crmPack: Object-Oriented Implementation of CRM Designs
Version 0.2.1

Implements a wide range of model-based dose escalation designs, ranging from classical and modern continual reassessment methods (CRMs) based on dose-limiting toxicity endpoints to dual-endpoint designs taking into account a biomarker/efficacy outcome. The focus is on Bayesian inference, making it very easy to setup a new design with its own JAGS code. However, it is also possible to implement 3+3 designs for comparison or models with non-Bayesian estimation. The whole package is written in a modular form in the S4 class system, making it very flexible for adaptation to new models, escalation or stopping rules.

AuthorDaniel Sabanes Bove <sabanesd@roche.com>, Wai Yin Yeung <winnie.yeung@roche.com>, Giuseppe Palermo <giuseppe.palermo@roche.com>, Thomas Jaki <jaki.thomas@gmail.com>
Date of publication2017-05-03 20:57:00 UTC
MaintainerDaniel Sabanes Bove <sabanesd@roche.com>
LicenseGPL (>= 2)
Version0.2.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("crmPack")

Getting started

Package overview

Popular man pages

CohortSizeMin-class: Size based on minimum of multiple cohort size rules
getMinInfBeta: Get the minimal informative unimodal beta distribution
plot-Samples-DualEndpoint-method: Plotting dose-toxicity and dose-biomarker model fits
plot-Samples-Model-method: Plotting dose-toxicity model fits
probit: Shorthand for probit function
simulate-DualResponsesDesign-method: This is a methods to simulate dose escalation procedure using...
simulate-DualResponsesSamplesDesign-method: This is a methods to simulate dose escalation procedure using...
See all...

All man pages Function index File listing

Man pages

AllModels-class: Class for All models This is a class where all models...
and-StoppingAll-Stopping-method: The method combining a stopping list and an atomic
and-Stopping-StoppingAll-method: The method combining an atomic and a stopping list
and-Stopping-Stopping-method: The method combining two atomic stopping rules
approximate: Approximate posterior with (log) normal distribution
as.list-GeneralData-method: as.list method for the "GeneralData" class
biomLevel: Compute the biomarker level for a given dose, given model and...
CohortSize-class: The virtual class for cohort sizes
CohortSizeConst: Initialization function for "CohortSizeConst"
CohortSizeConst-class: Constant cohort size
CohortSizeDLT: Initialization function for "CohortSizeDLT"
CohortSizeDLT-class: Cohort size based on number of DLTs
CohortSizeMax: Initialization function for "CohortSizeMax"
CohortSizeMax-class: Size based on maximum of multiple cohort size rules
CohortSizeMin: Initialization function for "CohortSizeMin"
CohortSizeMin-class: Size based on minimum of multiple cohort size rules
CohortSizeParts: Initialization function for "CohortSizeParts"
CohortSizeParts-class: Cohort size based on the parts
CohortSizeRange: Initialization function for "CohortSizeRange"
CohortSizeRange-class: Cohort size based on dose range
crmPackExample: Open the example pdf for crmPack
crmPackHelp: Open the browser with help pages for crmPack
crmPack-package: Object-oriented implementation of CRM designs
Data: Initialization function for the "Data" class
Data-class: Class for the data input
DataDual: Initialization function for the "DataDual" class
DataDual-class: Class for the dual endpoint data input
DataMixture: Initialization function for the "DataMixture" class
DataMixture-class: Class for the data with mixture sharing
DataParts: Initialization function for the "DataParts" class
DataParts-class: Class for the data with two study parts
Design: Initialization function for "Design"
Design-class: Class for the CRM design
dinvGamma: Compute the density of Inverse gamma distribution
dose: Compute the doses for a given probability, given model and...
DualDesign: Initialization function for "DualDesign"
DualDesign-class: Class for the dual-endpoint CRM design
DualEndpoint: Initialization function for the "DualEndpoint" class
DualEndpointBeta: Initialization function for the "DualEndpointBeta" class
DualEndpointBeta-class: Dual endpoint model with beta function for dose-biomarker...
DualEndpoint-class: General class for the dual endpoint model
DualEndpointEmax: Initialization function for the "DualEndpointEmax" class
DualEndpointEmax-class: Dual endpoint model with emax function for dose-biomarker...
DualEndpointOld-class: Dual endpoint model
DualEndpointRW: Initialization function for the "DualEndpointRW" class
DualEndpointRW-class: Dual endpoint model with RW prior for biomarker
DualResponsesDesign: Initialization function for 'DualResponsesDesign"
DualResponsesDesign-class: This is a class of design based on DLE responses using the...
DualResponsesSamplesDesign: Initialization function for 'DualResponsesSamplesDesign"
DualResponsesSamplesDesign-class: This is a class of design based on DLE responses using the...
DualSimulations: Initialization function for "DualSimulations"
DualSimulations-class: Class for the simulations output from dual-endpoint model...
DualSimulationsSummary-class: Class for the summary of dual-endpoint simulations output
EffFlexi: Initialization function for the "EffFlexi" class
EffFlexi-class: Class for the efficacy model in flexible form for prior...
Effloglog: Initialization function for the "Effloglog" class
Effloglog-class: Class for the linear log-log efficacy model using pseudo data...
examine: Obtain hypothetical trial course table for a design
ExpEff: Compute the expected efficacy based on a given dose, a given...
fit: Fit method for the Samples class
fitGain: Get the fiited values for the gain values at all dose levels...
gain: Compute the gain value with a given dose level, given a...
GeneralData-class: Class for general data input
GeneralModel-class: No Intitialization function for this General class for model...
GeneralSimulations: Initialization function for "GeneralSimulations"
GeneralSimulations-class: General class for the simulations output
GeneralSimulationsSummary-class: Class for the summary of general simulations output
getEff: Extracting efficacy responses for subjects without or with a...
getMinInfBeta: Get the minimal informative unimodal beta distribution
getResultList: Helper function to obtain simulation results list
get-Samples-character-method: Get specific parameter samples and produce a data.frame
Increments-class: The virtual class for controlling increments
IncrementsRelative: Initialization function for "IncrementsRelative"
IncrementsRelative-class: Increments control based on relative differences in intervals
IncrementsRelativeDLT: Initialization function for "IncrementsRelativeDLT"
IncrementsRelativeDLT-class: Increments control based on relative differences in terms of...
IncrementsRelativeParts: Initialization function for "IncrementsRelativeParts"
IncrementsRelativeParts-class: Increments control based on relative differences in...
initialize-DualEndpointOld-method: Initialization method for the "DualEndpointOld" class
is.bool: Predicate checking for a boolean option
is.probability: Predicate checking for a probability
is.probRange: Predicate checking for a probability range
is.range: Predicate checking for a numeric range
is.scalar: Checking for scalar
is.wholenumber: checks for whole numbers (integers)
joinBodies: Helper function to join two function bodies
joinModels: Helper function to join two BUGS models
LogisticIndepBeta: Intialization function for "LogisticIndepBeta" class
LogisticIndepBeta-class: No initialization function Standard logistic model with prior...
LogisticKadane: Initialization function for the "LogisticKadane" class
LogisticKadane-class: Reparametrized logistic model
LogisticLogNormal: Initialization function for the "LogisticLogNormal" class
LogisticLogNormal-class: Standard logistic model with bivariate (log) normal prior
LogisticLogNormalMixture: Initialization function for the "LogisticLogNormalMixture"...
LogisticLogNormalMixture-class: Standard logistic model with online mixture of two bivariate...
LogisticLogNormalSub: Initialization function for the "LogisticLogNormalSub" class
LogisticLogNormalSub-class: Standard logistic model with bivariate (log) normal prior...
LogisticNormal: Initialization function for the "LogisticNormal" class
LogisticNormal-class: Standard logistic model with bivariate normal prior
LogisticNormalFixedMixture: Initialization function for the "LogisticNormalFixedMixture"...
LogisticNormalFixedMixture-class: Standard logistic model with fixed mixture of multiple...
LogisticNormalMixture: Initialization function for the "LogisticNormalMixture" class
LogisticNormalMixture-class: Standard logistic model with flexible mixture of two...
logit: Shorthand for logit function
maxDose: Determine the maximum possible next dose
maxSize: "MAX" combination of cohort size rules
mcmc: Obtain posterior samples for all model parameters
McmcOptions: Initialization function for the "McmcOptions" class
McmcOptions-class: Class for the three canonical MCMC options
MinimalInformative: Construct a minimally informative prior
minSize: "MIN" combination of cohort size rules
Model-class: Class for the model input
ModelEff-class: No Initialization function class for Efficacy models using...
ModelPseudo-class: Class of models using expressing their prior in form of...
ModelTox-class: No intialization function Class for DLE models using pseudo...
multiplot: Multiple plot function
myBarplot: Convenience function to make barplots of percentages
nextBest: Find the next best dose
NextBest-class: The virtual class for finding next best dose
NextBestDualEndpoint: Initialization function for "NextBestDualEndpoint"
NextBestDualEndpoint-class: The class with the input for finding the next dose based on...
NextBestMaxGain: Initialization function for the class 'NextBestMaxGain'
NextBestMaxGain-class: Next best dose with maximum gain value based on a pseudo DLE...
NextBestMaxGainSamples: Initialization function for class "NextBestMaxGainSamples"
NextBestMaxGainSamples-class: Next best dose with maximum gain value based on a pseudo DLE...
NextBestMTD: Initialization function for class "NextBestMTD"
NextBestMTD-class: The class with the input for finding the next best MTD...
NextBestNCRM: Initialization function for "NextBestNCRM"
NextBestNCRM-class: The class with the input for finding the next dose in target...
NextBestTD: Initialization function for the class "NextBestTD"
NextBestTD-class: Next best dose based on Pseudo DLE model without sample
NextBestTDsamples: Initialization function for class "NextBestTDsamples"
NextBestTDsamples-class: Next best dose based on Pseudo DLE Model with samples
NextBestThreePlusThree: Initialization function for "NextBestThreePlusThree"
NextBestThreePlusThree-class: The class with the input for finding the next dose in target...
noOverlap: Check overlap of two character vectors
or-StoppingAny-Stopping: The method combining an atomic and a stopping list
or-Stopping-Stopping: The method combining two atomic stopping rules
or-Stopping-StoppingAny: The method combining a stopping list and an atomic
pinvGamma: Compute the distribution function of Inverse gamma...
plot-DataDual-missing-method: Plot method for the "DataDual" class
plot-DataDual-ModelEff-method: Plot of the fitted dose-efficacy based with a given pseudo...
plot-Data-missing-method: Plot method for the "Data" class
plot-Data-ModelTox-method: Plot of the fitted dose-tox based with a given pseudo DLE...
plotDualResponses: Plot of the DLE and efficacy curve side by side given a DLE...
plot-DualSimulations-missing-method: Plot dual-endpoint simulations
plot-DualSimulationsSummary-missing-method: Plot summaries of the dual-endpoint design simulations
plotGain: Plot the gain curve in addition with the dose-DLE and...
plot-GeneralSimulations-missing-method: Plot simulations
plot-GeneralSimulationsSummary-missing-method: Graphical display of the general simulation summary
plot.gtable: Plots gtable objects
plot-PseudoDualFlexiSimulations-missing-method: This plot method can be applied to...
plot-PseudoDualSimulations-missing-method: Plot simulations
plot-PseudoDualSimulationsSummary-missing-method: Plot the summary of Pseudo Dual Simulations summary
plot-PseudoSimulationsSummary-missing-method: Plot summaries of the pseudo simulations
plot-Samples-DualEndpoint-method: Plotting dose-toxicity and dose-biomarker model fits
plot-Samples-ModelEff-method: Plot the fitted dose-effcacy curve using a model from...
plot-Samples-Model-method: Plotting dose-toxicity model fits
plot-Samples-ModelTox-method: Plot the fitted dose-DLE curve using a 'ModelTox' class model...
plot-SimulationsSummary-missing-method: Plot summaries of the model-based design simulations
printVignette: Taken from utils package (print.vignette)
prob: Compute the probability for a given dose, given model and...
probit: Shorthand for probit function
ProbitLogNormal: Initialization function for the "ProbitLogNormal" class
ProbitLogNormal-class: Probit model with bivariate log normal prior
PseudoDualFlexiSimulations: Initialization function for 'PseudoDualFlexiSimulations'...
PseudoDualFlexiSimulations-class: This is a class which captures the trial simulations design...
PseudoDualSimulations: Initialization function for 'DualPseudoSimulations' class
PseudoDualSimulations-class: This is a class which captures the trial simulations design...
PseudoDualSimulationsSummary-class: Class for the summary of the dual responses simulations using...
PseudoSimulations: Initialization function of the 'PseudoSimulations' class
PseudoSimulations-class: This is a class which captures the trial simulations from...
PseudoSimulationsSummary-class: Class for the summary of pseudo-models simulations output
qinvGamma: Compute the quantile function of Inverse gamma distribution
Quantiles2LogisticNormal: Convert prior quantiles (lower, median, upper) to logistic...
Report: A Reference Class to represent sequentially updated reporting...
rinvGamma: The random generation of the Inverse gamma distribution
RuleDesign: Initialization function for "RuleDesign"
RuleDesign-class: Class for rule-based designs
safeInteger: Safe conversion to integer vector
Samples: Initialization function for "Samples"
Samples-class: Class for the MCMC output
sampleSize: Compute the number of samples for a given MCMC options triple
saveSample: Determine if we should save this sample
setSeed: Helper function to set and save the RNG seed
show-DualSimulationsSummary-method: Show the summary of the dual-endpoint simulations
show-GeneralSimulationsSummary-method: Show the summary of the simulations
show-PseudoDualSimulationsSummary-method: Show the summary of Pseudo Dual simulations summary
show-PseudoSimulationsSummary-method: Show the summary of the simulations
show-SimulationsSummary-method: Show the summary of the simulations
simulate-Design-method: Simulate outcomes from a CRM design
simulate-DualDesign-method: Simulate outcomes from a dual-endpoint design
simulate-DualResponsesDesign-method: This is a methods to simulate dose escalation procedure using...
simulate-DualResponsesSamplesDesign-method: This is a methods to simulate dose escalation procedure using...
simulate-RuleDesign-method: Simulate outcomes from a rule-based design
simulate-TDDesign-method: This is a methods to simulate dose escalation procedure only...
simulate-TDsamplesDesign-method: This is a methods to simulate dose escalation procedure only...
Simulations: Initialization function for the "Simulations" class
Simulations-class: Class for the simulations output from model based designs
SimulationsSummary-class: Class for the summary of model-based simulations output
size: Determine the size of the next cohort
StoppingAll: Initialization function for "StoppingAll"
StoppingAll-class: Stop based on fullfillment of all multiple stopping rules
StoppingAny: Initialization function for "StoppingAny"
StoppingAny-class: Stop based on fullfillment of any stopping rule
Stopping-class: The virtual class for stopping rules
StoppingCohortsNearDose: Initialization function for "StoppingCohortsNearDose"
StoppingCohortsNearDose-class: Stop based on number of cohorts near to next best dose
StoppingGstarCIRatio: Initialization function for "StoppingGstarCIRatio"
StoppingGstarCIRatio-class: Stop based on a target ratio, the ratio of the upper to the...
StoppingHighestDose: Initialization function for "StoppingHighestDose"
StoppingHighestDose-class: Stop when the highest dose is reached
StoppingList: Initialization function for "StoppingList"
StoppingList-class: Stop based on multiple stopping rules
StoppingMinCohorts: Initialization function for "StoppingMinCohorts"
StoppingMinCohorts-class: Stop based on minimum number of cohorts
StoppingMinPatients: Initialization function for "StoppingMinPatients"
StoppingMinPatients-class: Stop based on minimum number of patients
StoppingMTDdistribution: Initialization function for "StoppingMTDdistribution"
StoppingMTDdistribution-class: Stop based on MTD distribution
StoppingPatientsNearDose: Initialization function for "StoppingPatientsNearDose"
StoppingPatientsNearDose-class: Stop based on number of patients near to next best dose
StoppingTargetBiomarker: Initialization function for "StoppingTargetBiomarker"
StoppingTargetBiomarker-class: Stop based on probability of target biomarker
StoppingTargetProb: Initialization function for "StoppingTargetProb"
StoppingTargetProb-class: Stop based on probability of target tox interval
StoppingTDCIRatio: Initialization function for "StoppingTDCIRatio"
StoppingTDCIRatio-class: Stop based on a target ratio, the ratio of the upper to the...
stopTrial: Stop the trial?
summary-DualSimulations-method: Summarize the dual-endpoint design simulations, relative to...
summary-GeneralSimulations-method: Summarize the simulations, relative to a given truth
summary-PseudoDualFlexiSimulations-method: Summary for Pseudo Dual responses simulations given a pseudo...
summary-PseudoDualSimulations-method: Summary for Pseudo Dual responses simulations, relative to a...
summary-PseudoSimulations-method: Summarize the simulations, relative to a given truth
summary-Simulations-method: Summarize the model-based design simulations, relative to a...
TDDesign: Initialization function for 'TDDesign' class
TDDesign-class: Design class using DLE responses only based on the pseudo DLE...
TDsamplesDesign: Initialization function for 'TDsamplesDesign' class
TDsamplesDesign-class: This is a class of design based only on DLE responses using...
ThreePlusThreeDesign: Creates a new 3+3 design object from a dose grid
update-DataDual-method: Update method for the "DataDual" class
update-Data-method: Update method for the "Data" class
update-DataParts-method: Update method for the "DataParts" class
update-EffFlexi-method: Update method for the 'EffFlexi' Model class. This is a...
update-Effloglog-method: Update method for the 'Effloglog' Model class. This is a...
update-LogisticIndepBeta-method: Update method for the 'LogisticIndepBeta'Model class. This is...
Validate: A Reference Class to help programming validation for new S4...
writeModel: Creating a WinBUGS model file

Functions

&,Stopping,Stopping-method Man page
&,Stopping,StoppingAll-method Man page
&,StoppingAll,Stopping-method Man page
.AllModels Man page
.CohortSizeConst Man page
.CohortSizeDLT Man page
.CohortSizeMax Man page
.CohortSizeMin Man page
.CohortSizeParts Man page
.CohortSizeRange Man page
.Data Man page
.DataDual Man page
.DataMixture Man page
.DataParts Man page
.Design Man page
.DualDesign Man page
.DualEndpoint Man page
.DualEndpointBeta Man page
.DualEndpointEmax Man page
.DualEndpointRW Man page
.DualResponsesDesign Man page
.DualResponsesSamplesDesign Man page
.DualSimulations Man page
.DualSimulationsSummary Man page
.EffFlexi Man page
.Effloglog Man page
.GeneralData Man page
.GeneralModel Man page
.GeneralSimulations Man page
.GeneralSimulationsSummary Man page
.IncrementsRelative Man page
.IncrementsRelativeDLT Man page
.IncrementsRelativeParts Man page
.LogisticIndepBeta Man page
.LogisticKadane Man page
.LogisticLogNormal Man page
.LogisticLogNormalMixture Man page
.LogisticLogNormalSub Man page
.LogisticNormal Man page
.LogisticNormalFixedMixture Man page
.LogisticNormalMixture Man page
.McmcOptions Man page
.Model Man page
.ModelEff Man page
.ModelPseudo Man page
.ModelTox Man page
.NextBestDualEndpoint Man page
.NextBestMTD Man page
.NextBestMaxGain Man page
.NextBestMaxGainSamples Man page
.NextBestNCRM Man page
.NextBestTD Man page
.NextBestTDsamples Man page
.NextBestThreePlusThree Man page
.ProbitLogNormal Man page
.PseudoDualFlexiSimulations Man page
.PseudoDualSimulations Man page
.PseudoDualSimulationsSummary Man page
.PseudoSimulations Man page
.PseudoSimulationsSummary Man page
.RuleDesign Man page
.Samples Man page
.Simulations Man page
.SimulationsSummary Man page
.StoppingAll Man page
.StoppingAny Man page
.StoppingCohortsNearDose Man page
.StoppingGstarCIRatio Man page
.StoppingHighestDose Man page
.StoppingList Man page
.StoppingMTDdistribution Man page
.StoppingMinCohorts Man page
.StoppingMinPatients Man page
.StoppingPatientsNearDose Man page
.StoppingTDCIRatio Man page
.StoppingTargetBiomarker Man page
.StoppingTargetProb Man page
.TDDesign Man page
.TDsamplesDesign Man page
AllModels-class Man page
CohortSize-class Man page
CohortSizeConst Man page Source code
CohortSizeConst-class Man page
CohortSizeDLT Man page Source code
CohortSizeDLT-class Man page
CohortSizeMax Man page Source code
CohortSizeMax-class Man page
CohortSizeMin Man page Source code
CohortSizeMin-class Man page
CohortSizeParts Man page Source code
CohortSizeParts-class Man page
CohortSizeRange Man page Source code
CohortSizeRange-class Man page
Data Man page Source code
Data-class Man page
DataDual Man page Source code
DataDual-class Man page
DataMixture Man page Source code
DataMixture-class Man page
DataParts Man page Source code
DataParts-class Man page
Design Man page Source code
Design-class Man page
DualDesign Man page Source code
DualDesign-class Man page
DualEndpoint Man page Source code
DualEndpoint-class Man page
DualEndpointBeta Man page Source code
DualEndpointBeta-class Man page
DualEndpointEmax Man page Source code
DualEndpointEmax-class Man page
DualEndpointOld-class Man page
DualEndpointRW Man page Source code
DualEndpointRW-class Man page
DualResponsesDesign Man page Source code
DualResponsesDesign-class Man page
DualResponsesSamplesDesign Man page Source code
DualResponsesSamplesDesign-class Man page
DualSimulations Man page Source code
DualSimulations-class Man page
DualSimulationsSummary-class Man page
EffFlexi Man page Source code
EffFlexi-class Man page
Effloglog Man page Source code
Effloglog-class Man page
ExpEff Man page
ExpEff,numeric,EffFlexi,Samples-method Man page
ExpEff,numeric,Effloglog,Samples-method Man page
ExpEff,numeric,Effloglog,missing-method Man page
GeneralData-class Man page
GeneralModel-class Man page
GeneralSimulations Man page Source code
GeneralSimulations-class Man page
GeneralSimulationsSummary-class Man page
Increments-class Man page
IncrementsRelative Man page Source code
IncrementsRelative-class Man page
IncrementsRelativeDLT Man page Source code
IncrementsRelativeDLT-class Man page
IncrementsRelativeParts Man page Source code
IncrementsRelativeParts-class Man page
LogisticIndepBeta Man page Source code
LogisticIndepBeta-class Man page
LogisticKadane Man page Source code
LogisticKadane-class Man page
LogisticLogNormal Man page Source code
LogisticLogNormal-class Man page
LogisticLogNormalMixture Man page Source code
LogisticLogNormalMixture-class Man page
LogisticLogNormalSub Man page Source code
LogisticLogNormalSub-class Man page
LogisticNormal Man page Source code
LogisticNormal-class Man page
LogisticNormalFixedMixture Man page Source code
LogisticNormalFixedMixture-class Man page
LogisticNormalMixture Man page Source code
LogisticNormalMixture-class Man page
McmcOptions Man page Source code
McmcOptions-class Man page
MinimalInformative Man page Source code
Model-class Man page
ModelEff-class Man page
ModelPseudo-class Man page
ModelTox-class Man page
NextBest-class Man page
NextBestDualEndpoint Man page Source code
NextBestDualEndpoint-class Man page
NextBestMTD Man page Source code
NextBestMTD-class Man page
NextBestMaxGain Man page Source code
NextBestMaxGain-class Man page
NextBestMaxGainSamples Man page Source code
NextBestMaxGainSamples-class Man page
NextBestNCRM Man page Source code
NextBestNCRM-class Man page
NextBestTD Man page Source code
NextBestTD-class Man page
NextBestTDsamples Man page Source code
NextBestTDsamples-class Man page
NextBestThreePlusThree Man page Source code
NextBestThreePlusThree-class Man page
ProbitLogNormal Man page Source code
ProbitLogNormal-class Man page
PseudoDualFlexiSimulations Man page Source code
PseudoDualFlexiSimulations-class Man page
PseudoDualSimulations Man page Source code
PseudoDualSimulations-class Man page
PseudoDualSimulationsSummary-class Man page
PseudoSimulations Man page Source code
PseudoSimulations-class Man page
PseudoSimulationsSummary-class Man page
Quantiles2LogisticNormal Man page Source code
Report Man page
RuleDesign Man page Source code
RuleDesign-class Man page
Samples Man page Source code
Samples-class Man page
Simulations Man page Source code
Simulations-class Man page
SimulationsSummary-class Man page
Stopping-class Man page
StoppingAll Man page Source code
StoppingAll-class Man page
StoppingAny Man page Source code
StoppingAny-class Man page
StoppingCohortsNearDose Man page Source code
StoppingCohortsNearDose-class Man page
StoppingGstarCIRatio Man page Source code
StoppingGstarCIRatio-class Man page
StoppingHighestDose Man page Source code
StoppingHighestDose-class Man page
StoppingList Man page Source code
StoppingList-class Man page
StoppingMTDdistribution Man page Source code
StoppingMTDdistribution-class Man page
StoppingMinCohorts Man page Source code
StoppingMinCohorts-class Man page
StoppingMinPatients Man page Source code
StoppingMinPatients-class Man page
StoppingPatientsNearDose Man page Source code
StoppingPatientsNearDose-class Man page
StoppingTDCIRatio Man page Source code
StoppingTDCIRatio-class Man page
StoppingTargetBiomarker Man page Source code
StoppingTargetBiomarker-class Man page
StoppingTargetProb Man page Source code
StoppingTargetProb-class Man page
TDDesign Man page Source code
TDDesign-class Man page
TDsamplesDesign Man page Source code
TDsamplesDesign-class Man page
ThreePlusThreeDesign Man page Source code
Validate Man page
approximate Man page
approximate,Samples-method Man page
as.list,GeneralData-method Man page
biomLevel Man page
biomLevel,numeric,DualEndpoint,Samples-method Man page
crmPack Man page
crmPack-package Man page
crmPackExample Man page Source code
crmPackHelp Man page Source code
dinvGamma Man page Source code
dose Man page
dose,numeric,Model,Samples-method Man page
dose,numeric,ModelTox,Samples-method Man page
dose,numeric,ModelTox,missing-method Man page
examine Man page
examine,Design-method Man page
examine,RuleDesign-method Man page
fit Man page
fit,Samples,DualEndpoint,DataDual-method Man page
fit,Samples,EffFlexi,DataDual-method Man page
fit,Samples,Effloglog,DataDual-method Man page
fit,Samples,LogisticIndepBeta,Data-method Man page
fit,Samples,Model,Data-method Man page
fitGain Man page
fitGain,ModelTox,Samples,ModelEff,Samples,DataDual-method Man page
gain Man page
gain,numeric,ModelTox,Samples,EffFlexi,Samples-method Man page
gain,numeric,ModelTox,Samples,Effloglog,Samples-method Man page
gain,numeric,ModelTox,missing,Effloglog,missing-method Man page
get,Samples,character-method Man page
getEff Man page
getEff,DataDual-method Man page
getMinInfBeta Man page Source code
getResultList Man page Source code
initialize,DualEndpointOld-method Man page
is.bool Man page Source code
is.probRange Man page Source code
is.probability Man page Source code
is.range Man page Source code
is.scalar Man page Source code
is.wholenumber Man page Source code
joinBodies Man page Source code
joinModels Man page Source code
logit Man page Source code
maxDose Man page
maxDose,IncrementsRelative,Data-method Man page
maxDose,IncrementsRelativeDLT,Data-method Man page
maxDose,IncrementsRelativeParts,DataParts-method Man page
maxSize Man page
maxSize,CohortSize-method Man page
mcmc Man page
mcmc,Data,LogisticIndepBeta,McmcOptions-method Man page
mcmc,Data,LogisticNormal,McmcOptions-method Man page
mcmc,DataDual,EffFlexi,McmcOptions-method Man page
mcmc,DataDual,Effloglog,McmcOptions-method Man page
mcmc,DataMixture,GeneralModel,McmcOptions-method Man page
mcmc,GeneralData,GeneralModel,McmcOptions-method Man page
minSize Man page
minSize,CohortSize-method Man page
multiplot Man page Source code
myBarplot Man page Source code
nextBest Man page
nextBest,NextBestDualEndpoint,numeric,Samples,DualEndpoint,Data- Man page
nextBest,NextBestMTD,numeric,Samples,Model,Data-method Man page
nextBest,NextBestMaxGain,numeric,missing,ModelTox,DataDual-metho Man page
nextBest,NextBestMaxGainSamples,numeric,Samples,ModelTox,DataDua Man page
nextBest,NextBestNCRM,numeric,Samples,Model,Data-method Man page
nextBest,NextBestNCRM,numeric,Samples,Model,DataParts-method Man page
nextBest,NextBestTD,numeric,missing,LogisticIndepBeta,Data-metho Man page
nextBest,NextBestTDsamples,numeric,Samples,LogisticIndepBeta,Dat Man page
nextBest,NextBestThreePlusThree,missing,missing,missing,Data-met Man page
noOverlap Man page Source code
onAttach Source code
or-Stopping-Stopping Man page
or-Stopping-StoppingAny Man page
or-StoppingAny-Stopping Man page
pinvGamma Man page Source code
plot,Data,ModelTox-method Man page
plot,Data,missing-method Man page
plot,DataDual,ModelEff-method Man page
plot,DataDual,missing-method Man page
plot,DualSimulations,missing-method Man page
plot,DualSimulationsSummary,missing-method Man page
plot,GeneralSimulations,missing-method Man page
plot,GeneralSimulationsSummary,missing-method Man page
plot,PseudoDualFlexiSimulations,missing-method Man page
plot,PseudoDualSimulations,missing-method Man page
plot,PseudoDualSimulationsSummary,missing-method Man page
plot,PseudoSimulationsSummary,missing-method Man page
plot,Samples,DualEndpoint-method Man page
plot,Samples,Model-method Man page
plot,Samples,ModelEff-method Man page
plot,Samples,ModelTox-method Man page
plot,SimulationsSummary,missing-method Man page
plot.gtable Man page Source code
plotDualResponses Man page
plotDualResponses,ModelTox,Samples,ModelEff,Samples-method Man page
plotDualResponses,ModelTox,missing,ModelEff,missing-method Man page
plotGain Man page
plotGain,ModelTox,Samples,ModelEff,Samples-method Man page
plotGain,ModelTox,missing,ModelEff,missing-method Man page
print.gtable Source code
printVignette Man page Source code
prob Man page
prob,numeric,Model,Samples-method Man page
prob,numeric,ModelTox,Samples-method Man page
prob,numeric,ModelTox,missing-method Man page
probit Man page Source code
qinvGamma Man page Source code
replaceScientificNotationR Source code
rinvGamma Man page Source code
safeInteger Man page Source code
sampleSize Man page Source code
saveSample Man page Source code
setSeed Man page Source code
show,DualSimulationsSummary-method Man page
show,GeneralSimulationsSummary-method Man page
show,PseudoDualSimulationsSummary-method Man page
show,PseudoSimulationsSummary-method Man page
show,SimulationsSummary-method Man page
simulate,Design-method Man page
simulate,DualDesign-method Man page
simulate,DualResponsesDesign-method Man page
simulate,DualResponsesSamplesDesign-method Man page
simulate,RuleDesign-method Man page
simulate,TDDesign-method Man page
simulate,TDsamplesDesign-method Man page
size Man page
size,CohortSizeConst,ANY,Data-method Man page
size,CohortSizeDLT,ANY,Data-method Man page
size,CohortSizeMax,ANY,Data-method Man page
size,CohortSizeMin,ANY,Data-method Man page
size,CohortSizeParts,ANY,DataParts-method Man page
size,CohortSizeRange,ANY,Data-method Man page
stopTrial Man page
stopTrial,StoppingAll,ANY,ANY,ANY,ANY-method Man page
stopTrial,StoppingAny,ANY,ANY,ANY,ANY-method Man page
stopTrial,StoppingCohortsNearDose,numeric,ANY,ANY,Data-method Man page
stopTrial,StoppingGstarCIRatio,ANY,Samples,ModelTox,DataDual-met Man page
stopTrial,StoppingGstarCIRatio,ANY,missing,ModelTox,DataDual-met Man page
stopTrial,StoppingHighestDose,numeric,ANY,ANY,Data-method Man page
stopTrial,StoppingList,ANY,ANY,ANY,ANY-method Man page
stopTrial,StoppingMTDdistribution,numeric,Samples,Model,ANY-meth Man page
stopTrial,StoppingMinCohorts,ANY,ANY,ANY,Data-method Man page
stopTrial,StoppingMinPatients,ANY,ANY,ANY,Data-method Man page
stopTrial,StoppingPatientsNearDose,numeric,ANY,ANY,Data-method Man page
stopTrial,StoppingTDCIRatio,ANY,Samples,ModelTox,ANY-method Man page
stopTrial,StoppingTDCIRatio,ANY,missing,ModelTox,ANY-method Man page
stopTrial,StoppingTargetBiomarker,numeric,Samples,DualEndpoint,A Man page
stopTrial,StoppingTargetProb,numeric,Samples,Model,ANY-method Man page
summary,DualSimulations-method Man page
summary,GeneralSimulations-method Man page
summary,PseudoDualFlexiSimulations-method Man page
summary,PseudoDualSimulations-method Man page
summary,PseudoSimulations-method Man page
summary,Simulations-method Man page
update,Data-method Man page
update,DataDual-method Man page
update,DataParts-method Man page
update,EffFlexi-method Man page
update,Effloglog-method Man page
update,LogisticIndepBeta-method Man page
writeModel Man page Source code
|,Stopping,Stopping-method Man page
|,Stopping,StoppingAny-method Man page
|,StoppingAny,Stopping-method Man page

Files

TODO
inst
inst/crmPack.pdf
inst/NEWS
inst/doc
inst/doc/example.R
inst/doc/example.Rnw
inst/doc/example.pdf
NAMESPACE
R
R/Model-class.R
R/Rules-class.R
R/Samples-class.R
R/helpers.R
R/McmcOptions-methods.R
R/Data-methods.R
R/Simulations-methods.R
R/McmcOptions-class.R
R/fromQuantiles.R
R/writeModel.R
R/Model-methods.R
R/Simulations-class.R
R/Samples-methods.R
R/Design-methods.R
R/crmPack-package.R
R/Data-class.R
R/Rules-methods.R
R/mcmc.R
R/Design-class.R
vignettes
vignettes/tikzlibrarypositioning-plus.code.tex
vignettes/example.bib
vignettes/example.Rnw
vignettes/mySweave.sty
MD5
build
build/vignette.rds
DESCRIPTION
man
man/DualEndpointBeta-class.Rd
man/plot-Samples-Model-method.Rd
man/setSeed.Rd
man/DualResponsesSamplesDesign.Rd
man/show-PseudoDualSimulationsSummary-method.Rd
man/GeneralSimulations-class.Rd
man/NextBestMaxGain.Rd
man/IncrementsRelativeParts-class.Rd
man/StoppingMinPatients-class.Rd
man/StoppingList-class.Rd
man/StoppingAll-class.Rd
man/NextBestTD-class.Rd
man/fit.Rd
man/CohortSizeMin-class.Rd
man/RuleDesign-class.Rd
man/LogisticIndepBeta.Rd
man/update-DataParts-method.Rd
man/IncrementsRelativeDLT.Rd
man/LogisticNormalFixedMixture.Rd
man/probit.Rd
man/DualResponsesDesign-class.Rd
man/crmPackExample.Rd
man/NextBestDualEndpoint-class.Rd
man/NextBestTD.Rd
man/PseudoSimulationsSummary-class.Rd
man/LogisticNormal-class.Rd
man/LogisticLogNormalMixture.Rd
man/Effloglog-class.Rd
man/is.scalar.Rd
man/StoppingTargetBiomarker-class.Rd
man/StoppingTargetProb-class.Rd
man/StoppingAll.Rd
man/nextBest.Rd
man/or-Stopping-StoppingAny.Rd
man/NextBestDualEndpoint.Rd
man/PseudoDualSimulationsSummary-class.Rd
man/Design.Rd
man/NextBestMaxGain-class.Rd
man/PseudoDualSimulations-class.Rd
man/DualEndpointRW-class.Rd
man/stopTrial.Rd
man/update-LogisticIndepBeta-method.Rd
man/simulate-Design-method.Rd
man/simulate-DualResponsesDesign-method.Rd
man/summary-GeneralSimulations-method.Rd
man/Quantiles2LogisticNormal.Rd
man/Data-class.Rd
man/Simulations.Rd
man/CohortSizeMax-class.Rd
man/ModelTox-class.Rd
man/Samples.Rd
man/IncrementsRelative.Rd
man/plot-DataDual-ModelEff-method.Rd
man/NextBestTDsamples-class.Rd
man/DualSimulationsSummary-class.Rd
man/plot.gtable.Rd
man/NextBestThreePlusThree-class.Rd
man/plotGain.Rd
man/LogisticNormalMixture.Rd
man/StoppingPatientsNearDose-class.Rd
man/writeModel.Rd
man/is.probability.Rd
man/PseudoDualFlexiSimulations.Rd
man/Design-class.Rd
man/NextBestMaxGainSamples.Rd
man/update-Data-method.Rd
man/NextBestNCRM.Rd
man/show-GeneralSimulationsSummary-method.Rd
man/is.wholenumber.Rd
man/LogisticLogNormalMixture-class.Rd
man/Effloglog.Rd
man/CohortSizeMax.Rd
man/GeneralData-class.Rd
man/StoppingPatientsNearDose.Rd
man/LogisticNormalMixture-class.Rd
man/TDsamplesDesign-class.Rd
man/plot-DualSimulationsSummary-missing-method.Rd
man/RuleDesign.Rd
man/DualEndpointEmax.Rd
man/StoppingHighestDose-class.Rd
man/minSize.Rd
man/PseudoDualSimulations.Rd
man/summary-PseudoDualFlexiSimulations-method.Rd
man/StoppingList.Rd
man/ExpEff.Rd
man/get-Samples-character-method.Rd
man/prob.Rd
man/NextBestNCRM-class.Rd
man/ProbitLogNormal-class.Rd
man/or-Stopping-Stopping.Rd
man/DataParts-class.Rd
man/DataDual.Rd
man/EffFlexi-class.Rd
man/Model-class.Rd
man/plot-DualSimulations-missing-method.Rd
man/safeInteger.Rd
man/DataParts.Rd
man/initialize-DualEndpointOld-method.Rd
man/Simulations-class.Rd
man/StoppingAny-class.Rd
man/EffFlexi.Rd
man/is.range.Rd
man/DualSimulations-class.Rd
man/ModelPseudo-class.Rd
man/plot-PseudoDualSimulationsSummary-missing-method.Rd
man/gain.Rd
man/summary-DualSimulations-method.Rd
man/dose.Rd
man/show-SimulationsSummary-method.Rd
man/joinBodies.Rd
man/CohortSizeConst-class.Rd
man/update-DataDual-method.Rd
man/DualEndpoint.Rd
man/and-Stopping-Stopping-method.Rd
man/joinModels.Rd
man/Validate.Rd
man/plot-Samples-ModelEff-method.Rd
man/examine.Rd
man/summary-Simulations-method.Rd
man/plotDualResponses.Rd
man/AllModels-class.Rd
man/LogisticLogNormalSub.Rd
man/StoppingCohortsNearDose-class.Rd
man/show-PseudoSimulationsSummary-method.Rd
man/maxSize.Rd
man/IncrementsRelative-class.Rd
man/approximate.Rd
man/ThreePlusThreeDesign.Rd
man/biomLevel.Rd
man/or-StoppingAny-Stopping.Rd
man/DualDesign.Rd
man/CohortSizeParts-class.Rd
man/LogisticKadane-class.Rd
man/logit.Rd
man/CohortSize-class.Rd
man/qinvGamma.Rd
man/IncrementsRelativeParts.Rd
man/GeneralSimulationsSummary-class.Rd
man/StoppingGstarCIRatio-class.Rd
man/DualResponsesSamplesDesign-class.Rd
man/and-Stopping-StoppingAll-method.Rd
man/CohortSizeConst.Rd
man/LogisticKadane.Rd
man/DualDesign-class.Rd
man/CohortSizeDLT-class.Rd
man/DualSimulations.Rd
man/simulate-TDDesign-method.Rd
man/PseudoSimulations-class.Rd
man/DataMixture-class.Rd
man/getMinInfBeta.Rd
man/DualEndpointOld-class.Rd
man/dinvGamma.Rd
man/NextBestMTD-class.Rd
man/StoppingMTDdistribution-class.Rd
man/plot-Samples-ModelTox-method.Rd
man/StoppingMinCohorts-class.Rd
man/StoppingHighestDose.Rd
man/TDDesign-class.Rd
man/DataDual-class.Rd
man/LogisticLogNormalSub-class.Rd
man/CohortSizeDLT.Rd
man/Data.Rd
man/myBarplot.Rd
man/Increments-class.Rd
man/StoppingTargetProb.Rd
man/simulate-RuleDesign-method.Rd
man/size.Rd
man/CohortSizeRange-class.Rd
man/maxDose.Rd
man/plot-Data-ModelTox-method.Rd
man/multiplot.Rd
man/StoppingMinCohorts.Rd
man/NextBestMaxGainSamples-class.Rd
man/plot-PseudoDualFlexiSimulations-missing-method.Rd
man/update-EffFlexi-method.Rd
man/StoppingTargetBiomarker.Rd
man/noOverlap.Rd
man/getEff.Rd
man/LogisticIndepBeta-class.Rd
man/StoppingMTDdistribution.Rd
man/plot-Data-missing-method.Rd
man/ModelEff-class.Rd
man/NextBestMTD.Rd
man/printVignette.Rd
man/plot-GeneralSimulations-missing-method.Rd
man/update-Effloglog-method.Rd
man/Samples-class.Rd
man/StoppingTDCIRatio-class.Rd
man/plot-PseudoDualSimulations-missing-method.Rd
man/DualEndpointBeta.Rd
man/PseudoDualFlexiSimulations-class.Rd
man/and-StoppingAll-Stopping-method.Rd
man/summary-PseudoSimulations-method.Rd
man/StoppingTDCIRatio.Rd
man/DualEndpoint-class.Rd
man/DualEndpointEmax-class.Rd
man/DataMixture.Rd
man/MinimalInformative.Rd
man/TDDesign.Rd
man/PseudoSimulations.Rd
man/crmPack-package.Rd
man/DualEndpointRW.Rd
man/IncrementsRelativeDLT-class.Rd
man/StoppingCohortsNearDose.Rd
man/McmcOptions-class.Rd
man/CohortSizeRange.Rd
man/is.probRange.Rd
man/sampleSize.Rd
man/ProbitLogNormal.Rd
man/LogisticLogNormal-class.Rd
man/plot-SimulationsSummary-missing-method.Rd
man/rinvGamma.Rd
man/LogisticNormal.Rd
man/crmPackHelp.Rd
man/CohortSizeParts.Rd
man/plot-PseudoSimulationsSummary-missing-method.Rd
man/simulate-DualResponsesSamplesDesign-method.Rd
man/as.list-GeneralData-method.Rd
man/GeneralSimulations.Rd
man/GeneralModel-class.Rd
man/summary-PseudoDualSimulations-method.Rd
man/Stopping-class.Rd
man/is.bool.Rd
man/Report.Rd
man/NextBestTDsamples.Rd
man/StoppingMinPatients.Rd
man/saveSample.Rd
man/LogisticNormalFixedMixture-class.Rd
man/plot-DataDual-missing-method.Rd
man/fitGain.Rd
man/DualResponsesDesign.Rd
man/simulate-TDsamplesDesign-method.Rd
man/show-DualSimulationsSummary-method.Rd
man/NextBest-class.Rd
man/StoppingGstarCIRatio.Rd
man/CohortSizeMin.Rd
man/simulate-DualDesign-method.Rd
man/pinvGamma.Rd
man/McmcOptions.Rd
man/NextBestThreePlusThree.Rd
man/LogisticLogNormal.Rd
man/getResultList.Rd
man/SimulationsSummary-class.Rd
man/plot-GeneralSimulationsSummary-missing-method.Rd
man/TDsamplesDesign.Rd
man/StoppingAny.Rd
man/mcmc.Rd
man/plot-Samples-DualEndpoint-method.Rd
crmPack documentation built on May 20, 2017, 2:20 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.