Develop Emax model for continuous and binary endpoint — dev_ermod

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

# \donttest{
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")
  )
# }

# \donttest{
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")
  )
# }