_APPLICABLE)
self$.setParameterType("futilityStop", C_PARAM_NOT_APPLICABLE)
self$.setParameterType("numberOfSubjects", C_PARAM_NOT_APPLICABLE)
self$.setParameterType("expectedNumberOfSubjects", C_PARAM_NOT_APPLICABLE)
}
)
)
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Defines functions names.SimulationResults
Documented in names.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: 8474 $
## | Last changed: $Date: 2025-01-14 14:32:53 +0100 (Di, 14 Jan 2025) $
## | 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$.getVisibleFieldNames())
return(namesToShow)
}
#'
#' @name SimulationResults
#'
#' @title
#' Class for Simulation Results
#'
#' @description
#' A class for simulation results.
#'
#' @template field_seed
#' @template field_iterations
#'
#' @details
#' \code{SimulationResults} is the basic class for
#' \itemize{
#' \item \code{\link{SimulationResultsMeans}},
#' \item \code{\link{SimulationResultsRates}},
#' \item \code{\link{SimulationResultsSurvival}},
#' \item \code{\link{SimulationResultsCountData}},
#' \item \code{\link{SimulationResultsMultiArmMeans}},
#' \item \code{\link{SimulationResultsMultiArmRates}},
#' \item \code{\link{SimulationResultsMultiArmSurvival}},
#' \item \code{\link{SimulationResultsEnrichmentMeans}},
#' \item \code{\link{SimulationResultsEnrichmentRates}}, and
#' \item \code{\link{SimulationResultsEnrichmentSurvival}}.
#' }
#'
#' @include class_core_parameter_set.R
#' @include class_core_plot_settings.R
#' @include class_design.R
#' @include f_core_constants.R
#' @include class_time.R
#' @include f_simulation_base_survival.R
#' @include f_simulation_utilities.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResults <- R6::R6Class("SimulationResults",
inherit = ParameterSet,
public = list(
.plotSettings = NULL,
.design = NULL,
.data = NULL,
.rawData = NULL,
.showStatistics = NULL,
maxNumberOfIterations = NULL,
seed = NULL,
allocationRatioPlanned = numeric(),
conditionalPower = NULL,
iterations = NULL,
futilityPerStage = NULL,
futilityStop = NULL,
initialize = function(design, ..., showStatistics = FALSE) {
super$initialize(...)
self$.design <- design
self$.showStatistics <- showStatistics
self$.plotSettings <- PlotSettings$new()
},
getPlotSettings = function() {
return(self$.plotSettings)
},
setShowStatistics = function(showStatistics) {
.assertIsSingleLogical(showStatistics, "showStatistics")
self$.showStatistics <- showStatistics
},
show = function(showType = 1, digits = NA_integer_, showStatistics = FALSE) {
self$.show(
showType = showType, digits = digits, showStatistics = showStatistics,
consoleOutputEnabled = TRUE
)
},
.show = function(..., showType = 1, digits = NA_integer_,
showStatistics = FALSE, consoleOutputEnabled = TRUE, performanceScore = NULL) {
"Method for automatically printing simulation result objects"
self$.resetCat()
if (showType == 3) {
.createSummary(self, digits = digits)$.show(
showType = 1,
digits = digits, consoleOutputEnabled = consoleOutputEnabled
)
} else if (showType == 2) {
super$.show(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",
call. = FALSE
)
}
if (!is.character(showStatistics) || showStatistics != "exclusive") {
self$.cat(self$.toString(startWithUpperCase = TRUE), ":\n\n",
heading = 1,
consoleOutputEnabled = consoleOutputEnabled
)
self$.showParametersOfOneGroup(.getDesignParametersToShow(self), "Design parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
userDefinedParameters <- self$.getUserDefinedParameters()
if (inherits(self, "SimulationResultsSurvival") &&
self$.piecewiseSurvivalTime$delayedResponseEnabled) {
userDefinedParameters <- c(
userDefinedParameters,
".piecewiseSurvivalTime$delayedResponseEnabled"
)
}
self$.showParametersOfOneGroup(userDefinedParameters, "User defined parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
derivedParameters <- self$.getDerivedParameters()
if (length(derivedParameters) > 0) {
self$.showParametersOfOneGroup(derivedParameters, "Derived from user defined parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
}
self$.showParametersOfOneGroup(self$.getDefaultParameters(), "Default parameters",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
self$.showParametersOfOneGroup(self$.getGeneratedParameters(), "Results",
orderByParameterName = FALSE, consoleOutputEnabled = consoleOutputEnabled
)
self$.showUnknownParameters(consoleOutputEnabled = consoleOutputEnabled)
}
## statistics of simulated data
if (isTRUE(showStatistics) || self$.showStatistics ||
(is.character(showStatistics) && showStatistics == "exclusive")) {
self$.cat("Simulated data:\n", heading = 2, consoleOutputEnabled = consoleOutputEnabled)
params <- c()
if (inherits(self, "SimulationResultsMeans")) {
params <- c(
"effectMeasure",
"numberOfSubjects",
"testStatistic"
)
} else if (inherits(self, "SimulationResultsRates")) {
params <- c(
"effectMeasure",
"numberOfSubjects",
"testStatistic"
)
} else if (inherits(self, "SimulationResultsSurvival")) {
params <- c(
"effectMeasure",
"analysisTime",
"numberOfSubjects",
"eventsPerStage1",
"eventsPerStage2",
"cumulativeEventsPerStage",
"testStatistic",
"logRankStatistic",
"hazardRatioEstimateLR"
)
} else if (inherits(self, "SimulationResultsMultiArmMeans") ||
inherits(self, "SimulationResultsMultiArmRates")) {
params <- c(
"effectMeasure",
"subjectsActiveArm",
"testStatistic",
"conditionalCriticalValue",
"rejectPerStage",
"successStop",
"futilityPerStage"
)
} else if (inherits(self, "SimulationResultsEnrichmentMeans") ||
inherits(self, "SimulationResultsEnrichmentRates")) {
params <- c(
"effectMeasure",
"subjectsPopulation",
"testStatistic",
"conditionalCriticalValue",
"rejectPerStage",
"successStop",
"futilityPerStage"
)
} else if (inherits(self, "SimulationResultsMultiArmSurvival") ||
inherits(self, "SimulationResultsEnrichmentSurvival")) {
params <- c(
"effectMeasure",
"numberOfEvents",
"singleEventsPerArmAndStage",
"singleEventsPerSubsetAndStage",
"testStatistic",
"conditionalCriticalValue",
"rejectPerStage",
"successStop",
"futilityPerStage"
)
}
if (!is.null(self[["conditionalPowerAchieved"]]) &&
!all(is.na(self$conditionalPowerAchieved)) &&
any(!is.na(self$conditionalPowerAchieved)) &&
any(na.omit(self$conditionalPowerAchieved) != 0)) {
params <- c(params, "conditionalPowerAchieved")
}
stages <- sort(unique(self$.data$stageNumber))
variedParameterName1 <- self$.getVariedParameterName(1)
variedParameterName2 <- self$.getVariedParameterName(2)
parameterValues1 <- self$.getVariedParameterValues(variedParameterName1)
parameterValues2 <- self$.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) {
self$.catStatisticsLine(
stage = stage,
parameterName = parameterName,
paramCaption = paramCaption,
parameterValue1 = parameterValue1,
variedParameterName1 = variedParameterName1,
parameterValue2 = parameterValue2,
variedParameterName2 = variedParameterName2,
consoleOutputEnabled = consoleOutputEnabled
)
} else {
self$.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) {
self$.catStatisticsLine(
stage = stage,
parameterName = parameterName2,
paramCaption = paramCaption2,
parameterValue1 = parameterValue1,
variedParameterName1 = variedParameterName1,
parameterValue2 = unique(parameterValues2),
variedParameterName2 = variedParameterName2,
consoleOutputEnabled = consoleOutputEnabled
)
}
}
}
}
self$.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$.showUnknownParameters(
consoleOutputEnabled = consoleOutputEnabled
)
}
if (self$.design$kMax > 1 || twoGroupsEnabled || multiArmSurvivalEnabled) {
self$.cat("Legend:\n",
heading = 2,
consoleOutputEnabled = consoleOutputEnabled
)
if (multiArmSurvivalEnabled) {
self$.cat(" (i): values of treatment arm i compared to control\n",
consoleOutputEnabled = consoleOutputEnabled
)
self$.cat(" {j}: values of treatment arm j\n",
consoleOutputEnabled = consoleOutputEnabled
)
} else if (enrichmentEnabled) {
matrixName <- .getSimulationEnrichmentEffectMatrixName(self)
if (nrow(self$effectList[[matrixName]]) > 1) {
self$.cat(" (i): results of situation i\n",
consoleOutputEnabled = consoleOutputEnabled
)
}
} else if (twoGroupsEnabled) {
self$.cat(" (i): values of treatment arm i\n",
consoleOutputEnabled = consoleOutputEnabled
)
}
if (self$.design$kMax > 1) {
self$.cat(" [k]: values at stage k\n",
consoleOutputEnabled = consoleOutputEnabled
)
}
if (enrichmentEnabled) {
if (length(self$effectList$subGroups) > 1) {
self$.cat(paste0(" S[i]: population i\n"),
consoleOutputEnabled = consoleOutputEnabled
)
}
self$.cat(paste0(" F: full population\n"),
consoleOutputEnabled = consoleOutputEnabled
)
if (length(self$effectList$subGroups) > 1) {
self$.cat(paste0(" R: remaining population\n"),
consoleOutputEnabled = consoleOutputEnabled
)
}
}
self$.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, self$.getVariedParameterValueString(
variedParameterName1, parameterValue1
))
if (parameterName != "subjectsControlArm") {
postfix <- paste0(postfix, self$.getVariedParameterValueString(
variedParameterName2, parameterValue2
))
}
paramValue <- self$.data[[parameterName]][
self$.data$stageNumber == stage &
self$.data[[variedParameterName1]] == parameterValue1 &
self$.data[[variedParameterName2]] %in% parameterValue2
]
} else {
postfix <- paste0(postfix, self$.getVariedParameterValueString(
variedParameterName1, parameterValue1
))
paramValue <- self$.data[[parameterName]][
self$.data$stageNumber == stage &
self$.data[[variedParameterName1]] == parameterValue1
]
}
} else {
paramValue <- self$.data[[parameterName]][
self$.data$stageNumber == stage
]
}
if (self$.design$kMax > 1) {
postfix <- paste0(postfix, " [", stage, "]")
}
if (!consoleOutputEnabled) {
paramCaption <- paste0("*", paramCaption, "*")
}
variableNameFormatted <- .getFormattedVariableName(
name = paramCaption,
n = self$.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), "; ",
"n = ", length(paramValue)
)
} else {
paramValueFormatted <- "median [range]: NA [NA - NA]; mean +/sd: NA +/-NA"
}
output <- paste(variableNameFormatted, paramValueFormatted, "\n")
if (!grepl(": median \\[range\\]: NA \\[NA - NA\\]", output)) {
self$.cat(output, consoleOutputEnabled = consoleOutputEnabled)
}
}
},
.toString = function(startWithUpperCase = FALSE) {
s <- "simulation of"
if (grepl("MultiArm", .getClassName(self)) &&
!is.null(self[["activeArms"]]) && self$activeArms > 1) {
s <- paste(s, "multi-arm")
}
if (grepl("Enrichment", .getClassName(self)) &&
!is.null(self[["populations"]]) && self$populations > 1) {
s <- paste(s, "enrichment")
}
if (inherits(self, "SimulationResultsBaseMeans")) {
s <- paste(s, "means")
} else if (inherits(self, "SimulationResultsBaseRates")) {
s <- paste(s, "rates")
} else if (inherits(self, "SimulationResultsBaseSurvival")) {
s <- paste(s, "survival data")
} else if (inherits(self, "SimulationResultsCountData")) {
s <- paste(s, "count data")
} else {
s <- paste(s, "UNDEFINED")
}
if (self$.design$kMax > 1) {
if (.isTrialDesignGroupSequential(self$.design)) {
s <- paste(s, "(group sequential design)")
} else if (.isTrialDesignInverseNormal(self$.design)) {
s <- paste(s, "(inverse normal combination test design)")
} else if (.isTrialDesignFisher(self$.design)) {
s <- paste(s, "(Fisher's combination test design)")
} else if (.isTrialDesignConditionalDunnett(self$.design)) {
s <- paste(s, "(conditional Dunnett design)")
}
} else {
s <- paste(s, "(fixed sample size design)")
}
return(ifelse(startWithUpperCase, .firstCharacterToUpperCase(s), s))
},
.getParametersToShow = function() {
parametersToShow <- self$.getVisibleFieldNames()
y <- c(
"singleEventsPerStage",
"cumulativeEventsPerStage",
"iterations",
"overallReject", # base
"rejectAtLeastOne",
"rejectPerStage",
"rejectedArmsPerStage",
"rejectedPopulationsPerStage"
)
if (self$.design$kMax > 2) {
y <- c(y, "futilityStop")
}
y <- c(
y,
"futilityPerStage",
"earlyStop", # base
"successPerStage",
"selectedArms",
"selectedPopulations",
"numberOfActiveArms",
"numberOfPopulations",
"expectedNumberOfSubjects",
"expectedNumberOfEvents",
"numberOfSubjects",
"numberOfSubjects1",
"numberOfSubjects2",
"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$.data,
variantName = self$.getVariedParameterName(),
maxNumberOfIterations = maxNumberOfIterations
))
}
)
)
SimulationResultsBaseMeans <- R6::R6Class("SimulationResultsBaseMeans",
inherit = SimulationResults,
public = list(
stDev = NULL,
plannedSubjects = NULL,
minNumberOfSubjectsPerStage = NULL,
maxNumberOfSubjectsPerStage = NULL,
thetaH1 = NULL,
stDevH1 = NULL,
calcSubjectsFunction = NULL,
expectedNumberOfSubjects = NULL,
initialize = function(design, ...) {
super$initialize(design = design, ...)
generatedParams <- c(
"iterations",
"expectedNumberOfSubjects",
"sampleSizes",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
self$.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 <- R6::R6Class("SimulationResultsMeans",
inherit = SimulationResultsBaseMeans,
public = list(
meanRatio = NULL,
thetaH0 = NULL,
normalApproximation = NULL,
alternative = NULL,
groups = NULL,
directionUpper = NULL,
effect = NULL,
earlyStop = NULL,
sampleSizes = NULL,
overallReject = NULL, # = rejectedArmsPerStage in multi-arm
rejectPerStage = NULL,
conditionalPowerAchieved = NULL,
initialize = function(design, ...) {
super$initialize(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 <- R6::R6Class("SimulationResultsMultiArmMeans",
inherit = SimulationResultsBaseMeans,
public = list(
activeArms = NULL,
effectMatrix = NULL,
typeOfShape = NULL,
muMaxVector = NULL,
gED50 = NULL,
slope = NULL,
doseLevels = NULL,
intersectionTest = NULL,
adaptations = NULL,
typeOfSelection = NULL,
effectMeasure = NULL,
successCriterion = NULL,
epsilonValue = NULL,
rValue = NULL,
threshold = NULL,
selectArmsFunction = NULL,
earlyStop = NULL,
selectedArms = NULL,
numberOfActiveArms = NULL,
rejectAtLeastOne = NULL,
rejectedArmsPerStage = NULL,
successPerStage = NULL,
sampleSizes = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedArms",
"numberOfActiveArms",
"rejectedArmsPerStage",
"successPerStage"
)) {
self$.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
SimulationResultsBaseRates <- R6::R6Class("SimulationResultsBaseRates",
inherit = SimulationResults,
public = list(
directionUpper = NULL,
plannedSubjects = NULL,
minNumberOfSubjectsPerStage = NULL,
maxNumberOfSubjectsPerStage = NULL,
calcSubjectsFunction = NULL,
expectedNumberOfSubjects = NULL,
initialize = function(design, ...) {
super$initialize(design = design, ...)
generatedParams <- c(
"iterations",
"expectedNumberOfSubjects",
"sampleSizes",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
self$.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 <- R6::R6Class("SimulationResultsRates",
inherit = SimulationResultsBaseRates,
public = list(
riskRatio = NULL,
thetaH0 = NULL,
normalApproximation = NULL,
pi1 = NULL,
pi2 = NULL,
groups = NULL,
# directionUpper = NULL,
pi1H1 = NULL,
pi2H1 = NULL,
effect = NULL,
earlyStop = NULL,
sampleSizes = NULL,
expectedNumberOfSubjects = NULL,
overallReject = NULL,
rejectPerStage = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(design = design, ...)
generatedParams <- c(
"effect",
"iterations",
"sampleSizes",
"eventsNotAchieved",
"expectedNumberOfSubjects",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop",
"analysisTime",
"studyDuration"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
self$.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 <- R6::R6Class("SimulationResultsMultiArmRates",
inherit = SimulationResultsBaseRates,
public = list(
activeArms = NULL,
effectMatrix = NULL,
typeOfShape = NULL,
piMaxVector = NULL,
piControl = NULL,
piTreatmentsH1 = NULL,
piControlH1 = NULL,
gED50 = NULL,
slope = NULL,
doseLevels = NULL,
intersectionTest = NULL,
adaptations = NULL,
typeOfSelection = NULL,
effectMeasure = NULL,
successCriterion = NULL,
epsilonValue = NULL,
rValue = NULL,
threshold = NULL,
selectArmsFunction = NULL,
earlyStop = NULL,
selectedArms = NULL,
numberOfActiveArms = NULL,
rejectAtLeastOne = NULL,
rejectedArmsPerStage = NULL,
successPerStage = NULL,
sampleSizes = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedArms",
"numberOfActiveArms",
"rejectedArmsPerStage",
"successPerStage"
)) {
self$.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
SimulationResultsBaseSurvival <- R6::R6Class("SimulationResultsBaseSurvival",
inherit = SimulationResults,
public = list(
directionUpper = NULL,
plannedEvents = NULL,
minNumberOfEventsPerStage = NULL,
maxNumberOfEventsPerStage = NULL,
thetaH1 = NULL,
calcEventsFunction = NULL,
expectedNumberOfEvents = NULL,
initialize = function(design, ...) {
super$initialize(design = design, ...)
generatedParams <- c(
"iterations",
"expectedNumberOfEvents",
"cumulativeEventsPerStage",
"overallReject",
"rejectPerStage",
"futilityPerStage",
"earlyStop"
)
if (design$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
self$.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 <- R6::R6Class("SimulationResultsSurvival",
inherit = SimulationResultsBaseSurvival,
public = list(
.piecewiseSurvivalTime = NULL,
.accrualTime = NULL,
pi1 = NULL,
pi2 = NULL,
median1 = NULL,
median2 = NULL,
maxNumberOfSubjects = NULL,
accrualTime = NULL,
accrualIntensity = NULL,
dropoutRate1 = NULL,
dropoutRate2 = NULL,
dropoutTime = NULL,
eventTime = NULL,
thetaH0 = NULL,
allocation1 = NULL,
allocation2 = NULL,
kappa = NULL,
piecewiseSurvivalTime = NULL,
lambda1 = NULL,
lambda2 = NULL,
earlyStop = NULL,
hazardRatio = NULL,
analysisTime = NULL,
studyDuration = NULL,
eventsNotAchieved = NULL,
numberOfSubjects = NULL,
numberOfSubjects1 = NULL,
numberOfSubjects2 = NULL,
eventsPerStage = NULL,
overallEventsPerStage = NULL,
singleEventsPerStage = NULL,
cumulativeEventsPerStage = NULL,
expectedNumberOfSubjects = NULL,
rejectPerStage = NULL,
overallReject = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(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$kMax > 2) {
generatedParams <- c(generatedParams, "futilityStop")
}
for (generatedParam in generatedParams) {
self$.setParameterType(generatedParam, C_PARAM_GENERATED)
}
self$.setParameterType("numberOfSubjects1", C_PARAM_NOT_APPLICABLE)
self$.setParameterType("numberOfSubjects2", C_PARAM_NOT_APPLICABLE)
self$.setParameterType("median1", C_PARAM_NOT_APPLICABLE)
self$.setParameterType("median2", C_PARAM_NOT_APPLICABLE)
self$.setParameterType("eventsPerStage", C_PARAM_NOT_APPLICABLE)
self$.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 <- R6::R6Class("SimulationResultsMultiArmSurvival",
inherit = SimulationResultsBaseSurvival,
public = list(
activeArms = NULL,
effectMatrix = NULL,
typeOfShape = NULL,
omegaMaxVector = NULL,
gED50 = NULL,
slope = NULL,
doseLevels = NULL,
intersectionTest = NULL,
adaptations = NULL,
typeOfSelection = NULL,
effectMeasure = NULL,
successCriterion = NULL,
epsilonValue = NULL,
rValue = NULL,
threshold = NULL,
selectArmsFunction = NULL,
correlationComputation = NULL,
earlyStop = NULL,
selectedArms = NULL,
numberOfActiveArms = NULL,
rejectAtLeastOne = NULL,
rejectedArmsPerStage = NULL,
successPerStage = NULL,
eventsPerStage = NULL,
singleEventsPerStage = NULL,
cumulativeEventsPerStage = NULL,
singleEventsPerArmAndStage = NULL,
singleNumberOfEventsPerStage = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedArms",
"numberOfActiveArms",
"rejectedArmsPerStage",
"successPerStage"
)) {
self$.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 <- R6::R6Class("SimulationResultsEnrichmentMeans",
inherit = SimulationResultsBaseMeans,
public = list(
populations = NULL,
effectList = NULL,
intersectionTest = NULL,
stratifiedAnalysis = NULL,
adaptations = NULL,
typeOfSelection = NULL,
effectMeasure = NULL,
successCriterion = NULL,
epsilonValue = NULL,
rValue = NULL,
threshold = NULL,
selectPopulationsFunction = NULL,
earlyStop = NULL,
selectedPopulations = NULL,
numberOfPopulations = NULL,
rejectAtLeastOne = NULL,
rejectedPopulationsPerStage = NULL,
successPerStage = NULL,
sampleSizes = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedPopulations",
"numberOfPopulations",
"rejectedPopulationsPerStage",
"successPerStage"
)) {
self$.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 <- R6::R6Class("SimulationResultsEnrichmentRates",
inherit = SimulationResultsBaseRates,
public = list(
populations = NULL,
effectList = NULL,
intersectionTest = NULL,
stratifiedAnalysis = NULL,
adaptations = NULL,
piTreatmentH1 = NULL,
piControlH1 = NULL,
typeOfSelection = NULL,
effectMeasure = NULL,
successCriterion = NULL,
epsilonValue = NULL,
rValue = NULL,
threshold = NULL,
selectPopulationsFunction = NULL,
earlyStop = NULL,
selectedPopulations = NULL,
numberOfPopulations = NULL,
rejectAtLeastOne = NULL,
rejectedPopulationsPerStage = NULL,
successPerStage = NULL,
sampleSizes = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedPopulations",
"numberOfPopulations",
"rejectedPopulationsPerStage",
"successPerStage"
)) {
self$.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 <- R6::R6Class("SimulationResultsEnrichmentSurvival",
inherit = SimulationResultsBaseSurvival,
public = list(
populations = NULL,
effectList = NULL,
intersectionTest = NULL,
stratifiedAnalysis = NULL,
adaptations = NULL,
typeOfSelection = NULL,
effectMeasure = NULL,
successCriterion = NULL,
epsilonValue = NULL,
rValue = NULL,
threshold = NULL,
selectPopulationsFunction = NULL,
correlationComputation = NULL,
earlyStop = NULL,
selectedPopulations = NULL,
numberOfPopulations = NULL,
rejectAtLeastOne = NULL,
rejectedPopulationsPerStage = NULL,
successPerStage = NULL,
eventsPerStage = NULL,
singleEventsPerSubsetAndStage = NULL,
singleNumberOfEventsPerStage = NULL,
conditionalPowerAchieved = matrix(),
initialize = function(design, ...) {
super$initialize(design = design, ...)
for (generatedParam in c(
"rejectAtLeastOne",
"selectedPopulations",
"numberOfPopulations",
"rejectedPopulationsPerStage",
"successPerStage"
)) {
self$.setParameterType(generatedParam, C_PARAM_GENERATED)
}
}
)
)
#'
#' @name SimulationResultsCountData
#'
#' @title
#' Class for Simulation Results Count Data
#'
#' @description
#' A class for simulation results count data.
#'
#' @template field_maxNumberOfIterations
#' @template field_seed
#' @template field_allocationRatioPlanned
#' @template field_conditionalPower
#' @template field_iterations
#' @template field_futilityPerStage
#' @template field_thetaH0
#' @template field_accrualTime
#' @template field_accrualIntensity
#' @template field_groups
#' @template field_directionUpper
#' @template field_earlyStop
#' @template field_sampleSizes
#' @template field_expectedNumberOfSubjects
#' @template field_overallReject
#' @template field_rejectPerStage
#'
#' @details
#' Use \code{\link[=getSimulationCounts]{getSimulationCounts()}}
#' 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 f_simulation_base_counts.R
#'
#' @keywords internal
#'
#' @importFrom methods new
#'
SimulationResultsCountData <- R6::R6Class("SimulationResultsCountData",
inherit = SimulationResults,
public = list(
maxNumberOfSubjects = NULL,
plannedCalendarTime = NULL,
directionUpper = NULL,
lambda1 = NULL,
lambda2 = NULL,
lambda = NULL,
theta = NULL,
thetaH0 = NULL,
overdispersion = NULL,
fixedExposureTime = NULL,
accrualTime = NULL,
accrualIntensity = NULL,
followUpTime = NULL,
groups = NULL,
expectedNumberOfSubjects = NULL,
numberOfSubjects = NULL,
numberOfSubjects1 = NULL,
numberOfSubjects2 = NULL,
iterations = NULL,
futilityStop = NULL,
futilityPerStage = NULL,
rejectPerStage = NULL,
earlyStop = NULL,
overallReject = NULL,
calcSubjectsFunction = NULL,
initialize = function(design, ...) {
super$initialize(design = design, ...)
self$groups <- 2L
self$.setParameterType("conditionalPower", C_PARAM_NOT_APPLICABLE)
self$.setParameterType("futilityStop", C_PARAM_NOT_APPLICABLE)
self$.setParameterType("numberOfSubjects", C_PARAM_NOT_APPLICABLE)
self$.setParameterType("expectedNumberOfSubjects", C_PARAM_NOT_APPLICABLE)
}
)
)
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