getEstimates: getEstimates

In bhmbasket: Bayesian Hierarchical Models for Basket Trials

getEstimates

Description

This function calculates the point estimates and credible intervals per cohort, as well as estimates of the biases and the mean squared errors of the point estimates per cohort

Usage

getEstimates(
  analyses_list,
  add_parameters = NULL,
  point_estimator = "median",
  alpha_level = 0.05
)

Arguments

analyses_list	An object of class analysis_list, as created with performAnalyses
add_parameters	A vector of strings naming additional parameters from the Bayesian hierarchical models, e.g. c('mu', 'tau'). If NULL, no additional parameters will be evaluated, Default: NULL
point_estimator	A string indicating the type of estimator used for calculation of bias and MSE. Must be one of 'median' or 'mean'
alpha_level	A numeric in (0, 1) for the level of the credible interval. Only values corresponding to quantiles saved in performAnalyses will work, Default: 0.05

Details

Bias and MSE will only be calculated for response rate estimates of simulated trials. For additional parameters, bias and MSE will not be calculated.

Possible additional parameters are for the Bayesian hierarchical models are c('mu', 'tau') for 'berry', 'exnex', and 'exnex_adj'. The latter two models can also access the posterior weights paste0("w_", seq_len(n_cohorts)).

Value

A named list of matrices of estimates of response rates and credible intervals. Estimates of bias and MSE are included for response rate estimates of simulated trials.

Author(s)

Stephan Wojciekowski

See Also

createTrial performAnalyses

Examples

  scenarios_list <- simulateScenarios(
    n_subjects_list     = list(c(10, 20, 30)),
    response_rates_list = list(c(0.1, 0.2, 3)),
    n_trials            = 10)

  analyses_list <- performAnalyses(
    scenario_list       = scenarios_list,
    target_rates        = c(0.1, 0.1, 0.1),
    calc_differences    = matrix(c(3, 2, 2, 1), ncol = 2),
    n_mcmc_iterations   = 100)

  getEstimates(analyses_list)
  getEstimates(analyses_list   = analyses_list,
               add_parameters  = c("mu", "tau", "w_1", "w_2", "w_3"),
               point_estimator = "mean",
               alpha_level     = 0.1)

  outcome <- createTrial(
    n_subjects          = c(10, 20, 30),
    n_responders        = c( 1,  2,  3))

  outcome_analysis <- performAnalyses(
    scenario_list       = outcome,
    target_rates        = c(0.1, 0.1, 0.1),
    n_mcmc_iterations   = 100)

  getEstimates(outcome_analysis)
  getEstimates(analyses_list  = outcome_analysis,
               add_parameters = c("mu", "w_1", "w_2", "w_3"))

bhmbasket documentation built on March 18, 2022, 7:46 p.m.