pr_eoi: Calculate Probability of Meeting Effect of Interest (EOI)

In rich-payne/dreamer: Dose Response Models for Bayesian Model Averaging

Calculate Probability of Meeting Effect of Interest (EOI)

Description

Calculate Pr(effect_dose - effect_reference_dose > EOI | data) or Pr(effect_dose > EOI | data).

Usage

pr_eoi(x, eoi, dose, reference_dose = NULL, time = NULL)

Arguments

x	output from a call to dreamer_mcmc().
eoi	a vector of the effects of interest (EOI) in the probability function.
dose	a vector of the doses for which to calculate the posterior probabilities.
reference_dose	a vector of doses for relative effects of interest.
time	the time at which to calculate the posterior quantity. Defaults to the latest timepoint. Applies to longitudinal models only.

Value

A tibble listing the doses, times, and Pr(effect_dose - effect_reference_dose > eoi) if reference_dose is specified; otherwise, Pr(effect_dose > eoi).

Examples

set.seed(888)
data <- dreamer_data_linear(
  n_cohorts = c(20, 20, 20),
  dose = c(0, 3, 10),
  b1 = 1,
  b2 = 3,
  sigma = 5
)

# Bayesian model averaging
output <- dreamer_mcmc(
 data = data,
 n_adapt = 1e3,
 n_burn = 1e3,
 n_iter = 1e4,
 n_chains = 2,
 silent = FALSE,
 mod_linear = model_linear(
   mu_b1 = 0,
   sigma_b1 = 1,
   mu_b2 = 0,
   sigma_b2 = 1,
   shape = 1,
   rate = .001,
   w_prior = 1 / 2
 ),
 mod_quad = model_quad(
   mu_b1 = 0,
   sigma_b1 = 1,
   mu_b2 = 0,
   sigma_b2 = 1,
   mu_b3 = 0,
   sigma_b3 = 1,
   shape = 1,
   rate = .001,
   w_prior = 1 / 2
 )
)

pr_eoi(output, dose = 3, eoi = 10)

# difference of two doses
pr_eoi(output, dose = 3, eoi = 10, reference_dose = 0)

# single model
pr_eoi(output$mod_linear, dose = 3, eoi = 10)

rich-payne/dreamer documentation built on Dec. 20, 2024, 6:57 a.m.