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 |
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' |
CrmPackClass | 'CrmPackClass' |
crmPackExample | Open the example pdf for crmPack |
crmPackHelp | Open the browser with help pages for crmPack |
crmPack-package | Object-oriented implementation of CRM designs |
DADesign-class | 'DADesign' |
DALogisticLogNormal-class | 'DALogisticLogNormal' |
dapply | Apply a Function to Subsets of Data Frame. |
DASimulations | Initialization function for 'DASimulations' |
DASimulations-class | Class for the simulations output from DA based designs |
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' @description *[Stable]* This class... |
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_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_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_prepare_labels | Check That Labels Are Valid and Useful |
h_prepare_units | Append Units to a Numeric Dose |
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' |
is.wholenumber | checks for whole numbers (integers) |
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 | Do 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' |
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 | 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... |
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 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 | Plot '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-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 summaries of the model-based design simulations |
positive_number | 'positive_number' |
printVignette | Taken from utils package (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 | Initialization function for 'PseudoDualFlexiSimulations'... |
PseudoDualFlexiSimulations-class | This is a class which captures the trial simulations design... |
PseudoDualSimulations-class | 'PseudoDualSimulations' |
PseudoDualSimulationsSummary-class | Class for the summary of the dual responses simulations using... |
PseudoSimulations-class | 'PseudoSimulations' |
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-class | 'RuleDesign' |
RuleDesignOrdinal-class | 'RuleDesignOrdinal' |
safeInteger | Safe conversion to integer vector |
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 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-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 | 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-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 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-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 |
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