Man pages for crmPack
Object-Oriented Implementation of Dose Escalation Designs
| and-StoppingAll-Stopping-method | Combine a Stopping List and an Atomic Stopping Rule with AND |
| and-Stopping-StoppingAll-method | Combine an Atomic Stopping Rule and a Stopping List with AND |
| and-Stopping-Stopping-method | Combine Two Stopping Rules with AND |
| approximate | Approximate posterior with (log) normal distribution |
| assertions | Additional Assertions for 'checkmate' |
| biomarker | Get the Biomarker Levels for a Given Dual-Endpoint Model,... |
| check_equal | Check if All Arguments Are Equal |
| check_format | Check that an argument is a valid format specification |
| check_length | Check if vectors are of compatible lengths |
| check_probabilities | Check if an argument is a probability vector |
| check_probability | Check if an argument is a single probability value |
| check_probability_range | Check if an argument is a probability range |
| check_range | Check that an argument is a numerical range |
| CohortSize-class | 'CohortSize' |
| CohortSizeConst-class | 'CohortSizeConst' |
| CohortSizeDLT-class | 'CohortSizeDLT' |
| CohortSizeMax-class | 'CohortSizeMax' |
| CohortSizeMin-class | 'CohortSizeMin' |
| CohortSizeOrdinal-class | 'CohortSizeOrdinal' |
| CohortSizeParts-class | 'CohortSizeParts' |
| CohortSizeRange-class | 'CohortSizeRange' |
| crmPack | Object-oriented implementation of CRM designs |
| CrmPackClass | 'CrmPackClass' |
| crmPackExample | Open the Example PDF for crmPack |
| crmPackHelp | Open the Browser with Help Pages for crmPack |
| DADesign-class | 'DADesign' |
| DALogisticLogNormal-class | 'DALogisticLogNormal' |
| dapply | Apply a Function to Subsets of Data Frame. |
| DASimulations-class | 'DASimulations' |
| Data-class | 'Data' |
| DataDA-class | 'DataDA' |
| DataDual-class | 'DataDual' |
| DataGrouped-class | 'DataGrouped' |
| DataMixture-class | 'DataMixture' |
| DataOrdinal-class | 'DataOrdinal' |
| DataParts-class | 'DataParts' |
| Design-class | 'Design' |
| DesignGrouped-class | 'DesignGrouped' |
| DesignOrdinal-class | 'DesignOrdinal' |
| dinvGamma | Compute the Density of Inverse Gamma Distribution |
| DLTLikelihood | Likelihood of DLTs in each interval |
| dose | Computing the Doses for a given independent variable, Model... |
| doseFunction | Getting the Dose Function for a Given Model Type |
| dose_grid_range | Getting the Dose Grid Range |
| DualDesign-class | 'DualDesign' |
| DualEndpointBeta-class | 'DualEndpointBeta' |
| DualEndpoint-class | 'DualEndpoint' |
| DualEndpointEmax-class | 'DualEndpointEmax' |
| DualEndpointRW-class | 'DualEndpointRW' |
| DualResponsesDesign-class | 'DualResponsesDesign.R' |
| DualResponsesSamplesDesign-class | 'DualResponsesSamplesDesign' |
| DualSimulations-class | 'DualSimulations' |
| DualSimulationsSummary-class | 'DualSimulationsSummary' |
| EffFlexi-class | 'EffFlexi' |
| efficacy | Computing Expected Efficacy for a Given Dose, Model and... |
| efficacyFunction | Getting the Efficacy Function for a Given Model Type |
| Effloglog-class | 'Effloglog' |
| enable_logging | Verbose Logging |
| examine | Obtain Hypothetical Trial Course Table for a Design |
| fit | Fit method for the Samples class |
| fitGain | Get the fitted values for the gain values at all dose levels... |
| fitPEM | Get the fitted DLT free survival (piecewise exponential... |
| FractionalCRM-class | 'FractionalCRM' |
| gain | Compute Gain Values based on Pseudo DLE and a Pseudo Efficacy... |
| GeneralData-class | 'GeneralData' |
| GeneralModel-class | 'GeneralModel' |
| GeneralSimulations-class | 'GeneralSimulations' |
| GeneralSimulationsSummary-class | 'GeneralSimulationsSummary' |
| getEff | Extracting Efficacy Responses for Subjects Categorized by the... |
| get_result_list | Helper Function to Obtain Simulation Results List |
| get-Samples-character-method | Get specific parameter samples and produce a data.frame |
| h_all_equivalent | Comparison with Numerical Tolerance and Without Name... |
| h_barplot_percentages | Convenience function to make barplots of percentages |
| h_blind_plot_data | Helper Function to Blind Plot Data |
| h_calc_report_label_percentage | Helper function to calculate percentage of true stopping... |
| h_check_fun_formals | Checking Formals of a Function |
| h_convert_ordinal_data | Convert a Ordinal Data to the Equivalent Binary Data for a... |
| h_convert_ordinal_model | Convert an ordinal CRM model to the Equivalent Binary CRM... |
| h_convert_ordinal_samples | Convert a Samples Object from an ordinal Model to the... |
| h_covr_helpers | Helpers for stripping expressions of 'covr'-inserted trace... |
| h_default_if_empty | Getting the default value for an empty object |
| h_determine_dlts | Helper function to determine the dlts including first... |
| h_find_interval | Find Interval Numbers or Indices and Return Custom Number For... |
| h_format_number | Conditional Formatting Using C-style Formats |
| h_get_formatted_dosegrid | Format a 'doseGrid' for Printing |
| h_get_min_inf_beta | Helper for Minimal Informative Unimodal Beta Distribution |
| h_get_quantiles_start_values | Get Starting Values for Quantiles Optimization |
| h_group_data | Group Together Mono and Combo Data |
| h_info_theory_dist | Calculating the Information Theoretic Distance |
| h_in_range | Check which elements are in a given range |
| h_is_positive_definite | Testing Matrix for Positive Definiteness |
| h_jags_add_dummy | Appending a Dummy Number for Selected Slots in Data |
| h_jags_extract_samples | Extracting Samples from 'JAGS' 'mcarray' Object |
| h_jags_get_data | Getting Data for 'JAGS' |
| h_jags_get_model_inits | Setting Initial Values for 'JAGS' Model Parameters |
| h_jags_join_models | Joining 'JAGS' Models |
| h_jags_write_model | Writing JAGS Model to a File |
| h_knit_format_func | Used to obtain expected format. |
| h_model_dual_endpoint_beta | Update certain components of 'DualEndpoint' model with regard... |
| h_model_dual_endpoint_rho | Update 'DualEndpoint' class model components with regard to... |
| h_model_dual_endpoint_sigma2betaw | Update certain components of 'DualEndpoint' model with regard... |
| h_model_dual_endpoint_sigma2w | Update 'DualEndpoint' class model components with regard to... |
| h_next_best_eligible_doses | Get Eligible Doses from the Dose Grid. |
| h_next_best_mg_ci | Credibility Intervals for Max Gain and Target Doses at... |
| h_next_best_mg_doses_at_grid | Get Closest Grid Doses for a Given Target Doses for... |
| h_next_best_mg_plot | Building the Plot for 'nextBest-NextBestMaxGain' Method. |
| h_next_best_mgsamples_plot | Building the Plot for 'nextBest-NextBestMaxGainSamples'... |
| 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_next_best_tdsamples_plot | Building the Plot for 'nextBest-NextBestTDsamples' Method. |
| h_null_if_na | Getting 'NULL' for 'NA' |
| h_obtain_dose_grid_range | Helper Function Containing Common Functionality |
| h_plot_data_cohort_lines | Preparing Cohort Lines for Data Plot |
| h_plot_data_df | Preparing Data for Plotting |
| h_plot_doses_tried | Helper Function to Create Doses Tried Plot |
| h_plot_simulation_trajectory | Helper Function to Create Trajectory Plot |
| h_prepare_labels | Check That Labels Are Valid and Useful |
| h_prepare_units | Append Units to a Numeric Dose |
| h_pseudo_sim_fit_summary | Helper Function to Calculate Fit Summary |
| h_pseudo_sim_inverse_dose | Helper Function to Calculate Inverse Dose |
| h_quantiles_target_function | Target Function for Quantiles Optimization |
| h_rapply | Recursively Apply a Function to a List |
| h_simulations_output_format | Helper Function to create return list for Simulations output |
| h_slots | Getting the Slots from a S4 Object |
| h_summarize_add_stats | Helper function to calculate average across iterations for... |
| h_test_named_numeric | Check that an argument is a named vector of type numeric |
| h_this_truth | Helper Function to call truth calculation |
| h_unpack_stopit | Helper function to recursively unpack stopping rules and... |
| h_validate_combine_results | Combining S4 Class Validation Results |
| h_validate_common_data_slots | Helper Function performing validation Common to Data and... |
| Increments-class | 'Increments' |
| IncrementsDoseLevels-class | 'IncrementsDoseLevels' |
| IncrementsHSRBeta-class | 'IncrementsHSRBeta' |
| IncrementsMaxToxProb-class | 'IncrementsMaxToxProb' |
| IncrementsMin-class | 'IncrementsMin' |
| IncrementsOrdinal-class | 'IncrementsOrdinal' |
| IncrementsRelative-class | 'IncrementsRelative' |
| IncrementsRelativeDLT-class | 'IncrementsRelativeDLT' |
| IncrementsRelativeDLTCurrent-class | 'IncrementsRelativeDLTCurrent' |
| IncrementsRelativeParts-class | 'IncrementsRelativeParts' |
| knit_print | Render a 'CohortSizeConst' Object |
| LogisticIndepBeta-class | 'LogisticIndepBeta' |
| LogisticKadaneBetaGamma-class | 'LogisticKadaneBetaGamma' |
| LogisticKadane-class | 'LogisticKadane' |
| LogisticLogNormal-class | 'LogisticLogNormal' |
| LogisticLogNormalGrouped-class | 'LogisticLogNormalGrouped' |
| LogisticLogNormalMixture-class | 'LogisticLogNormalMixture' |
| LogisticLogNormalOrdinal-class | 'LogisticLogNormalOrdinal' |
| LogisticLogNormalSub-class | 'LogisticLogNormalSub' |
| LogisticNormal-class | 'LogisticNormal' |
| LogisticNormalFixedMixture-class | 'LogisticNormalFixedMixture' |
| LogisticNormalMixture-class | 'LogisticNormalMixture' |
| logit | Shorthand for Logit Function |
| match_within_tolerance | Helper Function for Value Matching with Tolerance |
| maxDose | Determine the Maximum Possible Next Dose |
| maxSize | "MAX" Combination of Cohort Size Rules |
| mcmc | Obtaining Posterior Samples for all Model Parameters |
| McmcOptions-class | 'McmcOptions' |
| MinimalInformative | Construct a Minimally Informative Prior |
| minSize | "MIN" Combination of Cohort Size Rules |
| ModelEff-class | 'ModelEff' |
| ModelLogNormal-class | 'ModelLogNormal' |
| ModelParamsNormal-class | 'ModelParamsNormal' |
| ModelPseudo-class | 'ModelPseudo' |
| ModelTox-class | 'ModelTox' |
| myBayesLogit | MCMC Sampling for Bayesian Logistic Regression Model |
| names-Samples-method | The Names of the Sampled Parameters |
| nextBest | Finding the Next Best Dose |
| NextBest-class | 'NextBest' |
| NextBestDualEndpoint-class | 'NextBestDualEndpoint' |
| NextBestEWOC-class | 'NextBestEWOC' |
| NextBestInfTheory-class | 'NextBestInfTheory' |
| NextBestMaxGain-class | 'NextBestMaxGain' |
| NextBestMaxGainSamples-class | 'NextBestMaxGainSamples' |
| NextBestMinDist-class | 'NextBestMinDist' |
| NextBestMTD-class | 'NextBestMTD' |
| NextBestNCRM-class | 'NextBestNCRM' |
| NextBestNCRMLoss-class | 'NextBestNCRMLoss' |
| NextBestOrdinal-class | 'NextBestOrdinal' |
| NextBestProbMTDLTE-class | 'NextBestProbMTDLTE' |
| NextBestProbMTDMinDist-class | 'NextBestProbMTDMinDist' |
| NextBestTD-class | 'NextBestTD' |
| NextBestTDsamples-class | 'NextBestTDsamples' |
| NextBestThreePlusThree-class | 'NextBestThreePlusThree' |
| ngrid | Number of Doses in Grid |
| OneParExpPrior-class | 'OneParExpPrior' |
| OneParLogNormalPrior-class | 'OneParLogNormalPrior' |
| or-StoppingAny-Stopping | Combine a Stopping List and an Atomic Stopping Rule with OR |
| or-Stopping-Stopping | Combine Two Stopping Rules with OR |
| or-Stopping-StoppingAny | Combine an Atomic Stopping Rule and a Stopping List with OR |
| pinvGamma | Compute the Distribution Function of Inverse Gamma... |
| pipe | Pipe operator |
| plot-Data | Helper Function for the Plot Method of the Data and... |
| plot-DataDA-missing-method | Plot Method for the 'DataDA' Class |
| 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-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 'DualSimulations' |
| plot-DualSimulationsSummary-missing-method | Plot Dual-Endpoint Design Simulation Summary |
| plotGain | Plot the gain curve in addition with the dose-DLE and... |
| plot-GeneralSimulations-missing-method | Plot 'GeneralSimulations' |
| plot-GeneralSimulationsSummary-missing-method | Plot 'GeneralSimulationsSummary' |
| plot.gtable | Plot 'gtable' Objects |
| plot-PseudoDualFlexiSimulations-missing-method | Plot 'PseudoDualFlexiSimulations' |
| plot-PseudoDualSimulations-missing-method | Plot 'PseudoDualSimulations' |
| plot-PseudoDualSimulationsSummary-missing-method | Plot 'PseudoDualSimulationsSummary' |
| plot-PseudoSimulationsSummary-missing-method | Plot 'PseudoSimulationsSummary' |
| plot-Samples-DALogisticLogNormal-method | Plotting dose-toxicity model fits |
| plot-Samples-DualEndpoint-method | Plotting dose-toxicity and dose-biomarker model fits |
| plot-Samples-GeneralModel-method | Plotting dose-toxicity model fits |
| plot-Samples-ModelEff-method | Plot the fitted dose-efficacy curve using a model from... |
| plot-Samples-ModelTox-method | Plot the fitted dose-DLE curve using a 'ModelTox' class model... |
| plot-SimulationsSummary-missing-method | Plot Model-Based Design Simulation Summary |
| positive_number | 'positive_number' |
| printVignette | Print Vignette |
| prob | Computing Toxicity Probabilities for a Given Dose, Model and... |
| probFunction | Getting the Prob Function for a Given Model Type |
| probit | Shorthand for Probit Function |
| ProbitLogNormal-class | 'ProbitLogNormal' |
| ProbitLogNormalRel-class | 'ProbitLogNormalRel' |
| PseudoDualFlexiSimulations-class | 'PseudoDualFlexiSimulations' |
| PseudoDualSimulations-class | 'PseudoDualSimulations' |
| PseudoDualSimulationsSummary-class | 'PseudoDualSimulationsSummary' |
| PseudoSimulations-class | 'PseudoSimulations' |
| PseudoSimulationsSummary-class | 'PseudoSimulationsSummary' |
| qinvGamma | Compute the Quantile Function of Inverse Gamma Distribution |
| Quantiles2LogisticNormal | Convert Prior Quantiles to Logistic (Log) Normal Model |
| rinvGamma | Random Generation for the Inverse Gamma Distribution |
| RuleDesign-class | 'RuleDesign' |
| RuleDesignOrdinal-class | 'RuleDesignOrdinal' |
| SafetyWindow-class | 'SafetyWindow' |
| SafetyWindowConst-class | 'SafetyWindowConst' |
| SafetyWindowSize-class | 'SafetyWindowSize' |
| Samples-class | 'Samples' |
| saveSample | Determining if this Sample Should be Saved |
| set_seed | Helper Function to Set and Save the RNG Seed |
| show-DualSimulationsSummary-method | Show the Summary of Dual-Endpoint Simulations |
| show-GeneralSimulationsSummary-method | Show the Summary of the Simulations |
| show-PseudoDualSimulationsSummary-method | Show the Summary of 'PseudoDualSimulations' |
| show-PseudoSimulationsSummary-method | Show the Summary of 'PseudoSimulations' |
| show-SimulationsSummary-method | Show the Summary of Model-Based Design Simulations |
| simulate-DADesign-method | Simulate outcomes from a time-to-DLT augmented CRM design |
| simulate-DesignGrouped-method | Simulate Method for the 'DesignGrouped' Class |
| simulate-Design-method | Simulate outcomes from a CRM design |
| simulate-DualDesign-method | Simulate outcomes from a dual-endpoint design |
| simulate-DualResponsesDesign-method | Simulate dose escalation procedure using both DLE and... |
| simulate-DualResponsesSamplesDesign-method | Simulate dose escalation procedure using DLE and efficacy... |
| simulate-RuleDesign-method | Simulate outcomes from a rule-based design |
| simulate-TDDesign-method | Simulate dose escalation procedure using DLE responses only... |
| simulate-TDsamplesDesign-method | Simulate dose escalation procedure using DLE responses only... |
| Simulations-class | 'Simulations' |
| SimulationsSummary-class | 'SimulationsSummary' |
| size | Size of an Object |
| StartingDose-class | 'StartingDose' |
| StoppingAll-class | 'StoppingAll' |
| StoppingAny-class | 'StoppingAny' |
| Stopping-class | 'Stopping' |
| StoppingCohortsNearDose-class | 'StoppingCohortsNearDose' |
| StoppingExternal-class | 'StoppingExternal' |
| StoppingHighestDose-class | 'StoppingHighestDose' |
| StoppingList-class | 'StoppingList' |
| StoppingLowestDoseHSRBeta-class | 'StoppingLowestDoseHSRBeta' |
| StoppingMaxGainCIRatio-class | 'StoppingMaxGainCIRatio' |
| StoppingMinCohorts-class | 'StoppingMinCohorts' |
| StoppingMinPatients-class | 'StoppingMinPatients' |
| StoppingMissingDose-class | 'StoppingMissingDose' |
| StoppingMTDCV-class | 'StoppingMTDCV' |
| StoppingMTDdistribution-class | 'StoppingMTDdistribution' |
| StoppingOrdinal-class | 'StoppingOrdinal' |
| StoppingPatientsNearDose-class | 'StoppingPatientsNearDose' |
| StoppingSpecificDose-class | 'StoppingSpecificDose' |
| StoppingTargetBiomarker-class | 'StoppingTargetBiomarker' |
| StoppingTargetProb-class | 'StoppingTargetProb' |
| StoppingTDCIRatio-class | 'StoppingTDCIRatio' |
| stopTrial | Stop the trial? |
| summary-DualSimulations-method | Summarize Dual-Endpoint Design Simulations |
| summary-GeneralSimulations-method | Summarize the 'GeneralSimulations', Relative to a Given Truth |
| summary-PseudoDualFlexiSimulations-method | Summarize 'PseudoDualFlexiSimulations' |
| summary-PseudoDualSimulations-method | Summarize 'PseudoDualSimulations' |
| summary-PseudoSimulations-method | Summarize 'PseudoSimulations' |
| summary-Simulations-method | Summarize Model-Based Design Simulations |
| TDDesign-class | 'TDDesign' |
| TDsamplesDesign-class | 'TDsamplesDesign' |
| tidy | Tidying 'CrmPackClass' objects |
| TITELogisticLogNormal-class | 'TITELogisticLogNormal' |
| update-DataDA-method | Updating 'DataDA' Objects |
| update-DataDual-method | Updating 'DataDual' Objects |
| update-Data-method | Updating 'Data' Objects |
| update-DataOrdinal-method | Updating 'DataOrdinal' Objects |
| update-DataParts-method | Updating 'DataParts' Objects |
| update-ModelPseudo-method | Update method for the 'ModelPseudo' model class. This is a... |
| Validate | 'Validate' |
| v_cohort_size | Internal Helper Functions for Validation of 'CohortSize'... |
| v_data_objects | Internal Helper Functions for Validation of 'GeneralData'... |
| v_design | Internal Helper Functions for Validation of 'RuleDesign'... |
| v_general_simulations | Internal Helper Functions for Validation of... |
| v_increments | Internal Helper Functions for Validation of 'Increments'... |
| v_mcmcoptions_objects | Internal Helper Functions for Validation of 'McmcOptions'... |
| v_model_objects | Internal Helper Functions for Validation of 'GeneralModel'... |
| v_model_params | Internal Helper Functions for Validation of Model Parameters... |
| v_next_best | Internal Helper Functions for Validation of 'NextBest'... |
| v_pseudo_simulations | Internal Helper Functions for Validation of... |
| v_safety_window | Internal Helper Functions for Validation of 'SafetyWindow'... |
| v_samples_objects | Internal Helper Functions for Validation of 'Samples' Objects |
| v_starting_dose | Internal Helper Functions for Validation of 'StartingDose'... |
| v_stopping | Internal Helper Functions for Validation of 'Stopping'... |
| windowLength | Determine the Safety Window Length of the Next Cohort |
