dev_ermod_emax: Develop Emax model for continuous and binary endpoint

In BayesERtools: Bayesian Exposure-Response Analysis Tools

Develop Emax model for continuous and binary endpoint

Description

These functions are used to develop an Emax model with continuous or binary endpoint. You can also specify covariates to be included in the model; note that only categorical covariates are allowed.

Usage

dev_ermod_emax(
  data,
  var_resp,
  var_exposure,
  l_var_cov = NULL,
  gamma_fix = 1,
  e0_fix = NULL,
  emax_fix = NULL,
  priors = NULL,
  verbosity_level = 1,
  chains = 4,
  iter = 2000,
  seed = sample.int(.Machine$integer.max, 1)
)

dev_ermod_bin_emax(
  data,
  var_resp,
  var_exposure,
  l_var_cov = NULL,
  gamma_fix = 1,
  e0_fix = NULL,
  emax_fix = NULL,
  priors = NULL,
  verbosity_level = 1,
  chains = 4,
  iter = 2000,
  seed = sample.int(.Machine$integer.max, 1)
)

Arguments

data	Input data for E-R analysis
var_resp	Response variable name in character
var_exposure	Exposure variable names in character
l_var_cov	a names list of categorical covariate variables in character vector. See details in the param.cov argument of rstanemax::stan_emax() or rstanemax::stan_emax_binary()
gamma_fix	Hill coefficient, default fixed to 1. See details in rstanemax::stan_emax() or rstanemax::stan_emax_binary()
e0_fix	See details in rstanemax::stan_emax() or rstanemax::stan_emax_binary()
emax_fix	See details in rstanemax::stan_emax() or rstanemax::stan_emax_binary()
priors	See details in rstanemax::stan_emax() or rstanemax::stan_emax_binary()
verbosity_level	Verbosity level. 0: No output, 1: Display steps, 2: Display progress in each step, 3: Display MCMC sampling.
chains	Number of chains for Stan.
iter	Number of iterations for Stan.
seed	Random seed for Stan model execution, see details in rstan::sampling() which is used in rstanemax::stan_emax() or rstanemax::stan_emax_binary()

Value

An object of class ermod_emax.or ermod_bin_emax.

Examples

data_er_cont <- rstanemax::exposure.response.sample

ermod_emax <-
  dev_ermod_emax(
    data = data_er_cont,
    var_exposure = "exposure",
    var_resp = "response"
  )

plot_er(ermod_emax, show_orig_data = TRUE)

data_er_cont_cov <- rstanemax::exposure.response.sample.with.cov

ermod_emax_w_cov <-
  dev_ermod_emax(
    data = data_er_cont_cov,
    var_exposure = "conc",
    var_resp = "resp",
    l_var_cov = list(emax = "cov2", ec50 = "cov3", e0 = "cov1")
  )




data_er_bin <- rstanemax::exposure.response.sample.binary

ermod_bin_emax <-
  dev_ermod_bin_emax(
    data = data_er_bin,
    var_exposure = "conc",
    var_resp = "y"
  )

plot_er(ermod_bin_emax, show_orig_data = TRUE)

ermod_bin_emax_w_cov <-
  dev_ermod_bin_emax(
    data = data_er_bin,
    var_exposure = "conc",
    var_resp = "y_cov",
    l_var_cov = list(emax = "sex")
  )

BayesERtools documentation built on June 8, 2025, 1:26 p.m.