Nothing
## |
## | *Constants*
## |
## | 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: 7126 $
## | Last changed: $Date: 2023-06-23 14:26:39 +0200 (Fr, 23 Jun 2023) $
## | Last changed by: $Author: pahlke $
## |
#' @include f_core_utilities.R
NULL
C_LOG_LEVEL_TRACE <- "TRACE"
C_LOG_LEVEL_DEBUG <- "DEBUG"
C_LOG_LEVEL_INFO <- "INFO"
C_LOG_LEVEL_WARN <- "WARN"
C_LOG_LEVEL_ERROR <- "ERROR"
C_LOG_LEVEL_PROGRESS <- "PROGRESS"
C_LOG_LEVEL_DISABLED <- "DISABLED"
C_SUMMARY_OUTPUT_SIZE_DEFAULT <- "large"
C_SUMMARY_LIST_ITEM_PREFIX_DEFAULT <- " "
# used in 'class_core_plot_settings.R'
C_POSITION_OUTSIDE_PLOT <- 0
C_POSITION_LEFT_TOP <- 1
C_POSITION_LEFT_CENTER <- 2
C_POSITION_LEFT_BOTTOM <- 3
C_POSITION_RIGHT_TOP <- 4
C_POSITION_RIGHT_CENTER <- 5
C_POSITION_RIGHT_BOTTOM <- 6
C_DESIGN_TOLERANCE_DEFAULT <- 1e-08
C_CONST_NEWTON_COTES <- 15
C_TWO_SIDED_POWER_DEFAULT <- FALSE
C_BINDING_FUTILITY_DEFAULT <- FALSE
C_BINDING_FUTILITY_FISHER_DEFAULT <- TRUE
C_CONST_BOUND_HP_DEFAULT <- 3
C_ALPHA_DEFAULT <- 0.025
C_BETA_DEFAULT <- 0.2
C_SIDED_DEFAULT <- 1L
C_KMAX_DEFAULT <- 3L
C_KMAX_UPPER_BOUND <- 20L
C_KMAX_UPPER_BOUND_FISHER <- 6L
C_NA_MAX_DEFAULT <- 100L
C_POWER_ASN_THETA_DEFAULT <- seq(-1, 1, 0.02)
C_ANALYSIS_TOLERANCE_DEFAULT <- 1e-06
C_ANALYSIS_TOLERANCE_FISHER_DEFAULT <- 1e-14
C_UPPER_BOUNDS_DEFAULT <- 8
C_FUTILITY_BOUNDS_DEFAULT <- -6
C_ALPHA_0_VEC_DEFAULT <- 1
C_THETA_H0_MEANS_DEFAULT <- 0
C_THETA_H0_RATES_DEFAULT <- 0
C_THETA_H0_SURVIVAL_DEFAULT <- 1
C_ALLOCATION_RATIO_DEFAULT <- 1
C_ALLOCATION_RATIO_MAXIMUM <- 100
C_DIRECTION_UPPER_DEFAULT <- TRUE
C_NORMAL_APPROXIMATION_MEANS_DEFAULT <- FALSE
C_NORMAL_APPROXIMATION_RATES_DEFAULT <- TRUE
C_EQUAL_VARIANCES_DEFAULT <- TRUE
C_ITERATIONS_DEFAULT <- 1000L
C_ACCEPT_DEVIATION_INFORMATIONRATES <- 0.05
C_THETA_RANGE_SEQUENCE_LENGTH_DEFAULT <- 50
C_VARIED_PARAMETER_SEQUENCE_LENGTH_DEFAULT <- 30
C_CLASS_NAME_TRIAL_DESIGN_GROUP_SEQUENTIAL <- "TrialDesignGroupSequential"
C_CLASS_NAME_TRIAL_DESIGN_INVERSE_NORMAL <- "TrialDesignInverseNormal"
C_CLASS_NAME_TRIAL_DESIGN_FISHER <- "TrialDesignFisher"
C_CLASS_NAME_TRIAL_DESIGN_CONDITIONAL_DUNNETT <- "TrialDesignConditionalDunnett"
.getTrialDesignClassNames <- function(inclusiveConditionalDunnett = TRUE) {
trialDesignClassNames <- c(
C_CLASS_NAME_TRIAL_DESIGN_GROUP_SEQUENTIAL,
C_CLASS_NAME_TRIAL_DESIGN_INVERSE_NORMAL,
C_CLASS_NAME_TRIAL_DESIGN_FISHER
)
if (inclusiveConditionalDunnett) {
trialDesignClassNames <- c(trialDesignClassNames, C_CLASS_NAME_TRIAL_DESIGN_CONDITIONAL_DUNNETT)
}
return(trialDesignClassNames)
}
C_EXCEPTION_TYPE_RUNTIME_ISSUE <- "Runtime exception: "
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT <- "Illegal argument: "
C_EXCEPTION_TYPE_ILLEGAL_DATA_INPUT <- "Illegal data input: "
C_EXCEPTION_TYPE_CONFLICTING_ARGUMENTS <- "Conflicting arguments: "
C_EXCEPTION_TYPE_ARGUMENT_OUT_OF_BOUNDS <- "Argument out of bounds: "
C_EXCEPTION_TYPE_ARGUMENT_LENGTH_OUT_OF_BOUNDS <- "Argument length out of bounds: "
C_EXCEPTION_TYPE_INDEX_OUT_OF_BOUNDS <- "Index out of bounds: "
C_EXCEPTION_TYPE_MISSING_ARGUMENT <- "Missing argument: "
C_EXCEPTION_TYPE_INCOMPLETE_ARGUMENTS <- "Incomplete associated arguments: "
C_DIRECTION_LOWER <- "lower"
C_DIRECTION_UPPER <- "upper"
C_QNORM_EPSILON <- 1e-100 # a value between 1e-323 and 1e-16
C_QNORM_MAXIMUM <- -stats::qnorm(C_QNORM_EPSILON)
C_QNORM_MINIMUM <- -C_QNORM_MAXIMUM
C_QNORM_THRESHOLD <- floor(C_QNORM_MAXIMUM)
#
# Constants used in 'f_analysis_multiarm' and 'f_analysis_enrichment'
#
C_INTERSECTION_TEST_MULTIARMED_DEFAULT <- "Dunnett"
C_INTERSECTION_TEST_ENRICHMENT_DEFAULT <- "Simes"
C_INTERSECTION_TESTS_MULTIARMED <- c(
"Bonferroni",
"Simes",
"Sidak",
"Dunnett",
"Hierarchical"
)
C_INTERSECTION_TESTS_ENRICHMENT <- c(
"Bonferroni",
"Simes",
"Sidak",
"SpiessensDebois"
)
C_VARIANCE_OPTION_DUNNETT <- "overallPooled"
C_VARIANCE_OPTION_MULTIARMED_DEFAULT <- "overallPooled"
C_VARIANCE_OPTIONS_MULTIARMED <- c("overallPooled", "pairwisePooled", "notPooled")
C_VARIANCE_OPTION_ENRICHMENT_DEFAULT <- "pooled"
C_VARIANCE_OPTIONS_ENRICHMENT <- c("pooled", "notPooled", "pooledFromFull")
C_STRATIFIED_ANALYSIS_DEFAULT <- TRUE
#
# Constants used in 'parameters.R'
#
C_PARAM_USER_DEFINED <- "u"
C_PARAM_DEFAULT_VALUE <- "d"
C_PARAM_GENERATED <- "g"
C_PARAM_DERIVED <- ">"
C_PARAM_NOT_APPLICABLE <- "."
C_PARAM_TYPE_UNKNOWN <- "?"
#
# Constants used in 'f_simulation_survival.R'
#
C_PI_2_DEFAULT <- 0.2
C_PI_1_DEFAULT <- seq(0.2, 0.5, 0.1)
C_PI_1_SAMPLE_SIZE_DEFAULT <- c(0.4, 0.5, 0.6)
C_DROP_OUT_RATE_1_DEFAULT <- 0
C_DROP_OUT_RATE_2_DEFAULT <- 0
C_DROP_OUT_TIME_DEFAULT <- 12
C_EVENT_TIME_DEFAULT <- 12
C_ALLOCATION_1_DEFAULT <- 1
C_ALLOCATION_2_DEFAULT <- 1
C_MAX_ITERATIONS_DEFAULT <- 10L
C_MAX_SIMULATION_ITERATIONS_DEFAULT <- 1000L
C_ACCRUAL_TIME_DEFAULT <- c(0, 12)
C_ACCRUAL_INTENSITY_DEFAULT <- 0.1
C_FOLLOW_UP_TIME_DEFAULT <- 6
#
# Constants used in 'f_simulation_multiarm[...].R'
#
C_ACTIVE_ARMS_DEFAULT <- 3L
C_POPULATIONS_DEFAULT <- 3L
C_TYPES_OF_SELECTION <- c("best", "rBest", "epsilon", "all", "userDefined")
C_TYPE_OF_SELECTION_DEFAULT <- C_TYPES_OF_SELECTION[1]
C_TYPES_OF_SHAPE <- c("linear", "sigmoidEmax", "userDefined")
C_TYPE_OF_SHAPE_DEFAULT <- C_TYPES_OF_SHAPE[1]
C_SUCCESS_CRITERIONS <- c("all", "atLeastOne")
C_SUCCESS_CRITERION_DEFAULT <- C_SUCCESS_CRITERIONS[1]
C_EFFECT_MEASURES <- c("effectEstimate", "testStatistic")
C_EFFECT_MEASURE_DEFAULT <- C_EFFECT_MEASURES[1]
#
# Additional constants used in 'f_design_sample_size_calculator.R'
#
C_ALTERNATIVE_DEFAULT <- seq(0.2, 1, 0.2)
C_ALTERNATIVE_POWER_SIMULATION_DEFAULT <- seq(0, 1, 0.2)
C_ALTERNATIVE_POWER_SIMULATION_MEAN_RATIO_DEFAULT <- seq(1, 2, 0.2)
C_RANGE_OF_HAZARD_RATIOS_DEFAULT <- seq(1, 2.6, 0.4)
C_STDEV_DEFAULT <- 1
#
# Constants used in 'core_group_sequential_design.R'
#
# Type of design is one of the following:
# O'Brien & Fleming,
# Pocock,
# Wang & Tsiatis Delta class,
# Haybittle & Peto,
# Optimum design within Wang & Tsiatis class,
# Pocock type alpha spending,
# O'Brien & Fleming type alpha spending,
# Kim & DeMets alpha spending,
# Hwang, Shi & DeCani alpha spending,
# user defined alpha spending
#
C_TYPE_OF_DESIGN_OF <- "OF" # O'Brien & Fleming
C_TYPE_OF_DESIGN_P <- "P" # Pocock,
C_TYPE_OF_DESIGN_WT <- "WT" # Wang & Tsiatis Delta class
C_TYPE_OF_DESIGN_PT <- "PT" # Pampallona & Tsiatis class
C_TYPE_OF_DESIGN_HP <- "HP" # Haybittle & Peto
C_TYPE_OF_DESIGN_WT_OPTIMUM <- "WToptimum" # Optimum design within Wang & Tsiatis class
C_TYPE_OF_DESIGN_AS_P <- "asP" # Pocock type alpha spending
C_TYPE_OF_DESIGN_AS_OF <- "asOF" # O'Brien & Fleming type alpha spending
C_TYPE_OF_DESIGN_AS_KD <- "asKD" # Kim & DeMets alpha spending
C_TYPE_OF_DESIGN_AS_HSD <- "asHSD" # Hwang, Shi & DeCani alpha spending
C_TYPE_OF_DESIGN_AS_USER <- "asUser" # user defined alpha spending
C_TYPE_OF_DESIGN_NO_EARLY_EFFICACY <- "noEarlyEfficacy" # no early efficacy stop
C_DEFAULT_TYPE_OF_DESIGN <- C_TYPE_OF_DESIGN_OF # the default type of design
C_TYPE_OF_DESIGN_LIST <- list(
"OF" = "O'Brien & Fleming",
"P" = "Pocock",
"WT" = "Wang & Tsiatis Delta class",
"PT" = "Pampallona & Tsiatis class",
"HP" = "Haybittle & Peto",
"WToptimum" = "Optimum design within Wang & Tsiatis class",
"asP" = "Pocock type alpha spending",
"asOF" = "O'Brien & Fleming type alpha spending",
"asKD" = "Kim & DeMets alpha spending",
"asHSD" = "Hwang, Shi & DeCani alpha spending",
"asUser" = "User defined alpha spending",
"noEarlyEfficacy" = "No early efficacy stop"
)
C_PLOT_SHOW_SOURCE_ARGUMENTS <- c("commands", "axes", "test", "validate")
C_PLOT_MAIN_CONDITIONAL_POWER_WITH_LIKELIHOOD <- "Conditional Power with Likelihood"
C_PLOT_YLAB_CONDITIONAL_POWER_WITH_LIKELIHOOD <- "Conditional power / Likelihood"
.getDesignTypes <- function() {
return(c(
C_TYPE_OF_DESIGN_OF,
C_TYPE_OF_DESIGN_P,
C_TYPE_OF_DESIGN_WT,
C_TYPE_OF_DESIGN_PT,
C_TYPE_OF_DESIGN_HP,
C_TYPE_OF_DESIGN_WT_OPTIMUM,
C_TYPE_OF_DESIGN_AS_P,
C_TYPE_OF_DESIGN_AS_OF,
C_TYPE_OF_DESIGN_AS_KD,
C_TYPE_OF_DESIGN_AS_HSD,
C_TYPE_OF_DESIGN_AS_USER,
C_TYPE_OF_DESIGN_NO_EARLY_EFFICACY
))
}
.printDesignTypes <- function() {
.arrayToString(.getDesignTypes(), encapsulate = TRUE)
}
.isAlphaSpendingDesignType <- function(typeOfDesign, userDefinedAlphaSpendingIncluded = TRUE) {
if (userDefinedAlphaSpendingIncluded &&
((typeOfDesign == C_TYPE_OF_DESIGN_AS_USER) || (typeOfDesign == C_TYPE_OF_DESIGN_NO_EARLY_EFFICACY))) {
return(TRUE)
}
return(typeOfDesign %in% c(
C_TYPE_OF_DESIGN_AS_P, C_TYPE_OF_DESIGN_AS_OF,
C_TYPE_OF_DESIGN_AS_KD, C_TYPE_OF_DESIGN_AS_HSD
))
}
#
# Type of beta spending design is one of the following:
# Pocock type beta spending,
# O'Brien & Fleming type beta spending,
# Kim & DeMets beta spending,
# Hwang, Shi & DeCani beta spending,
# user defined beta spending
# "none", "bsP", "bsOF", "bsKD", "bsHSD", "bsUser"
C_TYPE_OF_DESIGN_BS_NONE <- "none"
C_TYPE_OF_DESIGN_BS_P <- "bsP" # Pocock type beta spending
C_TYPE_OF_DESIGN_BS_OF <- "bsOF" # O'Brien & Fleming type beta spending
C_TYPE_OF_DESIGN_BS_KD <- "bsKD" # Kim & DeMets beta spending
C_TYPE_OF_DESIGN_BS_HSD <- "bsHSD" # Hwang, Shi & DeCani beta spending
C_TYPE_OF_DESIGN_BS_USER <- "bsUser" # user defined beta spending
C_TYPE_OF_DESIGN_BS_LIST <- list(
"none" = "none",
"bsP" = "Pocock type beta spending",
"bsOF" = "O'Brien & Fleming type beta spending",
"bsKD" = "Kim & DeMets beta spending",
"bsHSD" = "Hwang, Shi & DeCani beta spending",
"bsUser" = "user defined beta spending"
)
C_CIPHERS <- list(token = "310818669631424001", secret = "9318655074497250732")
.getBetaSpendingDesignTypes <- function() {
return(c(
C_TYPE_OF_DESIGN_BS_NONE,
C_TYPE_OF_DESIGN_BS_P,
C_TYPE_OF_DESIGN_BS_OF,
C_TYPE_OF_DESIGN_BS_KD,
C_TYPE_OF_DESIGN_BS_HSD,
C_TYPE_OF_DESIGN_BS_USER
))
}
.printBetaSpendingDesignTypes <- function() {
.arrayToString(.getBetaSpendingDesignTypes(), encapsulate = TRUE)
}
.isBetaSpendingDesignType <- function(typeOfDesign,
userDefinedBetaSpendingIncluded = TRUE, noneIncluded = FALSE) {
if (userDefinedBetaSpendingIncluded && typeOfDesign == C_TYPE_OF_DESIGN_BS_USER) {
return(TRUE)
}
if (noneIncluded && typeOfDesign == C_TYPE_OF_DESIGN_BS_NONE) {
return(TRUE)
}
return(typeOfDesign %in% c(
C_TYPE_OF_DESIGN_BS_P,
C_TYPE_OF_DESIGN_BS_OF,
C_TYPE_OF_DESIGN_BS_KD,
C_TYPE_OF_DESIGN_BS_HSD
))
}
##
## -------------------------------------------
##
C_OPTIMIZATION_CRITERION_ASNH1 <- "ASNH1"
C_OPTIMIZATION_CRITERION_ASNIFH1 <- "ASNIFH1"
C_OPTIMIZATION_CRITERION_ASN_SUM <- "ASNsum"
C_OPTIMIZATION_CRITERION_DEFAULT <- C_OPTIMIZATION_CRITERION_ASNH1
.getOptimizationCriterions <- function() {
return(c(
C_OPTIMIZATION_CRITERION_ASNH1,
C_OPTIMIZATION_CRITERION_ASNIFH1,
C_OPTIMIZATION_CRITERION_ASN_SUM
))
}
.printOptimizationCriterion <- function() {
.arrayToString(.getOptimizationCriterions(), encapsulate = TRUE)
}
.isOptimizationCriterion <- function(x) {
return(x %in% .getOptimizationCriterions())
}
##
## -------------------------------------------
##
C_FISHER_METHOD_FULL_ALPHA <- "fullAlpha"
C_FISHER_METHOD_EQUAL_ALPHA <- "equalAlpha"
C_FISHER_METHOD_NO_INTERACTION <- "noInteraction"
C_FISHER_METHOD_USER_DEFINED_ALPHA <- "userDefinedAlpha"
C_FISHER_METHOD_DEFAULT <- C_FISHER_METHOD_EQUAL_ALPHA
.getFisherMethods <- function() {
return(c(
C_FISHER_METHOD_FULL_ALPHA,
C_FISHER_METHOD_EQUAL_ALPHA,
C_FISHER_METHOD_NO_INTERACTION,
C_FISHER_METHOD_USER_DEFINED_ALPHA
))
}
.printFisherMethods <- function() {
.arrayToString(.getFisherMethods(), encapsulate = TRUE)
}
.isFisherMethod <- function(method) {
return(method %in% .getFisherMethods())
}
##
## -------------------------------------------
##
C_PARAMETER_NAMES <- list(
iterations = "Iterations",
seed = "Seed",
groups = "Treatment groups",
stages = "Stages",
sampleSizes = "Sample sizes",
means = "Means",
stDevs = "Standard deviations",
overallEvents = "Cumulative events",
overallAllocationRatios = "Cumulative allocation ratios",
expectedEvents = "Expected events",
varianceEvents = "Variance of events",
overallExpectedEvents = "Cumulative expected events",
overallVarianceEvents = "Cumulative variance of events",
bindingFutility = "Binding futility",
constantBoundsHP = "Haybittle Peto constants",
betaAdjustment = "Beta adjustment",
kMax = "Maximum number of stages",
alpha = "Significance level",
finalStage = "Final stage",
informationRates = "Information rates",
criticalValues = "Critical values",
criticalValuesDelayedInformation = "Upper bounds of continuation",
stageLevels = "Stage levels (one-sided)",
alphaSpent = "Cumulative alpha spending",
tolerance = "Tolerance",
method = "Method",
alpha0Vec = "Alpha_0",
scale = "Scale",
nonStochasticCurtailment = "Non stochastic curtailment",
simAlpha = "Simulated alpha",
beta = "Type II error rate",
betaSpent = "Cumulative beta spending",
sided = "Test",
futilityBounds = "Futility bounds (binding)",
futilityBoundsNonBinding = "Futility bounds (non-binding)",
futilityBoundsDelayedInformation = "Lower bounds of continuation (binding)",
futilityBoundsDelayedInformationNonBinding = "Lower bounds of continuation (non-binding)",
typeOfDesign = "Type of design",
deltaWT = "Delta for Wang & Tsiatis Delta class",
deltaPT0 = "Delta0 for Pampallona & Tsiatis class",
deltaPT1 = "Delta1 for Pampallona & Tsiatis class",
optimizationCriterion = "Optimization criterion for optimum design within Wang & Tsiatis class",
gammaA = "Parameter for alpha spending function",
gammaB = "Parameter for beta spending function",
typeBetaSpending = "Type of beta spending",
userAlphaSpending = "User defined alpha spending",
userBetaSpending = "User defined beta spending",
probs = "Exit probabilities",
power = "Power",
theta = "Effect",
direction = "Direction",
normalApproximation = "Normal approximation",
equalVariances = "Equal variances",
shift = "Shift",
inflationFactor = "Inflation factor",
information = "Informations",
rejectionProbabilities = "Rejection probabilities under H1",
futilityProbabilities = "Futility probabilities under H1",
averageSampleNumber1 = "Ratio expected vs fixed sample size under H1",
averageSampleNumber01 = "Ratio expected vs fixed sample size under a value between H0 and H1",
averageSampleNumber0 = "Ratio expected vs fixed sample size under H0",
allocationRatioPlanned = "Planned allocation ratio",
thetaH0 = "Theta H0",
thetaH1 = "Assumed effect under alternative",
stDevH1 = "Assumed standard deviation under alternative",
assumedStDev = "Assumed standard deviation",
assumedStDevs = "Assumed standard deviations",
pi1 = "Assumed treatment rate",
pi2 = "Assumed control rate",
overallPi1 = "Cumulative treatment rate",
overallPi2 = "Cumulative control rate",
pi1H1 = "pi(1) under H1",
pi2H1 = "pi(2) under H1",
nPlanned = "Planned sample size",
piControl = "Assumed control rate",
piControls = "Assumed control rates",
piTreatment = "Assumed treatment rate",
piTreatments = "Assumed treatment rates",
piTreatmentH1 = "pi(treatment) under H1",
piTreatmentsH1 = "pi(treatment) under H1",
overallPiControl = "Cumulative control rate",
overallPiTreatments = "Cumulative treatment rate",
overallPisControl = "Cumulative control rate",
overallPisTreatment = "Cumulative treatment rate",
effectSizes = "Cumulative effect sizes",
testStatistics = "Stage-wise test statistics",
pValues = "Stage-wise p-values",
testActions = "Actions",
conditionalPower = "Conditional power",
conditionalPowerAchieved = "Conditional power (achieved)",
conditionalPowerSimulated = "Conditional power (simulated)",
conditionalRejectionProbabilities = "Conditional rejection probability",
repeatedConfidenceIntervalLowerBounds = "Repeated confidence intervals (lower)",
repeatedConfidenceIntervalUpperBounds = "Repeated confidence intervals (upper)",
repeatedPValues = "Repeated p-values",
finalPValues = "Final p-value",
finalConfidenceIntervalLowerBounds = "Final CIs (lower)",
finalConfidenceIntervalUpperBounds = "Final CIs (upper)",
medianUnbiasedEstimates = "Median unbiased estimate",
overallSampleSizes = "Cumulative sample sizes",
overallSampleSizes1 = "Cumulative sample sizes (1)",
overallSampleSizes2 = "Cumulative sample sizes (2)",
overallTestStatistics = "Overall test statistics",
overallPValues = "Overall p-values",
overallMeans = "Cumulative means",
overallMeans1 = "Cumulative means (1)",
overallMeans2 = "Cumulative means (2)",
overallStDevs1 = "Cumulative standard deviations (1)",
overallStDevs2 = "Cumulative standard deviations (2)",
overallStDevs = "Cumulative (pooled) standard deviations",
testStatistics = "Stage-wise test statistics",
combInverseNormal = "Combination test statistics", # Inverse normal combination
combFisher = "Combination test statistics", # Fisher combination
weightsFisher = "Fixed weights",
weightsInverseNormal = "Fixed weights",
overallLogRanks = "Cumulative log-ranks",
overallEvents = "Cumulative number of events",
overallEvents1 = "Cumulative number of events (1)",
overallEvents2 = "Cumulative number of events (2)",
overallAllocationRatios = "Cumulative allocation ratios",
events = "Number of events",
allocationRatios = "Allocation ratios",
logRanks = "Log-ranks",
nMax = "N_max",
averageSampleNumber = "Average sample sizes (ASN)",
calculatedPower = "Power",
earlyStop = "Early stop",
rejectPerStage = "Reject per stage",
futilityPerStage = "Futility stop per stage",
overallEarlyStop = "Early stop",
overallReject = "Overall reject",
overallFutility = "Overall futility",
riskRatio = "Risk ratio",
meanRatio = "Mean ratio",
alternative = "Alternatives",
stDev = "Standard deviation",
nFixed = "Number of subjects fixed",
nFixed1 = "Number of subjects fixed (1)",
nFixed2 = "Number of subjects fixed (2)",
maxNumberOfSubjects = "Maximum number of subjects",
maxNumberOfSubjects1 = "Maximum number of subjects (1)",
maxNumberOfSubjects2 = "Maximum number of subjects (2)",
numberOfSubjects = "Number of subjects",
numberOfSubjects1 = "Number of subjects (1)",
numberOfSubjects2 = "Number of subjects (2)",
expectedNumberOfSubjectsH0 = "Expected number of subjects under H0",
expectedNumberOfSubjectsH01 = "Expected number of subjects under H0/H1",
expectedNumberOfSubjectsH1 = "Expected number of subjects under H1",
expectedNumberOfSubjects = "Expected number of subjects",
chi = "Probability of an event",
hazardRatio = "Hazard ratio",
hazardRatios = "Hazard ratios",
typeOfComputation = "Type of computation",
accountForObservationTimes = "Account for observation times",
eventTime = "Event time",
accrualTime = "Accrual time",
totalAccrualTime = "Total accrual time",
remainingTime = "Remaining time",
followUpTime = "Follow up time",
dropoutRate1 = "Drop-out rate (1)",
dropoutRate2 = "Drop-out rate (2)",
dropoutTime = "Drop-out time",
eventsFixed = "Number of events fixed",
expectedEventsH0 = "Expected number of events under H0",
expectedEventsH01 = "Expected number of events under H0/H1",
expectedEventsH1 = "Expected number of events under H1",
analysisTime = "Analysis times",
studyDurationH1 = "Expected study duration under H1",
expectedNumberOfSubjectsH1 = "Expected number of subjects under H1",
twoSidedPower = "Two-sided power",
plannedEvents = "Planned cumulative events",
plannedSubjects = "Planned cumulative subjects", # per arm (multi-arm); overall (base)
minNumberOfEventsPerStage = "Minimum number of events per stage",
maxNumberOfEventsPerStage = "Maximum number of events per stage",
minNumberOfSubjectsPerStage = "Minimum number of subjects per stage",
maxNumberOfSubjectsPerStage = "Maximum number of subjects per stage",
accrualIntensity = "Accrual intensity",
accrualIntensityRelative = "Accrual intensity (relative)",
maxNumberOfIterations = "Maximum number of iterations",
allocation1 = "Allocation 1",
allocation2 = "Allocation 2",
expectedNumberOfEvents = "Expected number of events",
expectedNumberOfEventsPerStage = "Expected number of events by stage",
eventsNotAchieved = "Events not achieved",
subjects = "Subjects",
overallReject = "Overall reject",
futilityStop = "Overall futility stop",
studyDuration = "Expected study duration",
maxStudyDuration = "Maximal study duration",
directionUpper = "Direction upper",
piecewiseSurvivalTime = "Piecewise survival times",
lambda1 = "lambda(1)",
lambda2 = "lambda(2)",
kappa = "kappa",
earlyStopPerStage = "Early stop per stage",
effect = "Effect",
maxNumberOfEvents = "Maximum number of events",
criticalValuesEffectScale = "Critical values (treatment effect scale)",
criticalValuesEffectScaleDelayedInformation = "Upper bounds of continuation (treatment effect scale)",
criticalValuesEffectScaleLower = "Lower critical values (treatment effect scale)",
criticalValuesEffectScaleUpper = "Upper critical values (treatment effect scale)",
criticalValuesPValueScale = "Local one-sided significance levels",
".design$stageLevels" = "Local one-sided significance levels",
futilityBoundsEffectScale = "Futility bounds (treatment effect scale)",
futilityBoundsEffectScaleDelayedInformation = "Lower bounds of continuation (treatment effect scale)",
futilityBoundsEffectScaleLower = "Lower futility bounds (treatment effect scale)",
futilityBoundsEffectScaleUpper = "Upper futility bounds (treatment effect scale)",
futilityBoundsPValueScale = "Futility bounds (one-sided p-value scale)",
futilityBoundsPValueScaleDelayedInformation = "Lower bounds of continuation (one-sided p-value scale)",
analysisTime = "Analysis time",
eventsPerStage1 = "Observed # events by stage (1)",
eventsPerStage2 = "Observed # events by stage (2)",
testStatistic = "Test statistic",
logRankStatistic = "Log-rank statistic",
hazardRatioEstimateLR = "Hazard ratio estimate LR",
delayedResponseAllowed = "Delayed response allowed",
delayedResponseEnabled = "Delayed response enabled",
piecewiseSurvivalEnabled = "Piecewise exponential survival enabled",
median1 = "median(1)",
median2 = "median(2)",
eventsPerStage = "Number of events per stage",
overallEventsPerStage = "Cumulative number of events",
expectedNumberOfEvents = "Observed number of events",
expectedNumberOfSubjects = "Observed number of subjects",
singleNumberOfEventsPerStage = "Single number of events",
endOfAccrualIsUserDefined = "End of accrual is user defined",
followUpTimeMustBeUserDefined = "Follow-up time must be user defined",
maxNumberOfSubjectsIsUserDefined = "Max number of subjects is user defined",
maxNumberOfSubjectsCanBeCalculatedDirectly = "Max number of subjects can be calculated directly",
absoluteAccrualIntensityEnabled = "Absolute accrual intensity is enabled",
time = "Time",
cumulativeEventProbabilities = "Cumulative event probabilities",
eventProbabilities1 = "Event probabilities (1)",
eventProbabilities2 = "Event probabilities (2)",
informationAtInterim = "Information at interim",
secondStageConditioning = "Conditional second stage p-values",
separatePValues = "Separate p-values",
singleStepAdjustedPValues = "Single step adjusted p-values",
intersectionTest = "Intersection test",
varianceOption = "Variance option",
overallPooledStDevs = "Cumulative (pooled) standard deviations",
optimumAllocationRatio = "Optimum allocation ratio",
rejected = "Rejected",
indices = "Indices of hypothesis",
adjustedStageWisePValues = "Adjusted stage-wise p-values",
overallAdjustedTestStatistics = "Overall adjusted test statistics",
rejectedIntersections = "Rejected intersections",
conditionalErrorRate = "Conditional error rate",
secondStagePValues = "Second stage p-values",
effectMatrix = "Effect matrix",
typeOfShape = "Type of shape",
gED50 = "ED50",
slope = "Slope",
adaptations = "Adaptations",
typeOfSelection = "Type of selection",
effectMeasure = "Effect measure",
successCriterion = "Success criterion",
epsilonValue = "Epsilon value",
rValue = "r value",
threshold = "Threshold",
rejectAtLeastOne = "Reject at least one",
selectedArms = "Selected arms",
rejectedArmsPerStage = "Rejected arms per stage",
selectedPopulations = "Selected populations",
rejectedPopulationsPerStage = "Rejected populations per stage",
successPerStage = "Success per stage",
effectEstimate = "Effect estimate",
subjectsControlArm = "Subjects (control arm)",
subjectsActiveArm = "Subjects (active arm)",
pValue = "p-value",
conditionalCriticalValue = "Conditional critical value",
piControlH1 = "pi(control) under H1",
piMaxVector = "pi_max",
omegaMaxVector = "omega_max",
muMaxVector = "mu_max",
activeArms = "Active arms",
populations = "Populations",
numberOfEvents = "Number of events",
calcSubjectsFunction = "Calculate subjects function",
calcEventsFunction = "Calculate events function",
selectArmsFunction = "Select arms function",
numberOfActiveArms = "Number of active arms",
selectPopulationsFunction = "Select populations function",
numberOfPopulations = "Number of populations",
correlationComputation = "Correlation computation method",
subsets = "Subsets",
subset = "Subset",
stratifiedAnalysis = "Stratified analysis",
maxInformation = "Maximum information",
informationEpsilon = "Information epsilon",
effectList = "Effect list",
subGroups = "Sub-groups",
prevalences = "Prevalences",
effects = "Effects",
situation = "Situation",
delayedInformation = "Delayed information",
decisionCriticalValues = "Decision critical values",
reversalProbabilities = "Reversal probabilities",
locationSampleSize = "Location sample sizes",
variationSampleSize = "Variation sample sizes",
subscoreSampleSize = "Sub-score sample sizes",
locationConditionalPower = "Location conditional power",
variationConditionalPower = "Variation conditional power",
subscoreConditionalPower = "Sub-score conditional power",
performanceScore = "Performance scores"
)
C_TABLE_COLUMN_NAMES <- list(
iterations = "Iterations",
seed = "Seed",
groups = "Treatment group",
stages = "Stage",
sampleSizes = "Sample size",
means = "Mean",
stDevs = "Standard deviation",
overallEvents = "Cumulative event",
overallAllocationRatios = "Cumulative allocation ratio",
overallMeans = "Cumulative mean",
expectedEvents = "Expected event",
varianceEvents = "Variance of event",
overallExpectedEvents = "Cumulative expected event",
overallVarianceEvents = "Cumulative variance of event",
bindingFutility = "Binding futility",
constantBoundsHP = "Haybittle Peto constant",
betaAdjustment = "Beta adjustment",
kMax = "Maximum # stages",
alpha = "Significance level",
finalStage = "Final stage",
informationRates = "Information rate",
criticalValues = "Critical value",
criticalValuesDelayedInformation = "Upper bounds of continuation",
stageLevels = "Stage level",
alphaSpent = "Cumulative alpha spending",
tolerance = "Tolerance",
method = "Method",
alpha0Vec = "Alpha_0",
scale = "Scale",
nonStochasticCurtailment = "Non stochastic curtailment",
simAlpha = "Simulated alpha",
beta = "Type II error rate",
betaSpent = "Cumulative beta spending",
sided = "Test",
futilityBounds = "Futility bound (binding)",
futilityBoundsNonBinding = "Futility bound (non-binding)",
futilityBoundsDelayedInformation = "Lower bounds of continuation (binding)",
futilityBoundsDelayedInformationNonBinding = "Lower bounds of continuation (non-binding)",
typeOfDesign = "Type of design",
deltaWT = "Delta (Wang & Tsiatis)",
deltaPT0 = "Delta0 (Pampallona & Tsiatis)",
deltaPT1 = "Delta1 (Pampallona & Tsiatis)",
optimizationCriterion = "Optimization criterion (Wang & Tsiatis)",
gammaA = "Parameter for alpha spending function",
gammaB = "Parameter for beta spending function",
typeBetaSpending = "Type of beta spending",
userAlphaSpending = "User defined alpha spending",
userBetaSpending = "User defined beta spending",
probs = "Internal calculation probabilities",
power = "Power",
theta = "Effect",
direction = "Direction",
normalApproximation = "Normal approximation",
equalVariances = "Equal variance",
assumedStDev = "Assumed standard deviation",
assumedStDevs = "Assumed standard deviation",
stDevH1 = "Assumed standard deviation under H1",
shift = "Shift",
inflationFactor = "Inflation factor",
information = "Information",
rejectionProbabilities = "Rejection probability under H1",
futilityProbabilities = "Futility probability under H1",
averageSampleNumber1 = "Ratio expected vs fixed sample size under H1",
averageSampleNumber01 = "Ratio expected vs fixed sample size under a value between H0 and H1",
averageSampleNumber0 = "Ratio expected vs fixed sample size under H0",
allocationRatioPlanned = "Planned allocation ratio",
thetaH0 = "Theta H0", # Effect
thetaH1 = "Assumed effect",
pi1 = "pi(1)",
pi2 = "pi(2)",
pi1H1 = "pi(1) under H1",
pi2H1 = "pi(2) under H1",
nPlanned = "Planned sample size",
piControl = "Assumed control rate",
piControls = "Assumed control rates",
piTreatment = "Assumed treatment rate",
piTreatments = "Assumed treatment rates",
piTreatmentH1 = "pi(treatment) under H1",
piTreatmentsH1 = "pi(treatment) under H1",
overallPiControl = "Cumulative control rate",
overallPiTreatments = "Cumulative treatment rate",
overallPisControl = "Cumulative control rate",
overallPisTreatment = "Cumulative treatment rate",
stages = "Stage",
effectSizes = "Overall effect size",
testStatistics = "Stage-wise test statistic",
pValues = "p-value",
testActions = "Action",
conditionalPower = "Conditional power",
conditionalPowerAchieved = "Conditional power (achieved)",
conditionalPowerSimulated = "Conditional power (simulated)",
conditionalRejectionProbabilities = "Conditional rejection probabilities",
repeatedConfidenceIntervalLowerBounds = "Repeated confidence interval (lower)",
repeatedConfidenceIntervalUpperBounds = "Repeated confidence interval (upper)",
repeatedPValues = "Repeated p-value",
finalPValues = "Final p-value",
finalConfidenceIntervalLowerBounds = "Final CI (lower)",
finalConfidenceIntervalUpperBounds = "Final CI (upper)",
medianUnbiasedEstimates = "Median unbiased estimate",
overallSampleSizes = "Cumulative sample size",
overallSampleSizes1 = "Cumulative sample size (1)",
overallSampleSizes2 = "Cumulative sample size (2)",
overallTestStatistics = "Overall test statistic",
overallPValues = "Overall p-value",
overallMeans1 = "Cumulative mean (1)",
overallMeans2 = "Cumulative mean (2)",
overallStDevs1 = "Cumulative standard deviation (1)",
overallStDevs2 = "Cumulative standard deviation (2)",
overallStDevs = "Cumulative (pooled) standard deviation",
testStatistics = "Test statistic",
combInverseNormal = "Inverse Normal Combination",
combFisher = "Fisher Combination",
weightsFisher = "Fixed weight",
weightsInverseNormal = "Fixed weight",
overallLogRanks = "Cumulative log-rank",
overallEvents = "Cumulative # events",
overallEvents1 = "Cumulative # events (1)",
overallEvents2 = "Cumulative # events (2)",
overallAllocationRatios = "Cumulative allocation ratio",
events = "# events",
allocationRatios = "Allocation ratio",
logRanks = "Log-rank",
nMax = "N_max",
averageSampleNumber = "Average sample size (ASN)",
calculatedPower = "Power",
earlyStop = "Early stop",
rejectPerStage = "Reject per stage",
futilityPerStage = "Futility stop per stage",
overallEarlyStop = "Early stop",
overallReject = "Overall reject",
overallFutility = "Overall futility",
riskRatio = "Risk ratio",
meanRatio = "Mean ratio",
alternative = "Alternative",
stDev = "Standard deviation",
nFixed = "# subjects fixed",
nFixed1 = "# subjects fixed (1)",
nFixed2 = "# subjects fixed (2)",
maxNumberOfSubjects = "Max # subjects",
maxNumberOfSubjects1 = "Max # subjects (1)",
maxNumberOfSubjects2 = "Max # subjects (2)",
numberOfSubjects = "# subjects",
numberOfSubjects1 = "# subjects (1)",
numberOfSubjects2 = "# subjects (2)",
expectedNumberOfSubjectsH0 = "Expected # subjects under H0",
expectedNumberOfSubjectsH01 = "Expected # subjects under H0/H1",
expectedNumberOfSubjectsH1 = "Expected # subjects under H1",
expectedNumberOfSubjects = "Expected # subjects",
chi = "Probability of an event",
hazardRatio = "Hazard ratio",
hazardRatios = "Hazard ratios",
typeOfComputation = "Type of computation",
accountForObservationTimes = "Account for observation times",
eventTime = "Event time",
accrualTime = "Accrual time",
totalAccrualTime = "Total accrual time",
remainingTime = "Remaining time",
followUpTime = "Follow up time",
dropoutRate1 = "Drop-out rate (1)",
dropoutRate2 = "Drop-out rate (2)",
dropoutTime = "Drop-out time",
eventsFixed = "# events fixed",
expectedEventsH0 = "Expected # events under H0",
expectedEventsH01 = "Expected # events under H0/H1",
expectedEventsH1 = "Expected # events under H1",
analysisTime = "Analysis time",
eventsPerStage1 = "Observed # events by stage (1)",
eventsPerStage2 = "Observed # events by stage (2)",
studyDurationH1 = "Expected study duration H1",
expectedNumberOfSubjectsH1 = "Expected # subjects H1",
twoSidedPower = "Two-sided power",
plannedEvents = "Planned cumulative events",
plannedSubjects = "Planned cumulative subjects",
minNumberOfEventsPerStage = "Minimum # events per stage",
maxNumberOfEventsPerStage = "Maximum # events per stage",
minNumberOfSubjectsPerStage = "Minimum # of subjects per stage",
maxNumberOfSubjectsPerStage = "Maximum # of subjects per stage",
accrualIntensity = "Accrual intensity",
accrualIntensityRelative = "Accrual intensity (relative)",
maxNumberOfIterations = "Maximum # iterations",
allocation1 = "Allocation 1",
allocation2 = "Allocation 2",
expectedNumberOfEvents = "Expected # events",
expectedNumberOfEventsPerStage = "Expected # events by stage",
eventsNotAchieved = "Events not achieved",
subjects = "Subjects",
futilityStop = "Overall futility stop",
studyDuration = "Expected study duration",
maxStudyDuration = "Maximal study duration",
directionUpper = "Direction upper",
piecewiseSurvivalTime = "Piecewise survival times",
lambda1 = "lambda(1)",
lambda2 = "lambda(2)",
kappa = "kappa",
earlyStopPerStage = "Early stop per stage",
effect = "Effect",
maxNumberOfEvents = "Maximum # events",
criticalValuesEffectScale = "Critical value (treatment effect scale)",
criticalValuesEffectScaleDelayedInformation = "Upper bound of continuation (treatment effect scale)",
criticalValuesEffectScaleLower = "Lower critical value (treatment effect scale)",
criticalValuesEffectScaleUpper = "Upper critical value (treatment effect scale)",
criticalValuesPValueScale = "Local one-sided significance level",
".design$stageLevels" = "Local one-sided significance level",
futilityBoundsEffectScale = "Futility bound (treatment effect scale)",
futilityBoundsEffectScaleDelayedInformation = "Lower bounds of continuation (treatment effect scale)",
futilityBoundsEffectScaleLower = "Lower futility bound (treatment effect scale)",
futilityBoundsEffectScaleUpper = "Upper futility bound (treatment effect scale)",
futilityBoundsPValueScale = "Futility bound (one-sided p-value scale)",
futilityBoundsPValueScaleDelayedInformation = "Lower bound of continuation (one-sided p-value scale)",
delayedResponseAllowed = "Delayed response allowed",
delayedResponseEnabled = "Delayed response enabled",
piecewiseSurvivalEnabled = "Piecewise exponential survival enabled",
median1 = "median(1)",
median2 = "median(2)",
eventsPerStage = "Cumulative # events",
eventsPerStage = "# events per stage",
overallEventsPerStage = "Cumulative # events",
expectedNumberOfEvents = "Observed # events",
expectedNumberOfSubjects = "Observed # subjects",
singleNumberOfEventsPerStage = "Single # events",
endOfAccrualIsUserDefined = "End of accrual is user defined",
followUpTimeMustBeUserDefined = "Follow-up time must be user defined",
maxNumberOfSubjectsIsUserDefined = "Max number of subjects is user defined",
maxNumberOfSubjectsCanBeCalculatedDirectly = "Max number of subjects can be calculated directly",
absoluteAccrualIntensityEnabled = "Absolute accrual intensity is enabled",
time = "Time",
cumulativeEventProbabilities = "Cumulative event probability",
eventProbabilities1 = "Event probability (1)",
eventProbabilities2 = "Event probability (2)",
informationAtInterim = "Information at interim",
secondStageConditioning = "Conditional second stage p-value",
separatePValues = "Separate p-value",
singleStepAdjustedPValues = "Single step adjusted p-value",
intersectionTest = "Intersection test",
varianceOption = "Variance option",
overallPooledStDevs = "Cumulative (pooled) standard deviation",
optimumAllocationRatio = "Optimum allocation ratio",
rejected = "Rejected",
indices = "Indices of hypothesis",
adjustedStageWisePValues = "Adjusted stage-wise p-value",
overallAdjustedTestStatistics = "Overall adjusted test statistics",
rejectedIntersections = "Rejected intersection",
conditionalErrorRate = "Conditional error rate",
secondStagePValues = "Second stage p-value",
effectMatrix = "Effect matrix",
typeOfShape = "Type of shape",
gED50 = "ED50",
slope = "Slope",
adaptations = "Adaptations",
typeOfSelection = "Type of selection",
effectMeasure = "Effect measure",
successCriterion = "Success criterion",
epsilonValue = "Epsilon value",
rValue = "r value",
threshold = "Threshold",
rejectAtLeastOne = "Reject at least one",
selectedArms = "Selected arm",
rejectedArmsPerStage = "Rejected arm per stage",
successPerStage = "Success per stage",
effectEstimate = "Effect estimate",
subjectsControlArm = "Subjects (control arm)",
subjectsActiveArm = "Subjects (active arm)",
pValue = "p-value",
conditionalCriticalValue = "Conditional critical value",
piControlH1 = "pi(control) under H1",
piMaxVector = "pi_max",
omegaMaxVector = "omega_max",
muMaxVector = "mu_max",
activeArms = "Active arm",
populations = "Population",
numberOfEvents = "Number of events",
calcSubjectsFunction = "Calc subjects fun",
calcEventsFunction = "Calc events fun",
selectArmsFunction = "Select arms fun",
numberOfActiveArms = "Number of active arms",
correlationComputation = "Correlation computation",
subsets = "Subset",
subset = "Subset",
stratifiedAnalysis = "Stratified analysis",
maxInformation = "Maximum information",
informationEpsilon = "Information epsilon",
effectList = "Effect list",
subGroups = "Sub-group",
prevalences = "Prevalence",
effects = "Effect",
situation = "Situation",
delayedInformation = "Delayed information",
decisionCriticalValues = "Decision critical value",
reversalProbabilities = "Reversal probability",
locationSampleSize = "Location sample size",
variationSampleSize = "Variation sample size",
subscoreSampleSize = "Sub-score sample size",
locationConditionalPower = "Location conditional power",
variationConditionalPower = "Variation conditional power",
subscoreConditionalPower = "Sub-score conditional power",
performanceScore = "Performance score"
)
.getParameterCaptions <- function(captionList, ...,
design = NULL,
designPlan = NULL,
stageResults = NULL,
analysisResults = NULL,
dataset = NULL,
designCharacteristics = NULL,
tableColumns = FALSE) {
parameterNames <- captionList
if (!is.null(design)) {
parameterNameFutilityBounds <- "futilityBounds"
if (.isDelayedInformationEnabled(design = design)) {
if (!is.na(design$bindingFutility) && !design$bindingFutility) {
parameterNameFutilityBounds <- "futilityBoundsDelayedInformationNonBinding"
} else {
parameterNameFutilityBounds <- "futilityBoundsDelayedInformation"
}
parameterNames$criticalValues <- captionList[["criticalValuesDelayedInformation"]]
parameterNames$criticalValuesEffectScale <- captionList[["criticalValuesEffectScaleDelayedInformation"]]
parameterNames$futilityBoundsEffectScale <- captionList[["futilityBoundsEffectScaleDelayedInformation"]]
parameterNames$futilityBoundsPValueScale <- captionList[["futilityBoundsPValueScaleDelayedInformation"]]
} else if (!is.na(design$bindingFutility) && !design$bindingFutility) {
parameterNameFutilityBounds <- "futilityBoundsNonBinding"
}
parameterNames$futilityBounds <- captionList[[parameterNameFutilityBounds]]
}
if (!is.null(designPlan) && inherits(designPlan, "TrialDesignPlanSurvival") &&
!is.null(designPlan$.piecewiseSurvivalTime) &&
designPlan$.piecewiseSurvivalTime$piecewiseSurvivalEnabled) {
parameterNames$lambda2 <- "Piecewise survival lambda (2)"
parameterNames$lambda1 <- "Piecewise survival lambda (1)"
}
if (!is.null(designPlan) &&
inherits(designPlan, "TrialDesignPlanSurvival") &&
identical(designPlan$.design$kMax, 1L)) {
parameterNames$maxNumberOfEvents <- "Number of events"
}
if (!is.null(designPlan) && inherits(designPlan, "TrialDesignPlan") &&
identical(designPlan$.design$kMax, 1L)) {
parameterNames$studyDuration <- "Study duration"
}
if (!is.null(analysisResults)) {
pluralExt <- ifelse(tableColumns, "", "s")
if (.isTrialDesignConditionalDunnett(analysisResults$.design)) {
parameterNames$repeatedConfidenceIntervalLowerBounds <-
paste0("Overall confidence interval", pluralExt, " (lower)")
parameterNames$repeatedConfidenceIntervalUpperBounds <-
paste0("Overall confidence interval", pluralExt, " (upper)")
parameterNames$repeatedPValues <- paste0("Overall p-value", pluralExt)
} else if (identical(analysisResults$.design$kMax, 1L)) {
parameterNames$repeatedConfidenceIntervalLowerBounds <- paste0("Confidence interval", pluralExt, " (lower)")
parameterNames$repeatedConfidenceIntervalUpperBounds <- paste0("Confidence interval", pluralExt, " (upper)")
parameterNames$repeatedPValues <- paste0("Overall p-value", pluralExt)
}
}
if (!is.null(designPlan) &&
(inherits(designPlan, "TrialDesignPlanMeans") ||
inherits(designPlan, "SimulationResultsMeans")) &&
isTRUE(designPlan$meanRatio)) {
parameterNames$stDev <- "Coefficient of variation"
}
if (!is.null(design) && .getClassName(design) != "TrialDesign" && design$sided == 2) {
parameterNames$criticalValuesPValueScale <- paste0("Local two-sided significance level", ifelse(tableColumns, "", "s"))
}
if ((!is.null(stageResults) && stageResults$isOneSampleDataset()) ||
(!is.null(dataset) && inherits(dataset, "DatasetMeans"))) {
parameterNames$overallStDevs <- paste0("Cumulative standard deviation", ifelse(tableColumns, "", "s"))
}
return(parameterNames)
}
.getParameterNames <- function(...,
design = NULL,
designPlan = NULL,
stageResults = NULL,
analysisResults = NULL,
dataset = NULL,
designCharacteristics = NULL) {
.getParameterCaptions(
captionList = C_PARAMETER_NAMES,
design = design,
designPlan = designPlan,
stageResults = stageResults,
analysisResults = analysisResults,
dataset = dataset,
designCharacteristics = designCharacteristics
)
}
.getTableColumnNames <- function(...,
design = NULL,
designPlan = NULL,
stageResults = NULL,
analysisResults = NULL,
dataset = NULL,
designCharacteristics = NULL) {
.getParameterCaptions(
captionList = C_TABLE_COLUMN_NAMES,
design = design,
designPlan = designPlan,
stageResults = stageResults,
analysisResults = analysisResults,
dataset = dataset,
designCharacteristics = designCharacteristics,
tableColumns = TRUE
)
}
C_PARAMETER_FORMAT_FUNCTIONS <- list(
means = ".formatMeans",
stDevs = ".formatStDevs",
stDev = ".formatStDevs",
thetaH0 = ".formatStDevs",
alternative = ".formatStDevs",
assumedStDev = ".formatStDevs",
assumedStDevs = ".formatStDevs",
overallAllocationRatios = ".formatRatios",
allocationRatioPlanned = ".formatRatios",
alpha = ".formatProbabilities",
beta = ".formatProbabilities",
informationRates = ".formatRates",
stageLevels = ".formatProbabilities",
alphaSpent = ".formatProbabilities",
alpha0Vec = ".formatProbabilities",
simAlpha = ".formatProbabilities",
criticalValues = ".formatCriticalValuesFisher", # will be set in class TrialDesignFisher
criticalValues = ".formatCriticalValues", # will be set in class TrialDesignGroupSequential
betaSpent = ".formatProbabilities",
futilityBounds = ".formatCriticalValues",
alpha0Vec = ".formatProbabilities",
constantBoundsHP = ".formatCriticalValues",
nMax = ".formatProbabilities",
nFixed = ".formatSampleSizes",
nFixed1 = ".formatSampleSizes",
nFixed2 = ".formatSampleSizes",
shift = ".formatProbabilities",
inflationFactor = ".formatProbabilities",
information = ".formatRates",
power = ".formatProbabilities",
rejectionProbabilities = ".formatProbabilities",
futilityProbabilities = ".formatFutilityProbabilities",
probs = ".formatProbabilities",
averageSampleNumber1 = ".formatProbabilities",
averageSampleNumber01 = ".formatProbabilities",
averageSampleNumber0 = ".formatProbabilities",
effectSizes = ".formatMeans",
thetaH1 = ".formatMeans",
stDevH1 = ".formatStDevs",
testStatistics = ".formatTestStatistics",
pValues = ".formatPValues",
conditionalPower = ".formatConditionalPower",
conditionalPowerAchieved = ".formatConditionalPower",
conditionalPowerSimulated = ".formatConditionalPower",
conditionalRejectionProbabilities = ".formatProbabilities",
repeatedConfidenceIntervalLowerBounds = ".formatMeans",
repeatedConfidenceIntervalUpperBounds = ".formatMeans",
repeatedPValues = ".formatRepeatedPValues",
finalPValues = ".formatPValues",
finalConfidenceIntervalLowerBounds = ".formatMeans",
finalConfidenceIntervalUpperBounds = ".formatMeans",
medianUnbiasedEstimates = ".formatMeans",
overallTestStatistics = ".formatTestStatistics",
overallPValues = ".formatPValues",
overallMeans = ".formatMeans",
overallMeans1 = ".formatMeans",
overallMeans2 = ".formatMeans",
overallStDevs1 = ".formatStDevs",
overallStDevs2 = ".formatStDevs",
overallStDevs = ".formatStDevs",
overallPooledStDevs = ".formatStDevs",
testStatistics = ".formatTestStatistics",
combInverseNormal = ".formatTestStatistics",
combFisher = ".formatTestStatisticsFisher",
weightsFisher = ".formatRates",
weightsInverseNormal = ".formatRates",
overallLogRanks = ".formatTestStatistics",
logRanks = ".formatTestStatistics",
theta = ".formatMeans",
averageSampleNumber = ".formatCriticalValues", # ".formatSampleSizes",
calculatedPower = ".formatProbabilities",
earlyStop = ".formatProbabilities",
rejectPerStage = ".formatProbabilities",
futilityPerStage = ".formatProbabilities",
overallEarlyStop = ".formatProbabilities",
overallReject = ".formatProbabilities",
overallFutility = ".formatProbabilities",
earlyStopPerStage = ".formatProbabilities",
effect = ".formatMeans",
maxNumberOfSubjects = ".formatSampleSizes",
maxNumberOfSubjects1 = ".formatSampleSizes",
maxNumberOfSubjects2 = ".formatSampleSizes",
maxNumberOfEvents = ".formatEvents",
numberOfSubjects = ".formatSampleSizes",
numberOfSubjects1 = ".formatSampleSizes",
numberOfSubjects2 = ".formatSampleSizes",
expectedNumberOfSubjectsH0 = ".formatSampleSizes",
expectedNumberOfSubjectsH01 = ".formatSampleSizes",
expectedNumberOfSubjectsH1 = ".formatSampleSizes",
expectedNumberOfSubjects = ".formatSampleSizes",
chi = ".formatRates",
hazardRatio = ".formatRates",
hazardRatios = ".formatRates",
pi1 = ".formatRates",
pi2 = ".formatRates",
pi1H1 = ".formatRates",
pi2H1 = ".formatRates",
piecewiseSurvivalTime = ".formatTime",
lambda2 = ".formatRates",
lambda1 = ".formatRates",
eventTime = ".formatEventTime",
accrualTime = ".formatTime",
totalAccrualTime = ".formatTime",
remainingTime = ".formatTime",
followUpTime = ".formatTime",
dropoutRate1 = ".formatRates",
dropoutRate2 = ".formatRates",
dropoutTime = ".formatTime",
eventsFixed = ".formatEvents",
expectedEventsH0 = ".formatEvents",
expectedEventsH01 = ".formatEvents",
expectedEventsH1 = ".formatEvents",
analysisTime = ".formatTime",
studyDurationH1 = ".formatDurations",
expectedNumberOfSubjectsH1 = ".formatSampleSizes",
expectedEvents = ".formatEvents",
varianceEvents = ".formatEvents",
overallExpectedEvents = ".formatEvents",
overallVarianceEvents = ".formatEvents",
events = ".formatEvents",
overallEvents = ".formatEvents",
expectedNumberOfEvents = ".formatEvents",
expectedNumberOfEventsPerStage = ".formatEvents",
eventsNotAchieved = ".formatRates",
subjects = ".formatSampleSizes",
futilityStop = ".formatProbabilities",
studyDuration = ".formatDurations",
maxStudyDuration = ".formatDurations",
criticalValuesEffectScale = ".formatCriticalValues",
criticalValuesEffectScaleLower = ".formatCriticalValues",
criticalValuesEffectScaleUpper = ".formatCriticalValues",
criticalValuesPValueScale = ".formatProbabilities",
futilityBoundsEffectScale = ".formatCriticalValues",
futilityBoundsPValueScale = ".formatProbabilities",
median1 = ".formatRatesDynamic",
median2 = ".formatRatesDynamic",
accrualIntensity = ".formatAccrualIntensities",
accrualIntensityRelative = ".formatAccrualIntensities",
eventsPerStage = ".formatEvents",
expectedNumberOfEvents = ".formatEvents",
expectedNumberOfSubjects = ".formatEvents",
singleNumberOfEventsPerStage = ".formatEvents",
time = ".formatTime",
cumulativeEventProbabilities = ".formatProbabilities",
eventProbabilities1 = ".formatProbabilities",
eventProbabilities2 = ".formatProbabilities",
informationAtInterim = ".formatRates",
separatePValues = ".formatPValues",
singleStepAdjustedPValues = ".formatPValues",
userAlphaSpending = ".formatHowItIs",
userBetaSpending = ".formatHowItIs",
piControl = ".formatRates",
piControls = ".formatRates",
piTreatment = ".formatRates",
piTreatments = ".formatRates",
piTreatmentH1 = ".formatRates",
piTreatmentsH1 = ".formatRates",
overallPiControl = ".formatRates",
overallPiTreatments = ".formatRates",
overallPisControl = ".formatRates",
overallPisTreatment = ".formatRates",
adjustedStageWisePValues = ".formatPValues",
overallAdjustedTestStatistics = ".formatTestStatisticsFisher", # will be set in class ClosedCombinationTestResults
overallAdjustedTestStatistics = ".formatTestStatistics",
conditionalErrorRate = ".formatProbabilities",
secondStagePValues = ".formatPValues",
sampleSizes = ".formatSampleSizes",
overallSampleSizes = ".formatSampleSizes",
effectMatrix = ".formatMeans",
gED50 = ".formatHowItIs",
slope = ".formatHowItIs",
epsilonValue = ".formatHowItIs",
threshold = ".formatHowItIs",
rejectAtLeastOne = ".formatProbabilities",
selectedArms = ".formatProbabilities",
rejectedArmsPerStage = ".formatProbabilities",
successPerStage = ".formatProbabilities",
effectEstimate = ".formatMeans",
subjectsControlArm = ".formatSampleSizes",
subjectsActiveArm = ".formatSampleSizes",
pValue = ".formatPValues",
conditionalCriticalValue = ".formatCriticalValues",
piControlH1 = ".formatRates",
piMaxVector = ".formatRates",
omegaMaxVector = ".formatRates",
muMaxVector = ".formatMeans",
numberOfEvents = ".formatEvents",
numberOfActiveArms = ".formatRates",
maxInformation = ".formatHowItIs",
informationEpsilon = ".formatProbabilities",
delayedInformation = ".formatRates",
decisionCriticalValues = ".formatCriticalValues",
reversalProbabilities = ".formatProbabilities",
locationSampleSize = ".formatProbabilities",
variationSampleSize = ".formatProbabilities",
subscoreSampleSize = ".formatProbabilities",
locationConditionalPower = ".formatProbabilities",
variationConditionalPower = ".formatProbabilities",
subscoreConditionalPower = ".formatProbabilities",
performanceScore = ".formatProbabilities"
)
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