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psborrow2 (version 0.0.4.0)

Bayesian Dynamic Borrowing Analysis and Simulation

Description

Bayesian dynamic borrowing is an approach to incorporating external data to supplement a randomized, controlled trial analysis in which external data are incorporated in a dynamic way (e.g., based on similarity of outcomes); see Viele 2013 for an overview. This package implements the hierarchical commensurate prior approach to dynamic borrowing as described in Hobbes 2011 . There are three main functionalities. First, 'psborrow2' provides a user-friendly interface for applying dynamic borrowing on the study results handles the Markov Chain Monte Carlo sampling on behalf of the user. Second, 'psborrow2' provides a simulation framework to compare different borrowing parameters (e.g. full borrowing, no borrowing, dynamic borrowing) and other trial and borrowing characteristics (e.g. sample size, covariates) in a unified way. Third, 'psborrow2' provides a set of functions to generate data for simulation studies, and also allows the user to specify their own data generation process. This package is designed to use the sampling functions from 'cmdstanr' which can be installed from .

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install.packages('psborrow2')

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188

Version

0.0.4.0

License

Apache License 2.0

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Maintainer

Matt Secrest

Last Published

February 12th, 2025

Functions in psborrow2 (0.0.4.0)

DataSimCutOff-class

Cut Off Object
Covariates-class

Covariate Class
MCMCSimulationResult-class

MCMCSimulationResult Class
Outcome-class

Outcome class
PriorGamma-class

PriorGamma Class
OutcomeSurvPEM-class

OutcomeSurvPEM Class
DataSimEvent-class

Event Time Distribution Object
OutcomeSurvExponential-class

OutcomeSurvExponential Class
OutcomeSurvWeibullPH-class

OutcomeSurvWeibullPH Class
Prior-class

Prior Class
OutcomeContinuousNormal-class

OutcomeContinuousNormal class
PriorCauchy-class

PriorCauchy Class
PriorHalfNormal-class

PriorHalfNormal Class
SimSampleSize-class

SimSampleSize Class
SimTreatmentList-class

SimTreatmentList Class
PriorExponential-class

PriorExponential Class
PriorNormal-class

PriorNormal Class
SimOutcomeList-class

SimOutcomeList Class
Treatment-class

Treatment Class
UniformPrior-class

UniformPrior Class
SimDataList-class

SimDataList Class
TimeToEvent-class

TimeToEvent class
SimVar-class

SimVar Class
SimBorrowingList-class

SimBorrowingList Class
PriorPoisson-class

PriorPoisson Class
baseline_covariates

Specify Correlated Baseline Covariates
PriorHalfCauchy-class

PriorHalfCauchy Class
as_data_frame

Coerce a psborrow2 object to a data frame
add_covariates

Add Covariates for Model Adjustment
bernoulli_prior

Legacy function for the bernoulli prior
PriorBeta-class

PriorBeta Class
SimCovariateList-class

SimCovariateList Class
PriorBernoulli-class

PriorBernoulli Class
SimCovariates-class

SimCovariates Class
borrowing_none

No borrowing
borrowing_hierarchical_commensurate

Hierarchical commensurate borrowing
check_data_matrix_has_columns

Check Data Matrix for Required Columns
check_fixed_external_data

Create a Fixed External Data Object
build_model_string

Build the model string by interpolating the Stan template
c

Combine objects in psborrow2
beta_prior

Legacy function for the beta prior
binary_cutoff

Binary Cut-Off Transformation
SimVarBin-class

SimVarBin class
bin_var

Create binary covariate
cut_off_funs

Cut Off Functions
create_analysis_obj

Compile MCMC sampler using STAN and create analysis object
create_alpha_string

Create alpha string
custom_enrollment

Create a DataSimEnrollment Object
enrollment_constant

Constant Enrollment Rates
create_baseline_object

Create Baseline Data Simulation Object
eval_constraints

Evaluate constraints
SimVarCont-class

SimVarCont class
check_cmdstanr

Check Stan
cauchy_prior

Legacy function for the cauchy prior
create_data_matrix

Create Data Matrix
create_simulation_obj

Compile MCMC sampler using STAN and create simulation object
possible_data_sim_vars

Get All Variable Names in Simulated Data Model Matrix
get_data

Get Simulated Data from SimDataList object
get_cmd_stan_models

Get CmdStanModel objects for MCMCSimulationResults
poisson_prior

Legacy function for the poisson prior
get_vars

Get Variables
generate,BaselineObject-method

Generate Data for a BaselineObject
outcome_surv_exponential

Exponential survival distribution
mcmc_sample

Sample from Stan model
normal_prior

Legacy function for the normal prior
gamma_prior

Legacy function for the gamma prior
example_matrix

Example data matrix
create_tau_string

Create tau string
outcome_surv_pem

Piecewise exponential survival distribution
prior_gamma

Prior gamma distribution
prior_half_cauchy

Prior half-cauchy distribution
half_cauchy_prior

Legacy function for the half-cauchy prior
example_surv

Simulated Survival Data
generate

Generate Data from Object
generate,DataSimObject-method

Generate Data for a DataSimObject
half_normal_prior

Legacy function for the normal half prior
load_and_interpolate_stan_model

Load and interpolate Stan model
set_dropout

Set Drop Out Distribution
set_enrollment

Set Enrollment Rates for Internal and External Trials
prior_cauchy

Prior cauchy distribution
borrowing_details

Legacy function for specifying borrowing details
prior_exponential

Prior exponential distribution
cont_var

Create continuous covariate
rename_draws_covariates

Rename Covariates in draws Object
Simulation-class

Simulation Class
borrowing_full

Full borrowing
set_cut_off

Set Clinical Cut Off Rule
sim_covariates_summ

Summarize the number of continuous and binary covariates in a SimCovariates object created by sim_covariates()
sim_treatment_list

Input treatment details for a simulation study
outcome_bin_logistic

Bernoulli distribution with logit parametrization
outcome_cont_normal

Normal Outcome Distribution
sim_data_list

Input generated data for a simulation study
logistic_bin_outcome

Legacy function for binary logistic regression
prior_poisson

Prior poisson distribution
prior_half_normal

Prior half-normal distribution
get_prior_string_covariates

Get prior string for all covariates
load_stan_file

Load a Stan psborrow2 template
get_quantiles

Get Quantiles of Random Data
sim_covariates

Specify covariates for simulation study
treatment_details

Specify Treatment Details
plot_pdf

Plot Probability Density Function Values
covariance_matrix

Create Covariance Matrix
weib_ph_surv_dist

Legacy function for the Weibull proportional Hazards survival distribution
set_transformations,BaselineObject-method

Set Transformations in Baseline Objects
plot_pmf

Plot Probability Mass Function Values
psborrow2-package

psborrow2: Bayesian Dynamic Borrowing Analysis and Simulation
set_transformations

Set transformations in BaselineObject objects
create_data_simulation

Data Simulation
sim_covariate_list

Input covariate adjustment details for a simulation study
create_event_dist

Specify a Time to Event Distribution
prior_normal

Prior normal distribution
variable_dictionary

Create Variable Dictionary
uniform_prior

Prior uniform distribution
trim_cols

Trim columns from Data Matrix Based on Borrowing object type
exp_surv_dist

Legacy function for the exponential survival distribution
get_results

Get results for MCMCSimulationResults objects
get_stan_code

Get method for Stan model
exponential_prior

Legacy function for the exponential prior
outcome_surv_weibull_ph

Weibull survival distribution (proportional hazards formulation)
prior_bernoulli

Prior bernoulli distribution
trim_rows

Trim Rows from Data Matrix Based on Borrowing object type
show_guide

Show guide for objects with guides
plot

Plot Prior Objects
prior_beta

Prior beta distribution
sim_outcome_list

Input outcome details for a simulation study
sim_borrowing_list

Input borrowing details for a simulation study
sim_samplesize

Set simulation study parameters for sample size
Borrowing-class

Borrowing Class
BorrowingHierarchicalCommensurate-class

BorrowingHierarchicalCommensurate class
BaselineDataList-class

Baseline Data Frame List
BinaryOutcome-class

BinaryOutcome class
BaselineObject-class

BaselineObject class for data simulation
ContinuousOutcome-class

ContinuousOutcome class
BaselineDataFrame-class

Baseline Data Frame Object
BorrowingNone-class

BorrowingNone class
Analysis-class

Analysis Class
BorrowingFull-class

BorrowingFull class
DataSimFixedExternalData-class

Fixed External Control Data Object
DataSimObject-class

Data Simulation Object Class
OutcomeBinaryLogistic-class

OutcomeBinaryLogistic class
DataSimEnrollment-class

Enrollment Object