| 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 |
| IncrementsNumDoseLevels | Initialization function for "IncrementsNumDoseLevels" |
| IncrementsNumDoseLevels-class | Increments control based on number of dose levels |
| 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 | Plot for PseudoDualFlexiSimulations |
| 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 |
