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

Files in this package

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 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