Function reference • psborrow2

All functions

Analysis-class .analysis_obj: Analysis Class

BaselineDataFrame-class .baseline_dataframe: Baseline Data Frame Object

BaselineObject-class .baseline_object: BaselineObject class for data simulation

BernoulliPrior-class .bernoulli_prior: BernoulliPrior Class

BetaPrior-class .beta_prior: BetaPrior Class

BinaryOutcome-class: BinaryOutcome class

Borrowing-class .borrowing_class: Borrowing Class

CauchyPrior-class .cauchy_prior: CauchyPrior Class

Covariates-class .covariate_class: Covariate Class

ExponentialPrior-class .exponential_prior: ExponentialPrior Class

ExponentialSurvDist-class .exp_surv_dist: ExponentialSurvDist Class

GammaPrior-class .gamma_prior: GammaPrior Class

HalfCauchyPrior-class .half_cauchy_prior: HalfCauchyPrior Class

HalfNormalPrior-class .half_normal_prior: HalfNormalPrior Class

LogisticBinaryOutcome-class .logistic_bin_outcome: LogisticBinaryOutcome class

MCMCSimulationResult-class .mcmc_simulation_result: MCMCSimulationResult Class

NormalPrior-class .normal_prior: NormalPrior Class

Outcome-class: Outcome class

PoissonPrior-class .poisson_prior: PoissonPrior Class

Prior-class: Prior 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

WeibullPHSurvDist-class .weib_ph_surv_dist: WeibullPHSurvDist Class

add_covariates(): Add Covariates for Model Adjustment

baseline_covariates(): Specify Correlated Baseline Covariates

bernoulli_prior(): Prior bernoulli distribution

beta_prior(): Prior beta distribution

bin_var(): Create binary covariate

binary_cutoff(): Binary Cut-Off Transformation

borrowing_details(): Specify Borrowing Model

cauchy_prior(): Prior cauchy distribution

check_cmdstanr(): Check Stan

check_data_matrix_has_columns(): Check Data Matrix for Required Columns

cont_var(): Create continuous covariate

covariance_matrix(): Create Covariance Matrix

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_simulation_obj(): Compile MCMC sampler using STAN and create simulation object

eval_constraints(): Evaluate constraints

example_matrix: Example data matrix

example_surv: Simulated Survival Data

exp_surv_dist(): Exponential survival distribution

exponential_prior(): Prior exponential distribution

gamma_prior(): Prior gamma distribution

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

generate(): Generate Data from Object

get_cmd_stan_models(): Get CmdStanModel objects for MCMCSimulationResults

get_covariate_constraints(): Get constraints from a list of Priors

get_prior_string(): Get Stan code for a Prior

get_quantiles(): Get Quantiles of Random Data

get_results(): Get results for MCMCSimulationResults objects

get_vars(): Get Variables

half_cauchy_prior(): Prior half-cauchy distribution

half_normal_prior(): Prior half-normal distribution

logistic_bin_outcome(): Bernoulli distribution with logit parametrization

make_analysis_object_list(): Make list of analysis objects for class Simulation

make_model_string_data(): Make model string of Stan's data block

make_model_string_functions(): Make model string of Stan's functions model bloc

make_model_string_model(): Make model string of Stan's model block

make_model_string_parameters(): Make model string of Stan's parameters model block

make_model_string_transf_param(): Make model string of Stan's transformed parameters model block

mcmc_sample(): Sample from Stan model

normal_prior(): Prior normal distribution

parse_constraint(): Extract Upper and Lower Bounds from a Prior object

plot(<Prior>,<missing>) plot(<NormalPrior>,<missing>) plot(<BernoulliPrior>,<missing>) plot(<BetaPrior>,<missing>) plot(<CauchyPrior>,<missing>) plot(<ExponentialPrior>,<missing>) plot(<GammaPrior>,<missing>) plot(<HalfCauchyPrior>,<missing>) plot(<HalfNormalPrior>,<missing>) plot(<PoissonPrior>,<missing>) plot(<UniformPrior>,<missing>): Plot Prior Objects

plot_pdf(): Plot Probability Density Function Values

plot_pmf(): Plot Probability Mass Function Values

poisson_prior(): Prior poisson distribution

prepare_stan_data_inputs(): Prepare Stan data inputs

rename_draws_covariates(): Rename Covariates in draws Object

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_estimate_bias(): What is the bias for a given model

sim_estimate_mse(): What is the MSE for a given model

sim_is_null_effect_covered(): Do the posterior quantiles contain a value of 1.0?

sim_is_true_effect_covered(): Do the posterior quantiles contain the true treatment effect?

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_data_matrix(): Trim model matrix to just include relevant columns

uniform_prior(): Prior uniform distribution

variable_dictionary(): Create Variable Dictionary

weib_ph_surv_dist(): Weibull survival distribution (proportional hazards formulation)