Package index • psborrow2

All functions

Analysis-class .analysis_obj: Analysis Class

BaselineDataFrame-class .baseline_dataframe: Baseline Data Frame Object

BaselineDataList-class .baseline_data_list: Baseline Data Frame List

BaselineObject-class .baseline_object: BaselineObject class for data simulation

BinaryOutcome-class: BinaryOutcome class

Borrowing-class: Borrowing Class

BorrowingFixedPowerPrior-class .borrowing_fixed_power_prior: BorrowingFixedPowerPrior class

BorrowingFull-class .borrowing_full: BorrowingFull class

BorrowingHierarchicalCommensurate-class .borrowing_hierarchical_commensurate: BorrowingHierarchicalCommensurate class

BorrowingNone-class .borrowing_none: BorrowingNone class

ContinuousOutcome-class: ContinuousOutcome class

Covariates-class .covariate_class: Covariate Class

DataSimCutOff-class .datasim_cut_off: Cut Off Object

DataSimEnrollment-class .datasim_enrollment: Enrollment Object

DataSimEvent-class .datasim_event: Event Time Distribution Object

DataSimFixedExternalData-class .datasim_fixed_external_data: Fixed External Control Data Object

DataSimObject-class .datasim_object: Data Simulation Object Class

MCMCSimulationResult-class .mcmc_simulation_result: MCMCSimulationResult Class

Outcome-class: Outcome class

OutcomeBinaryLogistic-class .outcome_bin_logistic: OutcomeBinaryLogistic class

OutcomeContinuousNormal-class .outcome_cont_normal: OutcomeContinuousNormal class

OutcomeSurvExponential-class .outcome_surv_exponential: OutcomeSurvExponential Class

OutcomeSurvPEM-class .outcome_surv_pem: OutcomeSurvPEM Class

OutcomeSurvWeibullPH-class .outcome_surv_weibull_ph: OutcomeSurvWeibullPH Class

Prior-class: Prior Class

PriorBernoulli-class .prior_bernoulli: PriorBernoulli Class

PriorBeta-class .prior_beta: PriorBeta Class

PriorCauchy-class .prior_cauchy: PriorCauchy Class

PriorExponential-class .prior_exponential: PriorExponential Class

PriorGamma-class .prior_gamma: PriorGamma Class

PriorHalfCauchy-class .prior_half_cauchy: PriorHalfCauchy Class

PriorHalfNormal-class .prior_half_normal: PriorHalfNormal Class

PriorNormal-class .prior_normal: PriorNormal Class

PriorPoisson-class .prior_poisson: PriorPoisson Class

SimBorrowingList-class .sim_borrowing_list: SimBorrowingList Class

SimCovariateList-class .sim_covariate_list: SimCovariateList Class

SimCovariates-class .sim_covariates: SimCovariates Class

SimDataList-class .sim_data_list: SimDataList Class

SimOutcomeList-class .sim_outcome_list: SimOutcomeList Class

SimSampleSize-class .sim_samplesize: SimSampleSize Class

SimTreatmentList-class .sim_treatment_list: SimTreatmentList Class

SimVar-class: SimVar Class

SimVarBin-class .bin_var: SimVarBin class

SimVarCont-class .cont_var: SimVarCont class

Simulation-class .simulation_obj: Simulation Class

TimeToEvent-class: TimeToEvent class

Treatment-class .treatment_class: Treatment Class

UniformPrior-class .uniform_prior: UniformPrior Class

add_covariates(): Add Covariates for Model Adjustment

as.data.frame(<BaselineDataList>): Coerce a psborrow2 object to a data frame

baseline_covariates(): Specify Correlated Baseline Covariates

bernoulli_prior(): Legacy function for the bernoulli prior

beta_prior(): Legacy function for the beta prior

bin_var(): Create binary covariate

binary_cutoff(): Binary Cut-Off Transformation

borrowing_details(): Legacy function for specifying borrowing details

borrowing_fixed_power_prior(): Fixed Power Prior Borrowing

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(<SimDataList>): Combine objects in psborrow2

cauchy_prior(): Legacy function for the cauchy prior

check_cmdstanr() check_cmdstan(): Check Stan

check_data_matrix_has_columns(): Check Data Matrix for Required Columns

check_fixed_external_data(): Create a Fixed External Data Object

cont_var(): Create continuous covariate

covariance_matrix(): Create Covariance Matrix

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() null_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_none() cut_off_after_first() cut_off_after_last() cut_off_after_events(): Cut Off Functions

enrollment_constant(): Constant Enrollment Rates

eval_constraints(): Evaluate constraints

example_matrix: Example data matrix

example_surv: Simulated Survival Data

exp_surv_dist(): Legacy function for the exponential survival distribution

exponential_prior(): Legacy function for the exponential prior

gamma_prior(): Legacy function for the gamma prior

generate(<BaselineObject>): Generate Data for a BaselineObject

generate(<DataSimObject>): Generate Data for a DataSimObject

generate(): Generate Data from Object

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

normal_prior(): Legacy function for the normal prior

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)

plot(<Prior>,<missing>) plot(<PriorNormal>,<missing>) plot(<PriorExponential>,<missing>) plot(<PriorHalfCauchy>,<missing>) plot(<PriorBernoulli>,<missing>) plot(<PriorBeta>,<missing>) plot(<PriorCauchy>,<missing>) plot(<PriorGamma>,<missing>) plot(<PriorHalfNormal>,<missing>) plot(<PriorPoisson>,<missing>) plot(<UniformPrior>,<missing>): 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

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

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(<BaselineObject>): Set Transformations in Baseline Objects

set_transformations(): Set transformations in BaselineObject objects

show_guide(): Show guide for objects with guides

sim_borrowing_list(): Input borrowing details for a simulation study

sim_covariate_list(): Input covariate adjustment 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_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

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

variable_dictionary(): Create Variable Dictionary

weib_ph_surv_dist(): Legacy function for the Weibull proportional Hazards survival distribution