Man pages for psborrow2
Bayesian Dynamic Borrowing Analysis and Simulation
| add_covariates | Add Covariates for Model Adjustment |
| Analysis-class | 'Analysis' Class |
| as_data_frame | Coerce a 'psborrow2' object to a data frame |
| baseline_covariates | Specify Correlated Baseline Covariates |
| BaselineDataFrame-class | Baseline Data Frame Object |
| BaselineDataList-class | Baseline Data Frame List |
| BaselineObject-class | 'BaselineObject' class for data simulation |
| bernoulli_prior | Legacy function for the bernoulli prior |
| beta_prior | Legacy function for the beta prior |
| binary_cutoff | Binary Cut-Off Transformation |
| BinaryOutcome-class | 'BinaryOutcome' class |
| bin_var | Create binary covariate |
| Borrowing-class | 'Borrowing' Class |
| borrowing_details | Legacy function for specifying borrowing details |
| borrowing_full | Full borrowing |
| BorrowingFull-class | 'BorrowingFull' class |
| borrowing_hierarchical_commensurate | Hierarchical commensurate borrowing |
| BorrowingHierarchicalCommensurate-class | 'BorrowingHierarchicalCommensurate' class |
| borrowing_none | No borrowing |
| BorrowingNone-class | 'BorrowingNone' class |
| build_model_string | Build the model string by interpolating the Stan template |
| c | Combine objects in 'psborrow2' |
| cauchy_prior | Legacy function for the cauchy prior |
| 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_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 |
| custom_enrollment | Create a 'DataSimEnrollment' Object |
| cut_off_funs | Cut Off Functions |
| 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 |
| enrollment_constant | Constant Enrollment Rates |
| eval_constraints | 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 |
| gamma_prior | Legacy function for the gamma prior |
| generate | Generate Data from Object |
| generate-BaselineObject-method | Generate Data for a 'BaselineObject' |
| generate-DataSimObject-method | Generate Data for a 'DataSimObject' |
| get_cmd_stan_models | Get 'CmdStanModel' objects for 'MCMCSimulationResults' |
| get_data | Get Simulated Data from 'SimDataList' object |
| get_prior_string_covariates | Get prior string for all covariates |
| get_quantiles | Get Quantiles of Random Data |
| get_results | Get results for 'MCMCSimulationResults' objects |
| get_stan_code | Get method for Stan model |
| get_vars | Get Variables |
| half_cauchy_prior | Legacy function for the half-cauchy prior |
| half_normal_prior | Legacy function for the normal half prior |
| load_and_interpolate_stan_model | Load and interpolate Stan model |
| load_stan_file | Load a Stan 'psborrow2' template |
| logistic_bin_outcome | Legacy function for binary logistic regression |
| mcmc_sample | Sample from Stan model |
| MCMCSimulationResult-class | 'MCMCSimulationResult' Class |
| normal_prior | Legacy function for the normal prior |
| OutcomeBinaryLogistic-class | 'OutcomeBinaryLogistic' class |
| outcome_bin_logistic | Bernoulli distribution with logit parametrization |
| Outcome-class | 'Outcome' class |
| OutcomeContinuousNormal-class | 'OutcomeContinuousNormal' class |
| outcome_cont_normal | Normal Outcome Distribution |
| outcome_surv_exponential | Exponential survival distribution |
| OutcomeSurvExponential-class | 'OutcomeSurvExponential' Class |
| outcome_surv_pem | Piecewise exponential survival distribution |
| OutcomeSurvPEM-class | 'OutcomeSurvPEM' Class |
| outcome_surv_weibull_ph | Weibull survival distribution (proportional hazards... |
| OutcomeSurvWeibullPH-class | 'OutcomeSurvWeibullPH' Class |
| plot | 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_bernoulli | Prior bernoulli distribution |
| PriorBernoulli-class | 'PriorBernoulli' Class |
| prior_beta | Prior beta distribution |
| PriorBeta-class | 'PriorBeta' Class |
| prior_cauchy | Prior cauchy distribution |
| PriorCauchy-class | 'PriorCauchy' Class |
| Prior-class | 'Prior' Class |
| prior_exponential | Prior exponential distribution |
| PriorExponential-class | 'PriorExponential' Class |
| prior_gamma | Prior gamma distribution |
| PriorGamma-class | 'PriorGamma' Class |
| prior_half_cauchy | Prior half-cauchy distribution |
| PriorHalfCauchy-class | 'PriorHalfCauchy' Class |
| prior_half_normal | Prior half-normal distribution |
| PriorHalfNormal-class | 'PriorHalfNormal' Class |
| prior_normal | Prior normal distribution |
| PriorNormal-class | 'PriorNormal' Class |
| prior_poisson | Prior poisson distribution |
| PriorPoisson-class | 'PriorPoisson' Class |
| psborrow2-package | psborrow2: Bayesian Dynamic Borrowing Analysis and Simulation |
| rename_draws_covariates | Rename Covariates in 'draws' Object |
| 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-BaselineObject-method | Set Transformations in Baseline Objects |
| show_guide | Show guide for objects with guides |
| sim_borrowing_list | Input borrowing details for a simulation study |
| SimBorrowingList-class | 'SimBorrowingList' Class |
| sim_covariate_list | Input covariate adjustment details for a simulation study |
| SimCovariateList-class | 'SimCovariateList' Class |
| sim_covariates | Specify covariates for simulation study |
| SimCovariates-class | 'SimCovariates' Class |
| sim_covariates_summ | Summarize the number of continuous and binary covariates in a... |
| sim_data_list | Input generated data for a simulation study |
| SimDataList-class | 'SimDataList' Class |
| sim_outcome_list | Input outcome details for a simulation study |
| SimOutcomeList-class | 'SimOutcomeList' Class |
| sim_samplesize | Set simulation study parameters for sample size |
| SimSampleSize-class | 'SimSampleSize' Class |
| sim_treatment_list | Input treatment details for a simulation study |
| SimTreatmentList-class | 'SimTreatmentList' Class |
| Simulation-class | 'Simulation' Class |
| SimVarBin-class | 'SimVarBin' class |
| SimVar-class | 'SimVar' Class |
| SimVarCont-class | 'SimVarCont' class |
| 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_rows | Trim Rows from Data Matrix Based on Borrowing object type |
| uniform_prior | Prior uniform distribution |
| UniformPrior-class | 'UniformPrior' Class |
| variable_dictionary | Create Variable Dictionary |
| weib_ph_surv_dist | Legacy function for the Weibull proportional Hazards survival... |
