Nothing
.parameterNames
and .parameterFormatFunctions
were removed from all rpact result objects in favor of a more efficient solutiongetSampleSizeSurvival()
/ getPowerSurvival()
:eventsPerStage
replaced by cumulativeEventsPerStage
singleEventsPerStage
addedgetSimulationSurvival()
: eventsPerStage
replaced by singleEventsPerStage
overallEventsPerStage
replaced by cumulativeEventsPerStage
getSimulationMultiArmSurvival()
: eventsPerStage
replaced by cumulativeEventsPerStage
singleNumberOfEventsPerStage
replaced by singleEventsPerArmAndStage
singleEventsPerStage
addedgetSimulationEnrichmentSurvival()
: singleNumberOfEventsPerStage
replaced by singleEventsPerSubsetAndStage
covr
and uploads the results to codecov.iogetSampleSizeCounts()
and getPowerCounts()
can be used to perform sample size calculations and the assessment of test characteristics for clinical trials with negative binomial distributed count data. This is possible for fixed sample size and group sequential designs. For the latter, the methodology described in Muetze et al. (2019) is implemented. These functions can also be used to perform blinded sample size reassessments according to Friede and Schmidli (2010).mvnprd
, mvstud
, as251Normal
, and as251StudentT
mnormt
dependency has been removed theta
can be used for plotting of sample size and power resultsgetPerformanceScore()
calculates the conditional performance score, its sub-scores and components according to Herrmann et al. (2020) for a given simulation result from a two-stage designallocationRatioPlanned
for simulating multi-arm and enrichment designs can be a vector of length kMax, the number of stages getObjectRCode()
(short: rcmd()
): with the new arguments pipeOperator
and output
many new output variants can be specified, e.g., the native R pipe operator or the magrittr pipe operator can be usedknitr::knit_print
for all result objects implemented and automatic code chunk option results = 'asis'
activateddf <= 500
because of erroneous results in mnormt
package otherwise. For df > 500
, multivariate normal distribution is used omega
to chi
in class TrialDesignPlanSurvival
sapply
removed from C++ code to stop deprecated warnings on r-devel-linux-x86_64-fedora-clang allocationRatioPlanned
for simulating means and rates for a two treatment groups design can be a vector of length kMax, the number of stages calcSubjectsFunction
can be used in C++ version for simulating means and ratescalcEventsFunction
added in getSimulationSurvival()getPerformanceScore()
added: calculates the performance score for simulation means results (1 and 2 groups; 2 stages)getDataset()
to enable pipe syntax for analysis, e.g.,
getDesignGroupSequential() |> getDataset(dataMeans) |> getAnalysisResults()
SystemRequirements: C++11
added to DESCRIPTION to enable C++ 11 compilation on R 3.xbetaAdjustment
can also be used in getDesignInverseNormal()
subsets
removed from result of getWideFormat()
for non-enrichment datasetspopulations
in getSimulationEnrichmentMeans()
, getSimulationEnrichmentRates()
, and getSimulationEnrichmentSurvival()
has been removed since it is always derived from effectList
getSimulationEnrichmentRates()
for calculated non-integer number of subjects getRawData()
: the resulting data.frame
now contains the correct stopStage
and lastObservationTime
(formerly observationTime
)deltaWT
is provided with three decimal points for typeOfDesign = "WToptimum"as.data.frame
functions improvedgetSimulationMultiArmSurvival()
: single stage treatment arm specific event numbers account for selection proceduregetSimulationEnrichmentRates()
and getSimulationEnrichmentSurvival()
getDesignCharacteristics()
getSimulationSurvival()
: the result object now contains the new parameter overallEventsPerStage
, which contains the values previously given in eventsPerStage
(it was "cumulative" by mistake); eventsPerStage
contains now the non-cumulative values as expectedstats::qnorm(1e-323)
to stats::qnorm(1e-100)
getAnalysisResults()
: issue with zero values in the argument 'userAlphaSpending' fixedgetSimulationEnrichmentMeans()
, getSimulationEnrichmentRates()
, getSimulationEnrichmentSurvival()
available for simulation of enrichment designs;
note that this is a novel implementation, hence experimentalgetDesignGroupSequential()
/ getDesignInverseNormal()
: new typeOfDesign = "noEarlyEfficacy" addedgetSimulationSurvival()
: bug fixed for accruallIntensity = 0 at some accrual intervalsgetSimulationMultiArmMeans()
, getSimulationMultiArmRates()
, and getSimulationMultiArmSurvival()
testPackage()
: a problem with downloading full set of unit tests under Debian/Linux has been fixedkable()
improved: optional knitr::kable arguments enabled, e.g., formatqnorm()
calculations improved as.data.frame()
getAnalysisResults()
generalized for enrichment designs; function getDataset()
generalized for entering stratified data; manual extended for enrichment designsgetAnalysisResults()
getObjectRCode()
(short: rcmd()
) returns the original R command which
produced any rpact result object, including all dependenciesgetWideFormat()
and getLongFormat()
return a dataset object in wide format (unstacked) or long format (narrow, stacked)kable()
returns the output of an rpact result object formatted in Markdown.t()
returns the transpose of an rpact result objectgetDesignFisher()
fixed: getDesignFisher(method = "noInteraction", kMax = 3)
and getDesignFisher(method = "noInteraction")
produced different resultstestPackage()
: the default call is now running only a small subset of all available unit tests; with the new
argument 'connection' the owners of the rpact validation documentation
can enter a 'token' and a 'secret' to get full access to all unit testsgetSampleSizeSurvival()
, getSimulationSurvival()
, getNumberOfSubjects()
, and getEventProbabilities()
getParameterCaption()
and getParameterName()
implementedas.matrix()
improved for several result objectsgetAvailablePlotTypes()
for sample size and power results fixedgetDesignFisher(kMax = 1)
in getSimulationMultiArm...()
fixed getSimulationMultiArmSurvival()
: correlation of log-rank statistics revised and improved getSimulationMultiArmMeans()
: name of the first effectMeasure option "effectDifference" changed to "effectEstimate" getSimulation[MultiArm][Means/Rates/Survival]()
: argument 'showStatistics' now works correctly and is consistently FALSE by default for multi-arm and non-multi-armgetSimulation[MultiArm]Survival()
: generic function summary()
improvedgetAnalysisResults()
: generic function summary()
improvedgetAccrualTime()
: improved and new argument 'accrualIntensityType' addedgetSampleSizeSurvival()
: field 'studyDurationH1' in result object was replaced by 'studyDuration', i.e., 'studyDurationH1' is deprecated and will be removed in future versionsgetSimulationMultiArmSurvival()
: plannedEvents redefined as overall events over treatment armsgetStageResults()
: element overallPooledStDevs added; print output improvedgetSampleSizeSurvival()
with user defined lambdas with different lengths: issue fixedsummary()
improved for several result objectstestPackage()
improvedgetSimulationMultiArm[Means/Rates/Survival]()
: stage index corrected for user defined calcSubjectsFunction or calcEventsFunctiongetSimulationMultiArmRates()
: adjustment for identical simulated rates to account for tiesgetSimulationMultiArmSurvival()
: corrected correlation of test statisticsgetSimulationRates()
: exact versions for testing a rate (one-sample case) and equality of rates (two-sample case)getEventProbabilities()
: plot of result objectgetNumberOfSubjects()
: plot of result objectplot(design1, design2)
getSimulationMeans()
: thetaH1 and stDevH1 can be specified for assessment of sample size recalculation (replaces thetaStandardized)getSimulationSurvival()
: separate p-values added to the aggregated simulation data for Fisher designsgetSimulationMeans()
, getSimulationRates()
: Cumulated number of subjects integrated in getData objectgetSimulation[MultiArm][Means/Rates/Survival]()
: new logical argument 'showStatistics' addedplot(x, type = "all")
plot(x, type = c(1, 3))
plot(x, grid = 1)
: new plot argument 'grid' enables the plotting of 2 or more plots in one graphicgetAnalysisResults()
: list output implemented analogous to the output of all other rpact objectsgetAnalysisResults()
: the following stage result arguments were removed from result object because they were redundant: effectSizes, testStatistics, and pValues. Please use the '.stageResults' object to access them, e.g., results\$.stageResults\$effectSizesgetAnalysisResults()
: the following design arguments were removed from result object because they were redundant: stages, informationRates, criticalValues, futilityBounds, alphaSpent, and stageLevels. Please use the '.design' object to access them, e.g., results\$.design\$informationRatesplot(x, showSource = TRUE)
improved for all rpact result objects xgetSimulationRates()
: issue for futility stopping for Fisher's combination test fixedgetSimulationSurvival()
: issue for expected number of events fixedgetSimulationSurvival()
: if eventsNotAchieved > 0, rejection/futility rate and analysis time is estimated for valid simulation runsgetSimulationSurvival()
: output improved for lambda1/median1/hazardRatio with length > 1getSampleSizeSurvival()
: calculation of the maximum number of subjects given the provided argument 'followUpTime' improvedgetPiecewiseSurvivalTime()
: delayed response via list-based piecewiseSurvivalTime definition enabledgetAccrualTime()
/ getSimulationSurvival()
: issue with the calculation of absolute accrual intensity by given relative accrual intensity fixedgetRawData()
: issue for multiple pi1 solved getAnalysisSurvival()
: calculation of stage wise results not more in getStageResultsgetStageResults()
: the calculation of 'effectSizes' for survival data and thetaH0 != 1 was corrected getDataset()
of survival data: issue with the internal storage of log ranks fixedgetSampleSizeSurvival()
with piecewise survival time: issue with calculation of 'maxNumberOfSubjects' for given 'followUpTime' fixed summary()
improvedgetSampleSizeSurvival()
with given maxNumberOfSubjects improvedget[SampleSize/Power]Survival()
for Kappa != 1 improvedsummary()
for getDesign[...]()
fixedsummary()
fixed for getSampleSize[...]()
and getPower[...]()
summary()
implemented for getDesign[...]()
, getSampleSize[...]()
, getPower[...]()
, and getSimulation[...]()
results: a simple boundary summary will be displayedgetDesign[...]()
, getSampleSize[...]()
, getPower[...]()
, and getSimulation[...]()
resultsgetStageResults()
improvedgetAccrualTime()
improvedgetSampleSizeSurvival()
improved: numeric search for accrualTime if followUpTime is givenset.seed()
calls 'kind' and 'normal.kind' were specified as follows: kind = "Mersenne-Twister", normal.kind = "Inversion"readDatasets()
fixed: variable names 'group' and 'groups' are now acceptedgetSampleSizeSurvival()
: argument 'maxNumberOfPatients' was renamed in 'maxNumberOfSubjects'Any scripts or data that you put into this service are public.
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