Bayesian Dynamic Borrowing Analysis and Simulation
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Documentation for package ‘psborrow2’ version 0.0.3.4
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A B C D E G H L M N O P R S T U V W misc
-- A --
| add_covariates | Add Covariates for Model Adjustment |
| Analysis-class | 'Analysis' Class |
| as.data.frame.BaselineDataList | Coerce a 'psborrow2' object to a data frame |
| as_data_frame | Coerce a 'psborrow2' object to a data frame |
-- B --
| BaselineDataFrame-class | Baseline Data Frame Object |
| BaselineDataList-class | Baseline Data Frame List |
| BaselineObject-class | 'BaselineObject' class for data simulation |
| baseline_covariates | Specify Correlated Baseline Covariates |
| bernoulli_prior | Legacy function for the bernoulli prior |
| beta_prior | Legacy function for the beta prior |
| BinaryOutcome-class | 'BinaryOutcome' class |
| binary_cutoff | Binary Cut-Off Transformation |
| bin_var | Create binary covariate |
| Borrowing-class | 'Borrowing' Class |
| BorrowingFull-class | 'BorrowingFull' class |
| BorrowingHierarchicalCommensurate-class | 'BorrowingHierarchicalCommensurate' class |
| BorrowingNone-class | 'BorrowingNone' class |
| borrowing_details | Legacy function for specifying borrowing details |
| borrowing_full | Full borrowing |
| borrowing_hierarchical_commensurate | Hierarchical commensurate borrowing |
| borrowing_none | No borrowing |
-- C --
| c | Combine objects in 'psborrow2' |
| c-method | Combine objects in 'psborrow2' |
| cauchy_prior | Legacy function for the cauchy prior |
| check_cmdstan | Check Stan |
| check_cmdstanr | Check Stan |
| check_data_matrix_has_columns | Check Data Matrix for Required Columns |
| check_fixed_external_data | Create a Fixed External Data Object |
| ContinuousOutcome-class | 'ContinuousOutcome' class |
| cont_var | Create continuous covariate |
| covariance_matrix | Create Covariance Matrix |
| Covariates-class | 'Covariate' Class |
| create_alpha_string | Create alpha string |
| create_alpha_string-method | Create alpha string |
| create_analysis_obj | Compile MCMC sampler using STAN and create analysis object |
| create_baseline_object | Create Baseline Data Simulation Object |
| create_data_matrix | Create Data Matrix |
| create_data_simulation | Data Simulation |
| create_event_dist | Specify a Time to Event Distribution |
| create_simulation_obj | Compile MCMC sampler using STAN and create simulation object |
| create_tau_string | Create tau string |
| create_tau_string-method | Create tau string |
| custom_enrollment | Create a 'DataSimEnrollment' Object |
| cut_off_after_events | Cut Off Functions |
| cut_off_after_first | Cut Off Functions |
| cut_off_after_last | Cut Off Functions |
| cut_off_funs | Cut Off Functions |
| cut_off_none | Cut Off Functions |
-- D --
| DataSimCutOff-class | Cut Off Object |
| DataSimEnrollment-class | Enrollment Object |
| DataSimEvent-class | Event Time Distribution Object |
| DataSimFixedExternalData-class | Fixed External Control Data Object |
| DataSimObject-class | Data Simulation Object Class |
-- E --
| enrollment_constant | Constant Enrollment Rates |
| eval_constraints | Evaluate constraints |
| eval_constraints-method | Evaluate constraints |
| example_matrix | Example data matrix |
| example_surv | Simulated Survival Data |
| exponential_prior | Legacy function for the exponential prior |
| exp_surv_dist | Legacy function for the exponential survival distribution |
-- G --
| gamma_prior | Legacy function for the gamma prior |
| generate | Generate Data from Object |
| generate-method | Generate Data for a 'BaselineObject' |
| generate-method | Generate Data for a 'DataSimObject' |
| get_cmd_stan_models | Get 'CmdStanModel' objects for 'MCMCSimulationResults' |
| get_cmd_stan_models-method | Get 'CmdStanModel' objects for 'MCMCSimulationResults' |
| get_data | Get Simulated Data from 'SimDataList' object |
| get_data-method | Get Simulated Data from 'SimDataList' object |
| get_quantiles | Get Quantiles of Random Data |
| get_results | Get results for 'MCMCSimulationResults' objects |
| get_results-method | Get results for 'MCMCSimulationResults' objects |
| get_stan_code | Get method for Stan model |
| get_stan_code-method | Get method for Stan model |
| get_vars | Get Variables |
| get_vars-method | Get Variables |
-- H --
| half_cauchy_prior | Legacy function for the half-cauchy prior |
| half_normal_prior | Legacy function for the normal half prior |
-- L --
| logistic_bin_outcome | Legacy function for binary logistic regression |
-- M --
| make_model_string_model | Create Stan Code for Model |
| make_model_string_model-method | Create Stan Code for Model |
| MCMCSimulationResult-class | 'MCMCSimulationResult' Class |
| mcmc_sample | Sample from Stan model |
| mcmc_sample-method | Sample from Stan model |
-- N --
| normal_prior | Legacy function for the normal prior |
| null_event_dist | Specify a Time to Event Distribution |
-- O --
| Outcome-class | 'Outcome' class |
| OutcomeBinaryLogistic-class | 'OutcomeBinaryLogistic' class |
| OutcomeContinuousNormal-class | 'OutcomeContinuousNormal' class |
| OutcomeSurvExponential-class | 'OutcomeSurvExponential' Class |
| OutcomeSurvWeibullPH-class | 'OutcomeSurvWeibullPH' Class |
| outcome_bin_logistic | Bernoulli distribution with logit parametrization |
| outcome_cont_normal | Normal Outcome Distribution |
| outcome_surv_exponential | Exponential survival distribution |
| outcome_surv_weibull_ph | Weibull survival distribution (proportional hazards formulation) |
-- P --
| plot | Plot Prior Objects |
| plot-method | Plot Prior Objects |
| plot_pdf | Plot Probability Density Function Values |
| plot_pmf | Plot Probability Mass Function Values |
| poisson_prior | Legacy function for the poisson prior |
| possible_data_sim_vars | Get All Variable Names in Simulated Data Model Matrix |
| Prior-class | 'Prior' Class |
| PriorBernoulli-class | 'PriorBernoulli' Class |
| PriorBeta-class | 'PriorBeta' Class |
| PriorCauchy-class | 'PriorCauchy' Class |
| PriorExponential-class | 'PriorExponential' Class |
| PriorGamma-class | 'PriorGamma' Class |
| PriorHalfCauchy-class | 'PriorHalfCauchy' Class |
| PriorHalfNormal-class | 'PriorHalfNormal' Class |
| PriorNormal-class | 'PriorNormal' Class |
| PriorPoisson-class | 'PriorPoisson' Class |
| prior_bernoulli | Prior bernoulli distribution |
| prior_beta | Prior beta distribution |
| prior_cauchy | Prior cauchy distribution |
| prior_exponential | Prior exponential distribution |
| prior_gamma | Prior gamma distribution |
| prior_half_cauchy | Prior half-cauchy distribution |
| prior_half_normal | Prior half-normal distribution |
| prior_normal | Prior normal distribution |
| prior_poisson | Prior poisson distribution |
-- R --
| rename_draws_covariates | Rename Covariates in 'draws' Object |
-- S --
| set_cut_off | Set Clinical Cut Off Rule |
| set_dropout | Set Drop Out Distribution |
| set_enrollment | Set Enrollment Rates for Internal and External Trials |
| set_transformations | Set transformations in 'BaselineObject' objects |
| set_transformations-method | Set Transformations in Baseline Objects |
| show_guide | Show guide for objects with guides |
| show_guide-method | Show guide for objects with guides |
| SimBorrowingList-class | 'SimBorrowingList' Class |
| SimCovariateList-class | 'SimCovariateList' Class |
| SimCovariates-class | 'SimCovariates' Class |
| SimDataList-class | 'SimDataList' Class |
| SimOutcomeList-class | 'SimOutcomeList' Class |
| SimSampleSize-class | 'SimSampleSize' Class |
| SimTreatmentList-class | 'SimTreatmentList' Class |
| Simulation-class | 'Simulation' Class |
| SimVar-class | 'SimVar' Class |
| SimVarBin-class | 'SimVarBin' class |
| SimVarCont-class | 'SimVarCont' class |
| sim_borrowing_list | Input borrowing details for a simulation study |
| sim_covariates | Specify covariates for simulation study |
| sim_covariates_summ | Summarize the number of continuous and binary covariates in a 'SimCovariates' object created by 'sim_covariates()' |
| sim_covariate_list | Input covariate adjustment details for a simulation study |
| sim_data_list | Input generated data for a simulation study |
| sim_outcome_list | Input outcome details for a simulation study |
| sim_samplesize | Set simulation study parameters for sample size |
| sim_treatment_list | Input treatment details for a simulation study |
-- T --
| TimeToEvent-class | 'TimeToEvent' class |
| Treatment-class | 'Treatment' Class |
| treatment_details | Specify Treatment Details |
| trim_cols | Trim columns from Data Matrix Based on Borrowing object type |
| trim_cols-method | Trim columns from Data Matrix Based on Borrowing object type |
| trim_rows | Trim Rows from Data Matrix Based on Borrowing object type |
| trim_rows-method | Trim Rows from Data Matrix Based on Borrowing object type |
-- U --
| UniformPrior-class | 'UniformPrior' Class |
| uniform_prior | Prior uniform distribution |
-- V --
| variable_dictionary | Create Variable Dictionary |
-- W --
| weib_ph_surv_dist | Legacy function for the Weibull proportional Hazards survival distribution |
-- misc --
| .analysis_obj | 'Analysis' Class |
| .baseline_dataframe | Baseline Data Frame Object |
| .baseline_data_list | Baseline Data Frame List |
| .baseline_object | 'BaselineObject' class for data simulation |
| .bin_var | 'SimVarBin' class |
| .borrowing_full | 'BorrowingFull' class |
| .borrowing_hierarchical_commensurate | 'BorrowingHierarchicalCommensurate' class |
| .borrowing_none | 'BorrowingNone' class |
| .cont_var | 'SimVarCont' class |
| .covariate_class | 'Covariate' Class |
| .datasim_cut_off | Cut Off Object |
| .datasim_enrollment | Enrollment Object |
| .datasim_event | Event Time Distribution Object |
| .datasim_fixed_external_data | Fixed External Control Data Object |
| .datasim_object | Data Simulation Object Class |
| .mcmc_simulation_result | 'MCMCSimulationResult' Class |
| .outcome_bin_logistic | 'OutcomeBinaryLogistic' class |
| .outcome_cont_normal | 'OutcomeContinuousNormal' class |
| .outcome_surv_exponential | 'OutcomeSurvExponential' Class |
| .outcome_surv_weibull_ph | 'OutcomeSurvWeibullPH' Class |
| .prior_bernoulli | 'PriorBernoulli' Class |
| .prior_beta | 'PriorBeta' Class |
| .prior_cauchy | 'PriorCauchy' Class |
| .prior_exponential | 'PriorExponential' Class |
| .prior_gamma | 'PriorGamma' Class |
| .prior_half_cauchy | 'PriorHalfCauchy' Class |
| .prior_half_normal | 'PriorHalfNormal' Class |
| .prior_normal | 'PriorNormal' Class |
| .prior_poisson | 'PriorPoisson' Class |
| .simulation_obj | 'Simulation' Class |
| .sim_borrowing_list | 'SimBorrowingList' Class |
| .sim_covariates | 'SimCovariates' Class |
| .sim_covariate_list | 'SimCovariateList' Class |
| .sim_data_list | 'SimDataList' Class |
| .sim_outcome_list | 'SimOutcomeList' Class |
| .sim_samplesize | 'SimSampleSize' Class |
| .sim_treatment_list | 'SimTreatmentList' Class |
| .treatment_class | 'Treatment' Class |
| .uniform_prior | 'UniformPrior' Class |