fit: Function to estimate a Bayesian case-control model.

In cjbarrie/extremeR: A Bayesian Hierarchical Case-Control Method for Analyzing Extreme Behavior

Function to estimate a Bayesian case-control model.

Description

Function to estimate a Bayesian case-control model.

Usage

fit(
  data = data_sim,
  contamination = F,
  show_code = T,
  offset = F,
  beta_prior = "normal",
  small_area_prior = "fixed",
  large_area_prior = NA,
  intercept_scale = NA,
  iter = 100,
  warmup = 50,
  thin = 4,
  cores = 4,
  chains = 4,
  control = list(max_treedepth = 7, adapt_delta = 0.8),
  verbose = TRUE
)

Arguments

data	list, survey and shapefile combined list object created with the data.prep() function.
contamination	logical, should the model include the Rota et al. (2013) style contamination layer? Defaults to TRUE.
show_code	logical, should the stan code print on the screen at the end of the run? Defaults to TRUE.
offset	logical, should the model include a King and Zeng (2001) style offset ? if contamination is also specified, this will be a contaminated-offset. Defaults to TRUE.
beta_prior	string, what prior should the regression coefficients have? Choice between: "normal" and "cauchy."
small_area_prior	string, what should be the small-area effects type? Choice between: "fixed," "random," "ICAR," and "BYM2." Specify NA for no area effects. Defaults to "fixed.
large_area_prior	string, what should be the large-area effects type? Choice between: "fixed" and "random." Specify NA for no area effects. Defaults to NA.
intercept_scale	integer, scale of intercept; see ?stan for further information.
iter	integer, number of draws; see ?stan for further information.
warmup	number of warmup draws; see ?stan for further information.
thin	integer, number to thin draws; see ?stan for further information.
cores	integer, number of cores to use; see ?stan for further information.
chains	integer, number of chains; see ?stan for further information.
control	list; tree depth and adapt delta; see ?stan for further information.
verbose	logical, print full stan output? Defaults to TRUE.

cjbarrie/extremeR documentation built on April 14, 2023, 9:26 p.m.