Man pages for crmPack
Object-Oriented Implementation of CRM Designs

AllModels-classClass for All models This is a class where all models...
and-StoppingAll-Stopping-methodThe method combining a stopping list and an atomic
and-Stopping-StoppingAll-methodThe method combining an atomic and a stopping list
and-Stopping-Stopping-methodThe method combining two atomic stopping rules
approximateApproximate posterior with (log) normal distribution
as.list-GeneralData-methodas.list method for the "GeneralData" class
biomLevelCompute the biomarker level for a given dose, given model and...
CohortSize-classThe virtual class for cohort sizes
CohortSizeConstInitialization function for "CohortSizeConst"
CohortSizeConst-classConstant cohort size
CohortSizeDLTInitialization function for "CohortSizeDLT"
CohortSizeDLT-classCohort size based on number of DLTs
CohortSizeMaxInitialization function for "CohortSizeMax"
CohortSizeMax-classSize based on maximum of multiple cohort size rules
CohortSizeMinInitialization function for "CohortSizeMin"
CohortSizeMin-classSize based on minimum of multiple cohort size rules
CohortSizePartsInitialization function for "CohortSizeParts"
CohortSizeParts-classCohort size based on the parts
CohortSizeRangeInitialization function for "CohortSizeRange"
CohortSizeRange-classCohort size based on dose range
crmPackExampleOpen the example pdf for crmPack
crmPackHelpOpen the browser with help pages for crmPack
crmPack-packageObject-oriented implementation of CRM designs
DataInitialization function for the "Data" class
Data-classClass for the data input
DataDualInitialization function for the "DataDual" class
DataDual-classClass for the dual endpoint data input
DataMixtureInitialization function for the "DataMixture" class
DataMixture-classClass for the data with mixture sharing
DataPartsInitialization function for the "DataParts" class
DataParts-classClass for the data with two study parts
DesignInitialization function for "Design"
Design-classClass for the CRM design
dinvGammaCompute the density of Inverse gamma distribution
doseCompute the doses for a given probability, given model and...
DualDesignInitialization function for "DualDesign"
DualDesign-classClass for the dual-endpoint CRM design
DualEndpointInitialization function for the "DualEndpoint" class
DualEndpointBetaInitialization function for the "DualEndpointBeta" class
DualEndpointBeta-classDual endpoint model with beta function for dose-biomarker...
DualEndpoint-classGeneral class for the dual endpoint model
DualEndpointEmaxInitialization function for the "DualEndpointEmax" class
DualEndpointEmax-classDual endpoint model with emax function for dose-biomarker...
DualEndpointOld-classDual endpoint model
DualEndpointRWInitialization function for the "DualEndpointRW" class
DualEndpointRW-classDual endpoint model with RW prior for biomarker
DualResponsesDesignInitialization function for 'DualResponsesDesign"
DualResponsesDesign-classThis is a class of design based on DLE responses using the...
DualResponsesSamplesDesignInitialization function for 'DualResponsesSamplesDesign"
DualResponsesSamplesDesign-classThis is a class of design based on DLE responses using the...
DualSimulationsInitialization function for "DualSimulations"
DualSimulations-classClass for the simulations output from dual-endpoint model...
DualSimulationsSummary-classClass for the summary of dual-endpoint simulations output
EffFlexiInitialization function for the "EffFlexi" class
EffFlexi-classClass for the efficacy model in flexible form for prior...
EffloglogInitialization function for the "Effloglog" class
Effloglog-classClass for the linear log-log efficacy model using pseudo data...
examineObtain hypothetical trial course table for a design
ExpEffCompute the expected efficacy based on a given dose, a given...
fitFit method for the Samples class
fitGainGet the fiited values for the gain values at all dose levels...
gainCompute the gain value with a given dose level, given a...
GeneralData-classClass for general data input
GeneralModel-classNo Intitialization function for this General class for model...
GeneralSimulationsInitialization function for "GeneralSimulations"
GeneralSimulations-classGeneral class for the simulations output
GeneralSimulationsSummary-classClass for the summary of general simulations output
getEffExtracting efficacy responses for subjects without or with a...
getMinInfBetaGet the minimal informative unimodal beta distribution
getResultListHelper function to obtain simulation results list
get-Samples-character-methodGet specific parameter samples and produce a data.frame
IncrementMinInitialization function for "IncrementMin"
IncrementMin-classMax increment based on minimum of multiple increment rules
Increments-classThe virtual class for controlling increments
IncrementsNumDoseLevelsInitialization function for "IncrementsNumDoseLevels"
IncrementsNumDoseLevels-classIncrements control based on number of dose levels
IncrementsRelativeInitialization function for "IncrementsRelative"
IncrementsRelative-classIncrements control based on relative differences in intervals
IncrementsRelativeDLTInitialization function for "IncrementsRelativeDLT"
IncrementsRelativeDLT-classIncrements control based on relative differences in terms of...
IncrementsRelativePartsInitialization function for "IncrementsRelativeParts"
IncrementsRelativeParts-classIncrements control based on relative differences in...
initialize-DualEndpointOld-methodInitialization method for the "DualEndpointOld" class
is.boolPredicate checking for a boolean option
is.probabilityPredicate checking for a probability
is.probRangePredicate checking for a probability range
is.rangePredicate checking for a numeric range
is.scalarChecking for scalar
is.wholenumberchecks for whole numbers (integers)
joinBodiesHelper function to join two function bodies
joinModelsHelper function to join two BUGS models
LogisticIndepBetaIntialization function for "LogisticIndepBeta" class
LogisticIndepBeta-classNo initialization function Standard logistic model with prior...
LogisticKadaneInitialization function for the "LogisticKadane" class
LogisticKadane-classReparametrized logistic model
LogisticLogNormalInitialization function for the "LogisticLogNormal" class
LogisticLogNormal-classStandard logistic model with bivariate (log) normal prior
LogisticLogNormalMixtureInitialization function for the "LogisticLogNormalMixture"...
LogisticLogNormalMixture-classStandard logistic model with online mixture of two bivariate...
LogisticLogNormalSubInitialization function for the "LogisticLogNormalSub" class
LogisticLogNormalSub-classStandard logistic model with bivariate (log) normal prior...
LogisticNormalInitialization function for the "LogisticNormal" class
LogisticNormal-classStandard logistic model with bivariate normal prior
LogisticNormalFixedMixtureInitialization function for the "LogisticNormalFixedMixture"...
LogisticNormalFixedMixture-classStandard logistic model with fixed mixture of multiple...
LogisticNormalMixtureInitialization function for the "LogisticNormalMixture" class
LogisticNormalMixture-classStandard logistic model with flexible mixture of two...
logitShorthand for logit function
matchToleranceHelper function for value matching with tolerance
maxDoseDetermine the maximum possible next dose
maxSize"MAX" combination of cohort size rules
mcmcObtain posterior samples for all model parameters
McmcOptionsInitialization function for the "McmcOptions" class
McmcOptions-classClass for the three canonical MCMC options
MinimalInformativeConstruct a minimally informative prior
minSize"MIN" combination of cohort size rules
Model-classClass for the model input
ModelEff-classNo Initialization function class for Efficacy models using...
ModelPseudo-classClass of models using expressing their prior in form of...
ModelTox-classNo intialization function Class for DLE models using pseudo...
multiplotMultiple plot function
myBarplotConvenience function to make barplots of percentages
myBayesLogitDo MCMC sampling for Bayesian logistic regression model
nextBestFind the next best dose
NextBest-classThe virtual class for finding next best dose
NextBestDualEndpointInitialization function for "NextBestDualEndpoint"
NextBestDualEndpoint-classThe class with the input for finding the next dose based on...
NextBestMaxGainInitialization function for the class 'NextBestMaxGain'
NextBestMaxGain-classNext best dose with maximum gain value based on a pseudo DLE...
NextBestMaxGainSamplesInitialization function for class "NextBestMaxGainSamples"
NextBestMaxGainSamples-classNext best dose with maximum gain value based on a pseudo DLE...
NextBestMTDInitialization function for class "NextBestMTD"
NextBestMTD-classThe class with the input for finding the next best MTD...
NextBestNCRMInitialization function for "NextBestNCRM"
NextBestNCRM-classThe class with the input for finding the next dose in target...
NextBestTDInitialization function for the class "NextBestTD"
NextBestTD-classNext best dose based on Pseudo DLE model without sample
NextBestTDsamplesInitialization function for class "NextBestTDsamples"
NextBestTDsamples-classNext best dose based on Pseudo DLE Model with samples
NextBestThreePlusThreeInitialization function for "NextBestThreePlusThree"
NextBestThreePlusThree-classThe class with the input for finding the next dose in target...
noOverlapCheck overlap of two character vectors
or-StoppingAny-StoppingThe method combining an atomic and a stopping list
or-Stopping-StoppingThe method combining two atomic stopping rules
or-Stopping-StoppingAnyThe method combining a stopping list and an atomic
pinvGammaCompute the distribution function of Inverse gamma...
plot-DataDual-missing-methodPlot method for the "DataDual" class
plot-DataDual-ModelEff-methodPlot of the fitted dose-efficacy based with a given pseudo...
plot-Data-missing-methodPlot method for the "Data" class
plot-Data-ModelTox-methodPlot of the fitted dose-tox based with a given pseudo DLE...
plotDualResponsesPlot of the DLE and efficacy curve side by side given a DLE...
plot-DualSimulations-missing-methodPlot dual-endpoint simulations
plot-DualSimulationsSummary-missing-methodPlot summaries of the dual-endpoint design simulations
plotGainPlot the gain curve in addition with the dose-DLE and...
plot-GeneralSimulations-missing-methodPlot simulations
plot-GeneralSimulationsSummary-missing-methodGraphical display of the general simulation summary
plot.gtablePlots gtable objects
plot-PseudoDualFlexiSimulations-missing-methodPlot for PseudoDualFlexiSimulations
plot-PseudoDualSimulations-missing-methodPlot simulations
plot-PseudoDualSimulationsSummary-missing-methodPlot the summary of Pseudo Dual Simulations summary
plot-PseudoSimulationsSummary-missing-methodPlot summaries of the pseudo simulations
plot-Samples-DualEndpoint-methodPlotting dose-toxicity and dose-biomarker model fits
plot-Samples-ModelEff-methodPlot the fitted dose-effcacy curve using a model from...
plot-Samples-Model-methodPlotting dose-toxicity model fits
plot-Samples-ModelTox-methodPlot the fitted dose-DLE curve using a 'ModelTox' class model...
plot-SimulationsSummary-missing-methodPlot summaries of the model-based design simulations
printVignetteTaken from utils package (print.vignette)
probCompute the probability for a given dose, given model and...
probitShorthand for probit function
ProbitLogNormalInitialization function for the "ProbitLogNormal" class
ProbitLogNormal-classProbit model with bivariate log normal prior
PseudoDualFlexiSimulationsInitialization function for 'PseudoDualFlexiSimulations'...
PseudoDualFlexiSimulations-classThis is a class which captures the trial simulations design...
PseudoDualSimulationsInitialization function for 'DualPseudoSimulations' class
PseudoDualSimulations-classThis is a class which captures the trial simulations design...
PseudoDualSimulationsSummary-classClass for the summary of the dual responses simulations using...
PseudoSimulationsInitialization function of the 'PseudoSimulations' class
PseudoSimulations-classThis is a class which captures the trial simulations from...
PseudoSimulationsSummary-classClass for the summary of pseudo-models simulations output
qinvGammaCompute the quantile function of Inverse gamma distribution
Quantiles2LogisticNormalConvert prior quantiles (lower, median, upper) to logistic...
ReportA Reference Class to represent sequentially updated reporting...
rinvGammaThe random generation of the Inverse gamma distribution
RuleDesignInitialization function for "RuleDesign"
RuleDesign-classClass for rule-based designs
safeIntegerSafe conversion to integer vector
SamplesInitialization function for "Samples"
Samples-classClass for the MCMC output
sampleSizeCompute the number of samples for a given MCMC options triple
saveSampleDetermine if we should save this sample
setSeedHelper function to set and save the RNG seed
show-DualSimulationsSummary-methodShow the summary of the dual-endpoint simulations
show-GeneralSimulationsSummary-methodShow the summary of the simulations
show-PseudoDualSimulationsSummary-methodShow the summary of Pseudo Dual simulations summary
show-PseudoSimulationsSummary-methodShow the summary of the simulations
show-SimulationsSummary-methodShow the summary of the simulations
simulate-Design-methodSimulate outcomes from a CRM design
simulate-DualDesign-methodSimulate outcomes from a dual-endpoint design
simulate-DualResponsesDesign-methodThis is a methods to simulate dose escalation procedure using...
simulate-DualResponsesSamplesDesign-methodThis is a methods to simulate dose escalation procedure using...
simulate-RuleDesign-methodSimulate outcomes from a rule-based design
simulate-TDDesign-methodThis is a methods to simulate dose escalation procedure only...
simulate-TDsamplesDesign-methodThis is a methods to simulate dose escalation procedure only...
SimulationsInitialization function for the "Simulations" class
Simulations-classClass for the simulations output from model based designs
SimulationsSummary-classClass for the summary of model-based simulations output
sizeDetermine the size of the next cohort
StoppingAllInitialization function for "StoppingAll"
StoppingAll-classStop based on fullfillment of all multiple stopping rules
StoppingAnyInitialization function for "StoppingAny"
StoppingAny-classStop based on fullfillment of any stopping rule
Stopping-classThe virtual class for stopping rules
StoppingCohortsNearDoseInitialization function for "StoppingCohortsNearDose"
StoppingCohortsNearDose-classStop based on number of cohorts near to next best dose
StoppingGstarCIRatioInitialization function for "StoppingGstarCIRatio"
StoppingGstarCIRatio-classStop based on a target ratio, the ratio of the upper to the...
StoppingHighestDoseInitialization function for "StoppingHighestDose"
StoppingHighestDose-classStop when the highest dose is reached
StoppingListInitialization function for "StoppingList"
StoppingList-classStop based on multiple stopping rules
StoppingMinCohortsInitialization function for "StoppingMinCohorts"
StoppingMinCohorts-classStop based on minimum number of cohorts
StoppingMinPatientsInitialization function for "StoppingMinPatients"
StoppingMinPatients-classStop based on minimum number of patients
StoppingMTDdistributionInitialization function for "StoppingMTDdistribution"
StoppingMTDdistribution-classStop based on MTD distribution
StoppingPatientsNearDoseInitialization function for "StoppingPatientsNearDose"
StoppingPatientsNearDose-classStop based on number of patients near to next best dose
StoppingTargetBiomarkerInitialization function for "StoppingTargetBiomarker"
StoppingTargetBiomarker-classStop based on probability of target biomarker
StoppingTargetProbInitialization function for "StoppingTargetProb"
StoppingTargetProb-classStop based on probability of target tox interval
StoppingTDCIRatioInitialization function for "StoppingTDCIRatio"
StoppingTDCIRatio-classStop based on a target ratio, the ratio of the upper to the...
stopTrialStop the trial?
summary-DualSimulations-methodSummarize the dual-endpoint design simulations, relative to...
summary-GeneralSimulations-methodSummarize the simulations, relative to a given truth
summary-PseudoDualFlexiSimulations-methodSummary for Pseudo Dual responses simulations given a pseudo...
summary-PseudoDualSimulations-methodSummary for Pseudo Dual responses simulations, relative to a...
summary-PseudoSimulations-methodSummarize the simulations, relative to a given truth
summary-Simulations-methodSummarize the model-based design simulations, relative to a...
TDDesignInitialization function for 'TDDesign' class
TDDesign-classDesign class using DLE responses only based on the pseudo DLE...
TDsamplesDesignInitialization function for 'TDsamplesDesign' class
TDsamplesDesign-classThis is a class of design based only on DLE responses using...
ThreePlusThreeDesignCreates a new 3+3 design object from a dose grid
update-DataDual-methodUpdate method for the "DataDual" class
update-Data-methodUpdate method for the "Data" class
update-DataParts-methodUpdate method for the "DataParts" class
update-EffFlexi-methodUpdate method for the 'EffFlexi' Model class. This is a...
update-Effloglog-methodUpdate method for the 'Effloglog' Model class. This is a...
update-LogisticIndepBeta-methodUpdate method for the 'LogisticIndepBeta'Model class. This is...
ValidateA Reference Class to help programming validation for new S4...
writeModelCreating a WinBUGS model file
crmPack documentation built on Sept. 3, 2022, 1:05 a.m.