crmPack: Object-Oriented Implementation of CRM Designs

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 publication2016-07-16 23:06:48
MaintainerDaniel Sabanes Bove <sabanesd@roche.com>
LicenseGPL (>= 2)
Version0.2.0

View on CRAN

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.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...

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

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

Files

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

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

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

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