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crmPack (version 2.2.1)

Object-Oriented Implementation of Dose Escalation Designs

Description

Implements a wide range of dose escalation designs. The focus is on model-based 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. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy to setup a new design with custom 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. Further details are presented in Sabanés Bové et al. (2019) .

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Version

Install

install.packages('crmPack')

Monthly Downloads

578

Version

2.2.1

License

GPL (>= 2)

Maintainer

Daniel Sabanes Bove

Last Published

July 27th, 2026

Functions in crmPack (2.2.1)

CrmPackClass-class

CohortSizeRandom-class

CohortSizeRandom

CohortSizeRange-class

CohortSizeRange

Likelihood of DLTs in each interval

DataCombo-class

DataParts-class

DataGrouped-class

DataMixture-class

CohortSizeMax-class

CohortSizeMax

DataOrdinal-class

ArmConditionList-class

ArmConditionList

CohortSizeMin-class

CohortSizeMin

DesignGrouped-class

DesignGrouped

DualSimulationsSummary-class

DualSimulationsSummary

DesignOrdinal-class

DesignOrdinal

DualDesign-class

DualEndpoint-class

DesignArm-class

DualEndpointRW-class

DualEndpointRW

DesignCombo-class

DualResponsesDesign-class

DualResponsesDesign.R

GeneralSimulationsSummary-class

GeneralSimulationsSummary

GeneralSimulations-class

GeneralSimulations

Effloglog-class

DualResponsesSamplesDesign-class

DualResponsesSamplesDesign

DualSimulations-class

DualSimulations

HierarchicalSimulations-class

HierarchicalSimulations

IncrementsRelativeDLTCurrent-class

IncrementsRelativeDLTCurrent

HierarchicalSimulationsSummary-class

HierarchicalSimulationsSummary

HierarchicalData-class

HierarchicalData

HierarchicalDesign-class

HierarchicalDesign

HierarchicalModel-class

HierarchicalModel

FractionalCRM-class

FractionalCRM

HierarchicalSamples-class

HierarchicalSamples

DALogisticLogNormal-class

DALogisticLogNormal

LogisticLogNormalOrdinal-class

LogisticLogNormalOrdinal

IncrementsRelativeParts-class

IncrementsRelativeParts

LogisticLogNormalSub-class

LogisticLogNormalSub

LogisticKadane-class

LogisticKadane

LogisticIndepBeta-class

LogisticIndepBeta

DASimulations-class

DASimulations

IncrementsHSRBeta-class

IncrementsHSRBeta

DualEndpointBeta-class

DualEndpointBeta

IncrementsRelative-class

IncrementsRelative

LogisticKadaneBetaGamma-class

LogisticKadaneBetaGamma

ModelParamsNormal-class

ModelParamsNormal

ModelLogNormal-class

ModelLogNormal

IncrementsRelativeDLT-class

IncrementsRelativeDLT

LogisticLogNormal-class

LogisticLogNormal

IncrementsDoseLevels-class

IncrementsDoseLevels

ModelPseudo-class

IncrementsComboOneDrugOnly-class

IncrementsComboOneDrugOnly

LogisticLogNormalGrouped-class

LogisticLogNormalGrouped

DualEndpointEmax-class

DualEndpointEmax

NextBestDualEndpoint-class

NextBestDualEndpoint

NextBestMaxGainSamples-class

NextBestMaxGainSamples

LogisticLogNormalMixture-class

LogisticLogNormalMixture

NoArmCondition-class

NoArmCondition

NextBestProbMTDLTE-class

NextBestProbMTDLTE

OneParExpPrior-class

OneParExpPrior

NextBestOrdinal-class

NextBestOrdinal

NextBestTDsamples-class

NextBestTDsamples

NextBestThreePlusThree-class

NextBestThreePlusThree

LogisticNormalFixedMixture-class

LogisticNormalFixedMixture

LogisticNormal-class

LogisticNormal

OneParLogNormalPrior-class

OneParLogNormalPrior

IncrementsMin-class

IncrementsMin

IncrementsComboCartesian-class

IncrementsComboCartesian

LogisticNormalMixture-class

LogisticNormalMixture

IncrementsOrdinal-class

IncrementsOrdinal

Increments-class

NextBestProbMTDMinDist-class

NextBestProbMTDMinDist

GeneralData-class

GeneralModel-class

PseudoDualSimulations-class

PseudoDualSimulations

RecruitmentRatio-class

RecruitmentRatio

RecruitmentUnlimited-class

RecruitmentUnlimited

PseudoDualSimulationsSummary-class

PseudoDualSimulationsSummary

NextBestMinDist-class

NextBestMinDist

StoppingAll-class

NextBestInfTheory-class

NextBestInfTheory

IncrementsMaxToxProb-class

IncrementsMaxToxProb

MinimalInformative

Construct a Minimally Informative Prior

ProbitLogNormalRel-class

ProbitLogNormalRel

StoppingAny-class

ProbitLogNormal-class

ProbitLogNormal

SafetyWindowSize-class

SafetyWindowSize

OpeningNone-class

OpeningAll-class

NextBestNCRMLoss-class

NextBestNCRMLoss

NextBestNCRM-class

McmcOptions-class

OpeningList-class

NextBestMaxGain-class

NextBestMaxGain

NextBestMTD-class

StoppingHighestDose-class

StoppingHighestDose

OpeningMinDose-class

OpeningMinDose

OpeningMinResponses-class

OpeningMinResponses

StoppingSpecificDose-class

StoppingSpecificDose

OpeningAny-class

SafetyWindow-class

SafetyWindowConst-class

SafetyWindowConst

NextBestEWOC-class

OpeningMinCohorts-class

OpeningMinCohorts

PseudoSimulationsSummary-class

PseudoSimulationsSummary

Simulations-class

SimulationsSummary-class

SimulationsSummary

Recruitment-class

Quantiles2LogisticNormal

Convert Prior Quantiles to Logistic (Log) Normal Model

StoppingMinCohorts-class

StoppingMinCohorts

NextBestTD-class

Check if All Arguments Are Equal

StoppingLowestDoseHSRBeta-class

StoppingLowestDoseHSRBeta

StoppingMTDCV-class

StoppingMTDCV

Check that an argument is a valid format specification

&,Stopping,StoppingAll-method

Combine an Atomic Stopping Rule and a Stopping List with AND

&,StoppingAll,Stopping-method

Combine a Stopping List and an Atomic Stopping Rule with AND

StoppingMTDdistribution-class

StoppingMTDdistribution

Object-oriented implementation of CRM designs

StoppingMaxGainCIRatio-class

StoppingMaxGainCIRatio

RuleDesign-class

RuleDesignOrdinal-class

RuleDesignOrdinal

StartingDose-class

StoppingList-class

StoppingMissingDose-class

StoppingMissingDose

StoppingTDCIRatio-class

StoppingTDCIRatio

Approximate posterior with (log) normal distribution

TITELogisticLogNormal-class

TITELogisticLogNormal

TDsamplesDesign-class

TDsamplesDesign

StoppingMinPatients-class

StoppingMinPatients

StoppingPatientsNearDose-class

StoppingPatientsNearDose

Open the Browser with Help Pages for crmPack

Open the Example PDF for crmPack

StoppingTargetBiomarker-class

StoppingTargetBiomarker

Check if vectors are of compatible lengths

Get the fitted values for the gain values at all dose levels based on a given pseudo DLE model, DLE sample, a pseudo efficacy model, a Efficacy sample and data. This method returns a data frame with dose, middle, lower and upper quantiles of the gain value samples

Apply a Function to Subsets of Data Frame.

PseudoSimulations-class

PseudoSimulations

PseudoDualFlexiSimulations-class

PseudoDualFlexiSimulations

TITELogisticLogNormalSub-class

TITELogisticLogNormalSub

Compute the Density of Inverse Gamma Distribution

StoppingCohortsNearDose-class

StoppingCohortsNearDose

StoppingExternal-class

StoppingExternal

check_probability

Check if an argument is a single probability value

efficacyFunction

Getting the Efficacy Function for a Given Model Type

Extract One Arm's Posterior Draws from a HierarchicalSamples Object

Computing Expected Efficacy for a Given Dose, Model and Samples

h_dose_combo_below_limit

Check if the Doses in a Dose Matrix are Below the Dose Limit.

dose_grid_range

Getting the Dose Grid Range

h_convert_ordinal_data

Convert a Ordinal Data to the Equivalent Binary Data for a Specific Grade

StoppingTargetProb-class

StoppingTargetProb

and,ArmCondition,ArmCondition-method

Logical AND Operator for ArmCondition Objects

check_probabilities

Check if an argument is a probability vector

h_blind_plot_data

Helper Function to Blind Plot Data

Check that an argument is a numerical range

Additional Assertions for checkmate

Get the Biomarker Levels for a Given Dual-Endpoint Model, Given Dose Levels and Samples

Computing the Doses for a given independent variable, Model and Samples

check_probability_range

Check if an argument is a probability range

h_check_fun_formals

Checking Formals of a Function

Getting the Dose Function for a Given Model Type

h_barplot_percentages

Convenience function to make barplots of percentages

StoppingOrdinal-class

StoppingOrdinal

TwoDrugsCombo-class

TwoDrugsCombo

Compute Gain Values based on Pseudo DLE and a Pseudo Efficacy Models and Using Optional Samples.

get,Samples,character-method

Get specific parameter samples and produce a data.frame

h_hierarchical_compile_datamodel

Compile the Hierarchical Data Model

h_hierarchical_compile_modelspecs

Compile the Hierarchical Model-Specification Function

Verbose Logging

h_jags_add_dummy

Appending a Dummy Number for Selected Slots in Data

h_is_positive_definite

Testing Matrix for Positive Definiteness

get_arm_simulations

Extract Arm-Level Simulations from Hierarchical Simulations

Extracting Efficacy Responses for Subjects Categorized by the DLT

h_hierarchical_compile_priormodel

Compile the Hierarchical Prior Model

h_enroll_backfill_patients

Helper Function to Enroll Backfill Patients

h_hierarchical_compile_init

Compile the Hierarchical Initial-Value Function

h_hierarchical_pooled_nodes

Find Pooled Nodes for an Arm

h_hierarchical_prior_relations

Collect Prior Relations

h_default_if_empty

Getting the default value for an empty object

h_convert_ordinal_model

Convert an ordinal CRM model to the Equivalent Binary CRM Model for a Specific Grade

h_get_formatted_dosegrid

Format a doseGrid for Printing

h_format_number

Conditional Formatting Using C-style Formats

h_calc_report_label_percentage

Helper function to calculate percentage of true stopping rules for report label output calculates true column means and converts output into percentages before combining the output with the report label; output is passed to show() and output with cat to console

h_get_min_inf_beta

Helper for Minimal Informative Unimodal Beta Distribution

h_convert_ordinal_samples

Convert a Samples Object from an ordinal Model to the Equivalent Samples Object from a Binary Model

Get the fitted DLT free survival (piecewise exponential model). This function returns a data frame with dose, middle, lower and upper quantiles for the PEM curve. If hazard=TRUE,

Group Together Mono and Combo Data

h_info_theory_dist

Calculating the Information Theoretic Distance

h_hierarchical_expr_key

Normalize an Expression Key

h_determine_dlts

Helper function to determine the dlts including first separate and placebo condition

h_mcmc_get_hierarchical_data

Flatten HierarchicalData into JAGS Input for a HierarchicalModel

h_hierarchical_get_decision_samples

Helper function to get the samples used for decision rules in a hierarchical design

h_hierarchical_reference_expr

Create the Namespaced Expression for a Parameter Reference

h_hierarchical_get_arm_arg

Select an Arm-Specific Argument

h_hierarchical_parse_ref

Parse a Hierarchical Parameter Reference

h_hierarchical_bind_stop_report

Bind Hierarchical Stop Reports for One Arm

h_get_quantiles_start_values

Get Starting Values for Quantiles Optimization

Helpers for stripping expressions of covr-inserted trace code

Fit method for the Samples class

h_knit_format_func

Used to obtain expected format.

h_mcmc_get_hierarchical_arm_samples

Build Arm-Specific Sample Name Mappings for a HierarchicalModel

h_model_dual_endpoint_beta

Update certain components of DualEndpoint model with regard to parameters of the function that models dose-biomarker relationship defined in the DualEndpointBeta class.

h_hierarchical_reference_stochastic_node

Infer the Stochastic Node for a Parameter Reference

h_summarize_add_stats

Helper function to calculate average across iterations for each additional reporting parameter extracts parameter names as specified by user and averaged the values for each specified parameter to show() and output with cat to console

h_test_named_numeric

Check that an argument is a named vector of type numeric

&,Stopping,Stopping-method

Combine Two Stopping Rules with AND

h_model_dual_endpoint_sigma2betaw

Update certain components of DualEndpoint model with regard to prior variance factor of the random walk.

and,Opening,Opening-method

Logical AND Operator for Opening Objects

h_jags_get_model_inits

Setting Initial Values for JAGS Model Parameters

Check which elements are in a given range

h_next_best_ncrm_loss_plot

Building the Plot for nextBest-NextBestNCRMLoss Method.

h_next_best_td_plot

Building the Plot for nextBest-NextBestTD Method.

h_jags_join_models

Joining JAGS Models

h_hierarchical_filter_pooled_specs

Drop Fixed-Prior Specs for Fully Pooled Generic Parameters

Obtain Hypothetical Trial Course Table for a Design

h_all_equivalent

Comparison with Numerical Tolerance and Without Name Comparison

h_jags_extract_samples

Extracting Samples from JAGS mcarray Object

h_hierarchical_root_symbols

Find the Root Symbol of an Expression

h_hierarchical_remove_pooled_prior_lines

Remove Fixed Priors for Pooled Nodes

h_next_best_tdsamples_plot

Building the Plot for nextBest-NextBestTDsamples Method.

Getting NULL for NA

h_model_dual_endpoint_rho

Update DualEndpoint class model components with regard to DLT and biomarker correlation.

h_jags_get_data

Getting Data for JAGS

h_next_best_mg_ci

Credibility Intervals for Max Gain and Target Doses at nextBest-NextBestMaxGain Method.

get_result_list

Helper Function to Obtain Simulation Results List

h_quantiles_target_function

Target Function for Quantiles Optimization

h_hierarchical_make_pool_map

Flatten Hierarchical Pool Definitions into a Lookup Table

h_prepare_units

Append Units to a Numeric Dose

h_prepare_labels

Check That Labels Are Valid and Useful

h_hierarchical_is_single_model

Is a Compatible Hierarchical Single-Agent Model

h_validate_combine_results

Combining S4 Class Validation Results

h_validate_common_data_slots

Helper Function performing validation Common to Data and DataOrdinal

h_eval_combo_truth

Helper for Evaluating the True Toxicity Probability at a Dose Combination

h_hierarchical_model_type

Identify the Internal Type of a Hierarchical Arm Model

h_plot_data_cohort_lines

Preparing Cohort Lines for Data Plot

h_next_best_mg_plot

Building the Plot for nextBest-NextBestMaxGain Method.

Shorthand for Logit Function

h_hierarchical_safe_name

Sanitize a Hierarchical Name for Generated JAGS Code

h_hierarchical_pool_names

Find the Pool Name for One or More Parameter References

h_hierarchical_stochastic_subexpressions

Find Stochastic Subexpressions in an Expression

Preparing Data for Plotting

h_obtain_dose_grid_range

Helper Function Containing Common Functionality

h_next_best_mgsamples_plot

Building the Plot for nextBest-NextBestMaxGainSamples Method.

h_prob_two_drugs_combo_single_prob

Evaluate Single-Agent Toxicity Probabilities in a Combo Model

h_pseudo_sim_fit_summary

Helper Function to Calculate Fit Summary

h_simulations_output_format

Helper Function to create return list for Simulations output

h_historical_arm_design

Construct a simplified DesignArm with hardcoded rule objects

h_prob_two_drugs_combo_single_samples

Extract Single-Agent Samples from Combo Samples

h_next_best_mg_doses_at_grid

Get Closest Grid Doses for a Given Target Doses for nextBest-NextBestMaxGain Method.

h_plot_simulation_trajectory

Helper Function to Create Trajectory Plot

h_plot_doses_tried

Helper Function to Create Doses Tried Plot

h_find_interval

Find Interval Numbers or Indices and Return Custom Number For 0.

knit_print.Backfill

Render a CohortSizeConst Object

h_pseudo_sim_inverse_dose

Helper Function to Calculate Inverse Dose

h_hierarchical_model_body_lines

Deparse a Model Body into JAGS Lines

h_hierarchical_model_specs

Suffix Single-Arm Model Specifications

h_tite_logistic_datamodel

Build the common JAGS likelihood for TITE logistic CRM models.

Getting the Slots from a S4 Object

"MIN" Combination of Cohort Size Rules

or-StoppingAny-Stopping

Combine a Stopping List and an Atomic Stopping Rule with OR

Obtaining Posterior Samples for all Model Parameters

h_tite_logistic_modelspecs

Build the shared JAGS data list for TITE logistic CRM models.

h_plot_combo_evolution

Helper Function to Plot 2D Combination Evolution

h_tite_logistic_weights

Calculate weights for TITE logistic CRM models.

Compute the Distribution Function of Inverse Gamma Distribution

h_hierarchical_namespace_model

Add an Arm Suffix to a Hierarchical Model Fragment

h_kable_param_default

Set Default Values for kable Parameters

h_jags_write_model

Writing JAGS Model to a File

h_model_dual_endpoint_sigma2w

Update DualEndpoint class model components with regard to biomarker regression variance.

h_next_best_eligible_doses

Get Eligible Doses from the Dose Grid.

h_hierarchical_supported_refs

List Supported Exchangeable Parameter References for an Arm Model

h_prob_two_drugs_combo_normalized_dose

Evaluate a Single-Agent Dose Normalization

MCMC Sampling for Bayesian Logistic Regression Model

match_within_tolerance

Helper Function for Value Matching with Tolerance

Helper Function to call truth calculation

h_plot_data_dataordinal

Helper Function for the Plot Method of the Data and DataOrdinal Classes

h_prob_two_drugs_combo

Calculate Two-Drug Combo Toxicity Probabilities

Number of Doses in Grid

or-Stopping-StoppingAny

Combine an Atomic Stopping Rule and a Stopping List with OR

Finding the Next Best Dose

plot,DataCombo,missing-method

Plot Method for the DataCombo Class

or,ArmCondition,ArmCondition-method

Logical OR Operator for ArmCondition Objects

plot,PseudoDualSimulations,missing-method

Plot PseudoDualSimulations

or,Opening,Opening-method

Logical OR Operator for Opening Objects

plot,PseudoDualSimulationsSummary,missing-method

Plot PseudoDualSimulationsSummary

plot,DataDA,missing-method

Plot Method for the DataDA Class

names,Samples-method

The Names of the Sampled Parameters

plot,Samples,TwoDrugsCombo-method

Plotting two-drug combination dose-toxicity model fits

plot,SimulationsSummary,missing-method

Plot Model-Based Design Simulation Summary

plot,ComboSimulations,missing-method

Plot ComboSimulations

Determine the Maximum Possible Next Dose

plot,DataDual,missing-method

Plot Method for the DataDual Class

plot,Samples,DALogisticLogNormal-method

Plotting dose-toxicity model fits

show,ComboSimulations-method

Show ComboSimulations Objects

plot,PseudoSimulationsSummary,missing-method

Plot PseudoSimulationsSummary

Plot gtable Objects

Helper Function to Set and Save the RNG Seed

plotDualResponses

Plot of the DLE and efficacy curve side by side given a DLE pseudo model, a DLE sample, an efficacy pseudo model and a given efficacy sample

plot,Samples,DualEndpoint-method

Plotting dose-toxicity and dose-biomarker model fits

plot,DataDual,ModelEff-method

Plot of the fitted dose-efficacy based with a given pseudo efficacy model and data without samples

show,ComboSimulationsSummary-method

Show the Summary of Combination Simulations

plot,Samples,GeneralModel-method

Plotting dose-toxicity model fits

show,HierarchicalSimulations-method

Show HierarchicalSimulations Objects

show,DualSimulationsSummary-method

Show the Summary of Dual-Endpoint Simulations

show,HierarchicalModel-method

Show HierarchicalModel Objects

or-Stopping-Stopping

Combine Two Stopping Rules with OR

plot,DualSimulations,missing-method

Plot DualSimulations

Computing Toxicity Probabilities for a Given Dose, Model and Samples

h_unpack_stopit

Helper function to recursively unpack stopping rules and return lists with logical value and label given

plot,HierarchicalData,missing-method

Plot Method for the HierarchicalData Class

"MAX" Combination of Cohort Size Rules

Recursively Apply a Function to a List

h_update_backfill_queue

Helper Function to Update Backfill Queue

Getting the Prob Function for a Given Model Type

Open a hierarchical design arm?

Calculate Maximum Number of Backfill Patients

plot,GeneralSimulationsSummary,missing-method

Plot GeneralSimulationsSummary

Determining if this Sample Should be Saved

show,GeneralSimulations-method

Show Simulations Objects

show,GeneralSimulationsSummary-method

Show the Summary of the Simulations

simulate,DesignGrouped-method

Simulate Method for the DesignGrouped Class

simulate,DesignCombo-method

Simulate outcomes from a two-drug combination CRM design

simulate,RuleDesign-method

Simulate outcomes from a rule-based design

Open / recruit backfill patients into a cohort?

simulate,HierarchicalDesign-method

Simulate outcomes from a hierarchical CRM design

positive_number

positive_number

plot,DualSimulationsSummary,missing-method

Plot Dual-Endpoint Design Simulation Summary

show,SimulationsSummary-method

Show the Summary of Model-Based Design Simulations

Shorthand for Probit Function

plot,GeneralSimulations,missing-method

Plot GeneralSimulations

Plot the gain curve in addition with the dose-DLE and dose-efficacy curve using a given DLE pseudo model, a DLE sample, a given efficacy pseudo model and an efficacy sample

simulate,TDDesign-method

Simulate dose escalation procedure using DLE responses only without samples

show,PseudoSimulationsSummary-method

Show the Summary of PseudoSimulations

summary,GeneralSimulations-method

Summarize the GeneralSimulations, Relative to a Given Truth

summary,DualSimulations-method

Summarize Dual-Endpoint Design Simulations

simulate,DADesign-method

Simulate outcomes from a time-to-DLT augmented CRM design

simulate,Design-method

Simulate outcomes from a CRM design

update,DataDA-method

Updating DataDA Objects

Extracting Single-Drug Data from Combination Data

Evaluate a Hypothetical Data Scenario for a Design

update,DataOrdinal-method

Updating DataOrdinal Objects

show,HierarchicalDesign-method

Show HierarchicalDesign Objects

show,HierarchicalData-method

Show HierarchicalData Objects

simulate,TDsamplesDesign-method

Simulate dose escalation procedure using DLE responses only with DLE samples

Size of an Object

Stop the trial?

summary,HierarchicalSimulations-method

Summarize Hierarchical Design Simulations

summary,PseudoDualFlexiSimulations-method

Summarize PseudoDualFlexiSimulations

update,DataDual-method

Updating DataDual Objects

v_general_simulations

Internal Helper Functions for Validation of GeneralSimulations Objects

Internal Helper Functions for Validation of RuleDesign Objects

update,DataParts-method

Updating DataParts Objects

update,ModelPseudo-method

Update method for the ModelPseudo model class. This is a method to update the model class slots (estimates, parameters, variables and etc.), when the new data (e.g. new observations of responses) are available. This method is mostly used to obtain new modal estimates for pseudo model parameters.

v_safety_window

Internal Helper Functions for Validation of SafetyWindow Objects

update,HierarchicalData-method

Updating HierarchicalData Objects

Internal Helper Functions for Validation of Recruitment Objects

plot,HierarchicalSamples,HierarchicalModel-method

Plotting hierarchical dose-toxicity model fits

plot,ComboSimulationsSummary,missing-method

Plot ComboSimulationsSummary

plot,Samples,ModelTox-method

Plot the fitted dose-DLE curve using a ModelTox class model with samples

plot,PseudoDualFlexiSimulations,missing-method

Plot PseudoDualFlexiSimulations

show,PseudoDualSimulationsSummary-method

Show the Summary of PseudoDualSimulations

summary,PseudoSimulations-method

Summarize PseudoSimulations

simulate,DualResponsesSamplesDesign-method

Simulate dose escalation procedure using DLE and efficacy responses with samples

v_hierarchical_design

Internal Helper Functions for Validation of HierarchicalDesign Objects

summary,PseudoDualSimulations-method

Summarize PseudoDualSimulations

Random Generation for the Inverse Gamma Distribution

plot,Data,ModelTox-method

Plot of the fitted dose-tox based with a given pseudo DLE model and data without samples

plot,Samples,ModelEff-method

Plot the fitted dose-efficacy curve using a model from ModelEff class with samples

Internal Helper Functions for Validation of Increments Objects

Internal Helper Functions for Validation of Opening Objects

v_pseudo_simulations

Internal Helper Functions for Validation of PseudoSimulations Objects

update,DataCombo-method

Updating DataCombo Objects

simulate,DualResponsesDesign-method

Simulate dose escalation procedure using both DLE and efficacy responses without samples

v_samples_objects

Internal Helper Functions for Validation of Samples Objects

v_starting_dose

Internal Helper Functions for Validation of StartingDose Objects

show,HierarchicalSimulationsSummary-method

Show the Summary of Hierarchical Simulations

simulate,DualDesign-method

Simulate outcomes from a dual-endpoint design

Compute the Quantile Function of Inverse Gamma Distribution

v_mcmcoptions_objects

Internal Helper Functions for Validation of McmcOptions Objects

v_model_objects

Internal Helper Functions for Validation of GeneralModel and ModelPseudo Objects

Internal Helper Functions for Validation of CohortSize Objects

Internal Helper Functions for Validation of GeneralData Objects

Internal Helper Functions for Validation of Stopping Objects

summary,ComboSimulations-method

Summarize ComboSimulations

summary,Simulations-method

Summarize Model-Based Design Simulations

Subsetting Operator for the Data Class

Tidying CrmPackClass objects

update,Data-method

Updating Data Objects

Internal Helper Functions for Validation of Model Parameters Objects

Determine the Safety Window Length of the Next Cohort

Internal Helper Functions for Validation of NextBest Objects

Internal Helper Functions for Validation of Backfill Objects

v_arm_condition

Internal Helper Functions for Validation of ArmCondition Objects

ArmMinDoseCondition-class

ArmMinDoseCondition

CohortSizeConst-class

CohortSizeConst

ArmConditionAll-class

ArmConditionAll

Backfill class

CohortSizeDLT-class

CohortSizeDLT

.DefaultCohortSize

ArmFinishedCondition-class

ArmFinishedCondition

ArmConditionAny-class

ArmConditionAny

ArmCondition-class

ComboSimulationsSummary-class

ComboSimulationsSummary

CohortSizeParts-class

CohortSizeParts

ComboSimulations-class

ComboSimulations

CohortSizeOrdinal-class

CohortSizeOrdinal