Object-Oriented Implementation of CRM Designs

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 |

IncrementMin | Initialization function for "IncrementMin" |

IncrementMin-class | Max increment based on minimum of multiple increment rules |

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 |

matchTolerance | Helper function for value matching with tolerance |

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 |

myBayesLogit | Do MCMC sampling for Bayesian logistic regression model |

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 |

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