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f_analysis_utilities.R
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f_analysis_utilities.R
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## |
## | *Analysis of multi-arm designs with adaptive test*
## |
## | 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: 7742 $
## | Last changed: $Date: 2024-03-22 13:46:29 +0100 (Fr, 22 Mrz 2024) $
## | Last changed by: $Author: pahlke $
## |
#' @include f_core_utilities.R
NULL
.getGMaxFromAnalysisResult <- function(results) {
return(nrow(results$.stageResults$testStatistics))
}
.setNPlanned <- function(results, nPlanned) {
design <- results$.design
if (design$kMax == 1) {
if (.isConditionalPowerEnabled(nPlanned)) {
warning("'nPlanned' (", .arrayToString(nPlanned), ") ",
"will be ignored because design is fixed",
call. = FALSE
)
}
results$.setParameterType("nPlanned", C_PARAM_NOT_APPLICABLE)
}
.setValueAndParameterType(results, "nPlanned", nPlanned, NA_real_)
while (length(results$nPlanned) < design$kMax) {
results$nPlanned <- c(NA_real_, results$nPlanned)
}
if (all(is.na(results$nPlanned))) {
results$.setParameterType("nPlanned", C_PARAM_NOT_APPLICABLE)
}
}
.isConditionalPowerEnabled <- function(nPlanned) {
return(!is.null(nPlanned) && length(nPlanned) > 0 && !all(is.na(nPlanned)))
}
.warnInCaseOfUnusedConditionalPowerArgument <- function(results, nPlanned, paramName, paramValues) {
if (!.isConditionalPowerEnabled(nPlanned)) {
if (length(paramValues) > 0 && !all(is.na(paramValues)) &&
results$.getParameterType(paramName) != C_PARAM_GENERATED) {
warning("'", paramName, "' (", .arrayToString(paramValues), ") ",
"will be ignored because 'nPlanned' is not defined",
call. = FALSE
)
}
return(invisible())
}
if (results$.design$kMax == 1) {
if (length(paramValues) > 0 && !all(is.na(paramValues)) &&
results$.getParameterType(paramName) != C_PARAM_GENERATED) {
warning("'", paramName, "' (", .arrayToString(paramValues), ") ",
"will be ignored because design is fixed",
call. = FALSE
)
}
return(invisible())
}
}
.setNPlannedAndThetaH1 <- function(results, nPlanned, thetaH1) {
.setNPlanned(results, nPlanned)
.warnInCaseOfUnusedConditionalPowerArgument(results, nPlanned, "thetaH1", thetaH1)
if (!is.matrix(results$thetaH1)) {
if (results$.getParameterType("thetaH1") %in% c(C_PARAM_TYPE_UNKNOWN, C_PARAM_NOT_APPLICABLE)) {
.setValueAndParameterType(results, "thetaH1", thetaH1, NA_real_)
} else {
results$thetaH1 <- thetaH1
if (results$.getParameterType("thetaH1") == C_PARAM_TYPE_UNKNOWN) {
results$.setParameterType("thetaH1", C_PARAM_USER_DEFINED)
}
}
} else {
if (results$.getParameterType("thetaH1") %in% c(C_PARAM_TYPE_UNKNOWN, C_PARAM_NOT_APPLICABLE)) {
.setValueAndParameterType(results, "thetaH1",
value = matrix(thetaH1, ncol = 1),
defaultValue = matrix(rep(NA_real_, .getGMaxFromAnalysisResult(results)), ncol = 1)
)
} else {
results$thetaH1 <- matrix(thetaH1, ncol = 1)
if (results$.getParameterType("thetaH1") == C_PARAM_TYPE_UNKNOWN) {
results$.setParameterType("thetaH1", C_PARAM_USER_DEFINED)
}
}
}
}
.setNPlannedAndThetaH1AndAssumedStDev <- function(results, nPlanned, thetaH1, assumedStDev) {
.setNPlannedAndThetaH1(results, nPlanned, thetaH1)
.warnInCaseOfUnusedConditionalPowerArgument(results, nPlanned, "assumedStDev", assumedStDev)
if (results$.getParameterType("assumedStDev") %in% c(C_PARAM_TYPE_UNKNOWN, C_PARAM_NOT_APPLICABLE)) {
.setValueAndParameterType(results, "assumedStDev", assumedStDev, NA_real_)
} else {
results$assumedStDev <- assumedStDev
if (results$.getParameterType("assumedStDev") == C_PARAM_TYPE_UNKNOWN) {
results$.setParameterType("assumedStDev", C_PARAM_USER_DEFINED)
}
}
}
.setNPlannedAndThetaH1AndAssumedStDevs <- function(results, nPlanned, thetaH1, assumedStDevs) {
.setNPlannedAndThetaH1(results, nPlanned, thetaH1)
.warnInCaseOfUnusedConditionalPowerArgument(results, nPlanned, "assumedStDevs", assumedStDevs)
if (results$.getParameterType("assumedStDevs") %in% c(C_PARAM_TYPE_UNKNOWN, C_PARAM_NOT_APPLICABLE)) {
.setValueAndParameterType(results, "assumedStDevs",
value = matrix(assumedStDevs, ncol = 1),
defaultValue = matrix(rep(NA_real_, .getGMaxFromAnalysisResult(results)), ncol = 1)
)
} else {
results$assumedStDevs <- matrix(assumedStDevs, ncol = 1)
if (results$.getParameterType("assumedStDevs") == C_PARAM_TYPE_UNKNOWN) {
results$.setParameterType("assumedStDevs", C_PARAM_USER_DEFINED)
}
}
}
.setNPlannedAndPi <- function(results, nPlanned, piControlName, piControlValues, piTreatments) {
.setNPlanned(results, nPlanned)
.warnInCaseOfUnusedConditionalPowerArgument(results, nPlanned, piControlName, piControlValues)
.warnInCaseOfUnusedConditionalPowerArgument(results, nPlanned, "piTreatments", piTreatments)
if (results$.getParameterType(piControlName) %in% c(C_PARAM_TYPE_UNKNOWN, C_PARAM_NOT_APPLICABLE)) {
.setValueAndParameterType(
results, piControlName,
matrix(piControlValues, ncol = 1),
matrix(rep(NA_real_, .getGMaxFromAnalysisResult(results)), ncol = 1)
)
} else {
results[[piControlName]] <- matrix(piControlValues, ncol = 1)
if (results$.getParameterType(piControlName) == C_PARAM_TYPE_UNKNOWN) {
results$.setParameterType(piControlName, C_PARAM_USER_DEFINED)
}
}
if (results$.getParameterType("piTreatments") == C_PARAM_TYPE_UNKNOWN) {
.setValueAndParameterType(
results, "piTreatments",
matrix(piTreatments, ncol = 1),
matrix(rep(NA_real_, .getGMaxFromAnalysisResult(results)), ncol = 1)
)
} else {
results$piTreatments <- matrix(piTreatments, ncol = 1)
if (results$.getParameterType("piTreatments") == C_PARAM_TYPE_UNKNOWN) {
results$.setParameterType("piTreatments", C_PARAM_USER_DEFINED)
}
}
}
.getSortedSubsets <- function(subsets) {
return(subsets[with(data.frame(subsets = subsets, index = as.integer(sub("\\D", "", subsets))), order(index))])
}
.getAllAvailableSubsets <- function(numbers, ..., sort = TRUE, digits = NA_integer_) {
if (length(numbers) == 0) {
return(character())
}
results <- paste0(numbers, collapse = "")
for (n in numbers) {
results <- c(results, .getAllAvailableSubsets(numbers[numbers != n], sort = sort))
}
if (!is.na(digits)) {
results <- results[nchar(results) == digits]
}
if (!sort) {
return(unique(results))
}
return(.getSortedSubsets(unique(results)))
}
.createSubsetsByGMax <- function(gMax, ..., stratifiedInput = TRUE,
subsetIdPrefix = "S", restId = ifelse(stratifiedInput, "R", "F"),
all = TRUE) {
.assertIsSingleInteger(gMax, "gMax", validateType = FALSE)
.assertIsInClosedInterval(gMax, "gMax", lower = 1, upper = 10)
if (gMax == 1) {
subsetName <- paste0(subsetIdPrefix, 1)
subsetName <- ifelse(stratifiedInput, subsetName, "F")
if (!all) {
return(subsetName)
}
return(list(subsetName))
}
numbers <- 1:(gMax - 1)
subsets <- list()
if (stratifiedInput) {
availableSubsets <- paste0(subsetIdPrefix, .getAllAvailableSubsets(numbers))
} else {
availableSubsets <- paste0(subsetIdPrefix, numbers)
}
for (i in numbers) {
subset <- availableSubsets[grepl(i, availableSubsets)]
subsets[[length(subsets) + 1]] <- subset
}
if (stratifiedInput) {
subsets[[length(subsets) + 1]] <- c(availableSubsets, restId)
} else {
subsets[[length(subsets) + 1]] <- restId
}
if (!all) {
if (!stratifiedInput) {
return(unlist(subsets))
}
return(subsets[[gMax]])
}
return(subsets)
}
.arraysAreEqual <- function(a1, a2) {
if (length(a1) != length(a2)) {
return(FALSE)
}
l <- length(a1)
if (l > 0) {
a1 <- sort(a1)
a2 <- sort(a2)
if (sum(a1 == a2) < l) {
return(FALSE)
}
}
return(TRUE)
}
.getNumberOfGroupsFromArgumentNames <- function(argNames) {
numbers <- gsub("\\D", "", argNames)
numbers <- numbers[numbers != ""]
return(ifelse(length(numbers) == 0, 1, max(as.numeric(numbers))))
}
.getGroupNumberFromArgumentName <- function(argName) {
n <- gsub("\\D", "", argName)
return(ifelse(n == "", 1, as.numeric(n)))
}
.isControlGroupArgument <- function(argName, numberOfGroups) {
if (numberOfGroups <= 2) {
return(FALSE)
}
return(ifelse(numberOfGroups == 1, FALSE, .getGroupNumberFromArgumentName(argName) == numberOfGroups))
}
.naOmitBackward <- function(x) {
indices <- which(is.na(x))
if (length(indices) == 0) {
return(x)
}
if (length(x) == 1 || !is.na(x[length(x)])) {
return(x)
}
if (length(indices) == 1) {
return(x[1:(length(x) - 1)])
}
indexBefore <- NA_real_
for (i in length(indices):1) {
index <- indices[i]
if (!is.na(indexBefore) && index != indexBefore - 1) {
return(x[1:(indexBefore - 1)])
}
indexBefore <- index
}
if (!is.na(indexBefore)) {
return(x[1:(indexBefore - 1)])
}
return(x)
}
.getNumberOfStagesFromArguments <- function(args, argNames) {
numberOfStages <- 1
for (argName in argNames) {
argValues <- args[[argName]]
n <- length(.naOmitBackward(argValues))
if (n > numberOfStages) {
numberOfStages <- n
}
}
return(numberOfStages)
}
.getNumberOfSubsetsFromArguments <- function(args, argNames) {
numberOfSubsets <- 1
for (argName in argNames) {
argValues <- args[[argName]]
n <- length(na.omit(argValues))
if (n > numberOfSubsets) {
numberOfSubsets <- n
}
}
return(numberOfSubsets)
}
.assertIsValidTreatmentArmArgumentDefined <- function(args, argNames, numberOfGroups, numberOfStages) {
tratmentArgNames <- argNames[!grepl(paste0(".*\\D{1}", numberOfGroups, "$"), argNames)]
for (argName in tratmentArgNames) {
argValues <- args[[argName]]
if (!is.null(argValues) && length(.naOmitBackward(argValues)) == numberOfStages) {
return(invisible())
}
}
stop(
C_EXCEPTION_TYPE_CONFLICTING_ARGUMENTS,
"at least for one treatment arm the values for ", numberOfStages, " stages must be defined ",
"because the control arm defines ", numberOfStages, " stages"
)
}
.createDataFrame <- function(...) {
args <- list(...)
args <- .removeDesignFromArgs(args)
argNames <- .getArgumentNames(...)
if (length(args) == 0 || length(argNames) == 0) {
stop(C_EXCEPTION_TYPE_MISSING_ARGUMENT, "data.frame or data vectors expected")
}
multiArmEnabled <- any(grep("3", argNames))
numberOfGroups <- .getNumberOfGroupsFromArgumentNames(argNames)
numberOfStages <- .getNumberOfStagesFromArguments(args, argNames)
survivalDataEnabled <- .isDataObjectSurvival(...)
enrichmentEnabled <- .isDataObjectEnrichment(...)
numberOfSubsets <- 1
if (enrichmentEnabled) {
numberOfSubsets <- .getNumberOfSubsetsFromArguments(args, argNames)
}
if (multiArmEnabled) {
.assertIsValidTreatmentArmArgumentDefined(args, argNames, numberOfGroups, numberOfStages)
}
numberOfValues <- length(args[[1]])
naIndicesBefore <- NULL
if (!survivalDataEnabled && multiArmEnabled) {
naIndicesBefore <- list()
}
for (argName in argNames) {
argValues <- args[[argName]]
if (is.null(argValues) || length(argValues) == 0) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"'", argName, "' is not a valid numeric vector"
)
}
if (is.na(argValues[1])) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"'", argName, "' is NA at first stage; a valid numeric value must be specified at stage 1"
)
}
if (length(argValues) != numberOfValues) {
stop(
C_EXCEPTION_TYPE_CONFLICTING_ARGUMENTS,
"all data vectors must have the same length: '",
argName, "' (", length(argValues), ") differs from '",
argNames[1], "' (", numberOfValues, ")"
)
}
if (.equalsRegexpIgnoreCase(argName, "^stages?$")) {
if (length(stats::na.omit(argValues)) != length(argValues)) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"NA's not allowed for '", argName, "'; stages must be defined completely"
)
}
definedStages <- sort(intersect(unique(argValues), 1:numberOfValues))
if (length(definedStages) < numberOfValues) {
if (length(definedStages) == 0) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT, "no valid stages are defined; ",
"stages must be defined completely (", .arrayToString(1:numberOfValues), ")"
)
}
if (!enrichmentEnabled) {
msg <- ifelse(length(definedStages) == 1,
paste0("only stage ", definedStages, " is defined"),
paste0("only stages ", .arrayToString(definedStages), " are defined")
)
stop(C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT, msg, "; stages must be defined completely")
}
}
}
if (!survivalDataEnabled && .isControlGroupArgument(argName, numberOfGroups) &&
length(na.omit(argValues)) < numberOfStages) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"control group '", argName, "' (", .arrayToString(argValues, digits = 2), ") must be defined for all stages"
)
}
naIndices <- which(is.na(argValues))
if (length(naIndices) > 0) {
stageIndex <- naIndices[length(naIndices)]
if (stageIndex != numberOfValues) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"'", argName, "' contains a NA at stage ", stageIndex,
" followed by a value for a higher stage; NA's must be the last values"
)
}
}
if (length(naIndices) > 1 && !enrichmentEnabled) {
indexBefore <- naIndices[length(naIndices)]
for (i in (length(naIndices) - 1):1) {
index <- naIndices[i]
if (indexBefore - index > 1) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"'", argName, "' contains alternating values and NA's; ",
"NA's must be the last values"
)
}
indexBefore <- index
}
}
if (!enrichmentEnabled) {
if (!multiArmEnabled && !survivalDataEnabled) {
if (!is.null(naIndicesBefore) && !.equalsRegexpIgnoreCase(argName, "^stages?$")) {
if (!.arraysAreEqual(naIndicesBefore, naIndices)) {
stop(
C_EXCEPTION_TYPE_CONFLICTING_ARGUMENTS,
"inconsistent NA definition; ",
"if NA's exist, then they are mandatory for each group at the same stage"
)
}
}
naIndicesBefore <- naIndices
} else {
groupNumber <- .getGroupNumberFromArgumentName(argName)
if (!is.null(naIndicesBefore[[as.character(groupNumber)]]) &&
!.equalsRegexpIgnoreCase(argName, "^stages?$") &&
!.isControlGroupArgument(argName, numberOfGroups)) {
if (!.arraysAreEqual(naIndicesBefore[[as.character(groupNumber)]], naIndices)) {
stop(
C_EXCEPTION_TYPE_CONFLICTING_ARGUMENTS,
"values of treatment ", groupNumber, " not correctly specified; ",
"if NA's exist, then they are mandatory for each parameter at the same stage"
)
}
}
if (!.isControlGroupArgument(argName, numberOfGroups)) {
naIndicesBefore[[as.character(groupNumber)]] <- naIndices
}
}
}
if (sum(is.infinite(argValues)) > 0) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT, "all data values must be finite; ",
"'", argName, "' contains infinite values"
)
}
if (!any(grepl(paste0("^", sub("\\d*$", "", argName), "$"), C_KEY_WORDS_SUBSETS)) && !is.numeric(argValues)) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT, "all data vectors must be numeric ('",
argName, "' is ", .getClassName(argValues), ")"
)
}
if (length(argValues) > C_KMAX_UPPER_BOUND * numberOfSubsets) {
stop(
C_EXCEPTION_TYPE_ARGUMENT_LENGTH_OUT_OF_BOUNDS,
"'", argName, "' is out of bounds [1, ", C_KMAX_UPPER_BOUND, "]"
)
}
}
if (!enrichmentEnabled) {
for (groupNumber in 1:numberOfGroups) {
groupVars <- argNames[grepl(paste0("\\D", groupNumber, "$"), argNames)]
naIndicesBefore <- NULL
for (argName in groupVars) {
argValues <- args[[argName]]
naIndices <- which(is.na(argValues))
if (!is.null(naIndicesBefore) && !.equalsRegexpIgnoreCase(argName, "^stages?$")) {
if (!.arraysAreEqual(naIndicesBefore, naIndices)) {
stop(
C_EXCEPTION_TYPE_CONFLICTING_ARGUMENTS,
"inconsistent NA definition for group ", groupNumber, "; ",
"if NA's exist, then they are mandatory for each group at the same stage"
)
}
}
naIndicesBefore <- naIndices
}
}
}
dataFrame <- as.data.frame(args)
if (length(intersect(tolower(names(dataFrame)), c("stage", "stages"))) == 0) {
dataFrame$stages <- 1:nrow(dataFrame)
}
return(dataFrame)
}
.getDataFrameFromArgs <- function(...) {
args <- list(...)
if (length(args) == 0) {
stop(
C_EXCEPTION_TYPE_MISSING_ARGUMENT,
"cannot initialize dataset because no data are defined"
)
}
dataFrame <- NULL
dataFrameCounter <- 0
for (arg in args) {
if (is.data.frame(arg)) {
dataFrameCounter <- dataFrameCounter + 1
if (is.null(dataFrame)) {
dataFrame <- arg
}
}
}
if (dataFrameCounter > 1) {
warning("Found ", dataFrameCounter, ", data.frame arguments; ",
"only the first data.frame will be used for the initialization of the dataset",
call. = FALSE
)
}
return(dataFrame)
}
.getDesignFromArgs <- function(...) {
args <- list(...)
if (length(args) == 0) {
return(NULL)
}
for (arg in args) {
if (.isTrialDesign(arg)) {
return(arg)
}
}
return(NULL)
}
.getDatasetFromArgs <- function(...) {
args <- list(...)
if (length(args) == 0) {
return(NULL)
}
for (arg in args) {
if (.isDataset(arg)) {
return(arg)
}
}
return(NULL)
}
.removeDesignFromArgs <- function(args) {
for (i in 1:length(args)) {
if (.isTrialDesign(args[[i]])) {
return(args[-i])
}
}
return(args)
}
.getArgumentNames <- function(...) {
dataFrame <- .getDataFrameFromArgs(...)
if (!is.null(dataFrame)) {
return(names(dataFrame))
}
args <- list(...)
if (length(args) == 0) {
return(character())
}
args <- .removeDesignFromArgs(args)
return(names(args))
}
.assertIsValidDatasetArgument <- function(...) {
argNames <- .getArgumentNames(...)
if (length(argNames) == 0) {
return(TRUE)
}
argNamesLower <- tolower(argNames)
dataObjectkeyWords <- unique(tolower(C_KEY_WORDS))
multiArmKeywords <- tolower(c(
C_KEY_WORDS_SUBSETS,
C_KEY_WORDS_EVENTS,
C_KEY_WORDS_OVERALL_EVENTS,
C_KEY_WORDS_SAMPLE_SIZES,
C_KEY_WORDS_OVERALL_SAMPLE_SIZES,
C_KEY_WORDS_MEANS,
C_KEY_WORDS_OVERALL_MEANS,
C_KEY_WORDS_ST_DEVS,
C_KEY_WORDS_OVERALL_ST_DEVS,
C_KEY_WORDS_ALLOCATION_RATIOS,
C_KEY_WORDS_OVERALL_ALLOCATION_RATIOS,
C_KEY_WORDS_LOG_RANKS,
C_KEY_WORDS_OVERALL_LOG_RANKS
))
enrichmentKeywords <- tolower(c(
C_KEY_WORDS_EXPECTED_EVENTS,
C_KEY_WORDS_VARIANCE_EVENTS,
C_KEY_WORDS_OVERALL_EXPECTED_EVENTS,
C_KEY_WORDS_OVERALL_VARIANCE_EVENTS
))
unknownArgs <- setdiff(argNamesLower, dataObjectkeyWords)
unknownArgsChecked <- unknownArgs
unknownArgs <- c()
for (unknownArg in unknownArgsChecked) {
unknown <- TRUE
for (multiArmKeyword in multiArmKeywords) {
if (grepl(paste0(multiArmKeyword, "\\d{1,4}"), unknownArg)) {
unknown <- FALSE
}
}
for (enrichmentKeyword in enrichmentKeywords) {
if (grepl(enrichmentKeyword, unknownArg)) {
unknown <- FALSE
}
}
if (unknown) {
unknownArgs <- c(unknownArgs, unknownArg)
}
}
if (length(unknownArgs) > 0) {
for (i in 1:length(unknownArgs)) {
unknownArgs[i] <- argNames[argNamesLower == unknownArgs[i]][1]
}
if (length(unknownArgs) == 1) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"the argument '", unknownArgs, "' is not a valid dataset argument"
)
} else {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"the arguments ", .arrayToString(unknownArgs, encapsulate = TRUE),
" are no valid dataset arguments"
)
}
}
invisible(TRUE)
}
.getParameterNameVariant <- function(x, sep = ".") { # x <- "overallExpectedEvents"
if (identical(x, tolower(x))) {
return(x)
}
indices <- gregexpr("[A-Z]", x)[[1]]
parts <- strsplit(x, "[A-Z]")[[1]]
result <- ""
for (i in 1:length(indices)) {
index <- indices[i]
y <- tolower(substring(x, index, index))
result <- paste0(result, parts[i], sep, y)
}
if (length(parts) > length(indices)) {
result <- paste0(result, parts[length(parts)])
}
return(trimws(result))
}
.getAllParameterNameVariants <- function(parameterNameVariants) {
overallParameterNameVariants <- parameterNameVariants[grepl("^overall", parameterNameVariants)]
if (length(overallParameterNameVariants) > 0) {
overallParameterNameVariants <- c(
gsub("^overall", "cumulative", overallParameterNameVariants),
gsub("^overall", "cum", overallParameterNameVariants)
)
}
parameterNameVariants <- c(parameterNameVariants, overallParameterNameVariants)
otherVariants <- character()
for (parameterNameVariant in parameterNameVariants) {
otherVariants <- c(otherVariants, .getParameterNameVariant(parameterNameVariant, "."))
otherVariants <- c(otherVariants, .getParameterNameVariant(parameterNameVariant, "_"))
}
return(unique(c(parameterNameVariants, otherVariants)))
}
.isDataObject <- function(..., dataObjectkeyWords) {
.assertIsValidDatasetArgument(...)
argNames <- .getArgumentNames(...)
if (length(argNames) == 0) {
return(FALSE)
}
dataObjectkeyWords <- .getAllParameterNameVariants(dataObjectkeyWords)
matching <- intersect(argNames, dataObjectkeyWords)
return(length(matching) > 0)
}
.isDataObjectEnrichment <- function(...) {
enrichmentEnabled <- .isDataObject(...,
dataObjectkeyWords = c(C_KEY_WORDS_SUBSETS, paste0(C_KEY_WORDS_SUBSETS, "1"))
)
if (!enrichmentEnabled) {
return(FALSE)
}
args <- list(...)
if (length(args) == 1 && is.data.frame(args[[1]])) {
data <- args[[1]]
if ("subsets" %in% colnames(data) && all(is.na(data[["subsets"]]))) {
return(FALSE)
}
}
return(enrichmentEnabled)
}
.isDataObjectMeans <- function(...) {
dataObjectkeyWords <- c(
C_KEY_WORDS_MEANS,
C_KEY_WORDS_ST_DEVS,
C_KEY_WORDS_OVERALL_MEANS,
C_KEY_WORDS_OVERALL_ST_DEVS
)
dataObjectkeyWords <- c(dataObjectkeyWords, paste0(dataObjectkeyWords, c(1, 2)))
return(.isDataObject(..., dataObjectkeyWords = dataObjectkeyWords))
}
.isDataObjectRates <- function(...) {
dataObjectkeyWordsExpected <- c(
C_KEY_WORDS_EVENTS,
C_KEY_WORDS_OVERALL_EVENTS
)
dataObjectkeyWordsForbidden <- c(
C_KEY_WORDS_OVERALL_LOG_RANKS,
C_KEY_WORDS_LOG_RANKS,
C_KEY_WORDS_OVERALL_ALLOCATION_RATIOS,
C_KEY_WORDS_ALLOCATION_RATIOS,
C_KEY_WORDS_EXPECTED_EVENTS,
C_KEY_WORDS_VARIANCE_EVENTS,
C_KEY_WORDS_OVERALL_EXPECTED_EVENTS,
C_KEY_WORDS_OVERALL_VARIANCE_EVENTS
)
dataObjectkeyWordsExpected <- c(dataObjectkeyWordsExpected, paste0(dataObjectkeyWordsExpected, c(1, 2)))
dataObjectkeyWordsForbidden <- c(dataObjectkeyWordsForbidden, paste0(dataObjectkeyWordsForbidden, c(1, 2)))
return(.isDataObject(..., dataObjectkeyWords = dataObjectkeyWordsExpected) &&
!.isDataObject(..., dataObjectkeyWords = dataObjectkeyWordsForbidden))
}
.isDataObjectSurvival <- function(...) {
dataObjectkeyWords <- c(
C_KEY_WORDS_OVERALL_LOG_RANKS,
C_KEY_WORDS_LOG_RANKS,
C_KEY_WORDS_OVERALL_ALLOCATION_RATIOS,
C_KEY_WORDS_ALLOCATION_RATIOS
)
dataObjectkeyWords <- c(dataObjectkeyWords, paste0(dataObjectkeyWords, c(1, 2)))
return(.isDataObject(..., dataObjectkeyWords = dataObjectkeyWords))
}
.isDataObjectNonStratifiedEnrichmentSurvival <- function(...) {
dataObjectkeyWords <- c(
C_KEY_WORDS_EXPECTED_EVENTS,
C_KEY_WORDS_VARIANCE_EVENTS,
C_KEY_WORDS_OVERALL_EXPECTED_EVENTS,
C_KEY_WORDS_OVERALL_VARIANCE_EVENTS
)
return(.isDataObject(..., dataObjectkeyWords = dataObjectkeyWords))
}
#'
#' @title
#' Get Wide Format
#'
#' @description
#' Returns the specified dataset as a \code{\link[base]{data.frame}} in so-called wide format.
#'
#' @details
#' In the wide format (unstacked), the data are presented with each different data variable in a separate column, i.e.,
#' the different groups are in separate columns.
#'
#' @seealso
#' \code{\link[=getLongFormat]{getLongFormat()}} for returning the dataset as a \code{\link[base]{data.frame}} in long format.
#'
#' @return A \code{\link[base]{data.frame}} will be returned.
#'
#' @keywords internal
#'
#' @export
#'
getWideFormat <- function(dataInput) {
.assertIsDataset(dataInput)
paramNames <- names(dataInput)
paramNames <- paramNames[!(paramNames %in% c("groups"))]
if (!dataInput$.enrichmentEnabled) {
paramNames <- paramNames[!(paramNames %in% c("subsets"))]
}
numberOfSubsets <- dataInput$getNumberOfSubsets()
numberOfGroups <- dataInput$getNumberOfGroups(survivalCorrectionEnabled = FALSE)
if (numberOfSubsets <= 1) {
numberOfStages <- dataInput$getNumberOfStages()
df <- data.frame(stages = 1:numberOfStages)
} else {
numberOfStages <- length(dataInput$subsets) / numberOfGroups / numberOfSubsets
df <- data.frame(stages = rep(1:numberOfStages, numberOfSubsets))
}
for (paramName in paramNames) {
if (numberOfGroups == 1) {
df[[paramName]] <- dataInput[[paramName]]
} else {
for (group in 1:numberOfGroups) {
if (paramName %in% c("stages", "subsets")) {
varName <- paramName
} else {
varName <- paste0(paramName, group)
}
df[[varName]] <- dataInput[[paramName]][dataInput$groups == group]
}
}
}
return(df)
}
.getNumberOfStages <- function(dataFrame, naOmitEnabled = TRUE) {
if (naOmitEnabled) {
colNames <- colnames(dataFrame)
validColNames <- character()
for (colName in colNames) {
colValues <- dataFrame[, colName]
if (length(colValues) > 0 && !all(is.na(colValues))) {
validColNames <- c(validColNames, colName)
}
}
subData <- stats::na.omit(dataFrame[, validColNames])
numberOfStages <- length(unique(as.character(subData$stage)))
if (numberOfStages == 0) {
print(dataFrame[, validColNames])
stop(
C_EXCEPTION_TYPE_RUNTIME_ISSUE,
"'dataFrame' seems to contain an invalid column"
)
}
return(numberOfStages)
}
return(length(levels(dataFrame$stage)))
}
.getWideFormat <- function(dataFrame) {
if (!is.data.frame(dataFrame)) {
stop(C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT, "'dataFrame' must be a data.frame (is ", .getClassName(dataFrame), ")")
}
paramNames <- names(dataFrame)
paramNames <- paramNames[!(paramNames %in% c("stage", "group", "subset"))]
numberOfSubsets <- ifelse(is.factor(dataFrame$subset),
length(levels(dataFrame$subset)), length(unique(na.omit(dataFrame$subset)))
)
numberOfGroups <- ifelse(is.factor(dataFrame$group),
length(levels(dataFrame$group)), length(unique(na.omit(dataFrame$group)))
)
if (numberOfSubsets <= 1) {
df <- data.frame(stage = 1:.getNumberOfStages(dataFrame))
} else {
df <- data.frame(stage = 1:(length(dataFrame$subset) / numberOfGroups))
}
for (paramName in paramNames) {
if (numberOfGroups == 1) {
df[[paramName]] <- dataFrame[[paramName]]
} else {
for (group in 1:numberOfGroups) {
varName <- paste0(paramName, group)
values <- dataFrame[[paramName]][dataFrame$group == group]
df[[varName]] <- values
}
}
}
if (numberOfSubsets > 1) {
stages <- dataFrame$stage[dataFrame$group == 1]
df$stage <- stages # sort(rep(stages, multiplier))
subsets <- dataFrame$subset[dataFrame$group == 1]
if (nrow(df) != length(subsets)) {
stop(C_EXCEPTION_TYPE_RUNTIME_ISSUE, "something went wrong: ", nrow(df), " != ", length(subsets))
}
df$subset <- subsets
df <- .moveColumn(df, "subset", "stage")
# df <- df[with(data.frame(subset = df$subset, index = as.integer(sub("\\D", "", df$subset))), order(index)), ]
}
return(df)
}
#'
#' @title
#' Get Long Format
#'
#' @description
#' Returns the specified dataset as a \code{\link[base]{data.frame}} in so-called long format.
#'
#' @details
#' In the long format (narrow, stacked), the data are presented with one column containing
#' all the values and another column listing the context of the value, i.e.,
#' the data for the different groups are in one column and the dataset contains an additional "group" column.
#'
#' @seealso
#' \code{\link[=getWideFormat]{getWideFormat()}} for returning the dataset as a \code{\link[base]{data.frame}} in wide format.
#'
#' @return A \code{\link[base]{data.frame}} will be returned.
#'
#' @keywords internal
#'
#' @export
#'
getLongFormat <- function(dataInput) {
.assertIsDataset(dataInput)
return(as.data.frame(dataInput, niceColumnNamesEnabled = FALSE))
}
.setConditionalPowerArguments <- function(results, dataInput, nPlanned, allocationRatioPlanned) {
.assertIsAnalysisResults(results)
.setNPlanned(results, nPlanned)
numberOfGroups <- dataInput$getNumberOfGroups()
.assertIsValidAllocationRatioPlanned(allocationRatioPlanned, numberOfGroups)
if (!.isConditionalPowerEnabled(nPlanned) || numberOfGroups == 1) {
if (numberOfGroups == 1) {
if (length(allocationRatioPlanned) == 1 && !identical(allocationRatioPlanned, 1)) {
warning("'allocationRatioPlanned' (", allocationRatioPlanned, ") ",
"will be ignored because the specified data has only one group",
call. = FALSE
)
}
} else if (!identical(allocationRatioPlanned, C_ALLOCATION_RATIO_DEFAULT)) {
warning("'allocationRatioPlanned' (", allocationRatioPlanned, ") ",
"will be ignored because 'nPlanned' is not defined",
call. = FALSE
)
}
results$.setParameterType("allocationRatioPlanned", C_PARAM_NOT_APPLICABLE)
return(invisible(results))
}
.setValueAndParameterType(results, "allocationRatioPlanned", allocationRatioPlanned, C_ALLOCATION_RATIO_DEFAULT)
return(invisible(results))
}
.getRecalculatedInformationRates <- function(dataInput, maxInformation, stage = NA_integer_) {
.assertIsSingleInteger(stage, "stage", naAllowed = TRUE, validateType = FALSE)
stageFromData <- dataInput$getNumberOfStages()
if (is.null(stage) || is.na(stage) || stage > stageFromData) {
stage <- stageFromData
}
informationRates <- rep(NA_real_, stage)
absoluteInformations <- rep(NA_real_, stage)
if (.isDatasetMeans(dataInput) || .isDatasetRates(dataInput)) {
for (k in 1:stage) {
sampleSizes <- dataInput$getOverallSampleSizes(stage = k)
absoluteInformations[k] <- sum(sampleSizes, na.rm = TRUE)
informationRates[k] <- absoluteInformations[k] / maxInformation
}
} else if (.isDatasetSurvival(dataInput)) {
for (k in 1:stage) {
events <- dataInput$getOverallEvents(stage = k)
absoluteInformations[k] <- sum(events, na.rm = TRUE)
informationRates[k] <- absoluteInformations[k] / maxInformation
}
} else {
stop(C_EXCEPTION_TYPE_RUNTIME_ISSUE, "'dataInput' class ", .getClassName(dataInput), " is not supported")
}