# Bayesian Dynamic Borrowing Analysis and Simulation

## Documentation for package ‘psborrow2’ version 0.0.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
build_model_string | Build the model string by interpolating the Stan template

## -- 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_prior_string_covariates | Get prior string for all covariates
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 --

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

## -- M --

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
OutcomeSurvPEM-class | 'OutcomeSurvPEM' 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_pem | Piecewise 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_pem | 'OutcomeSurvPEM' 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