Compile artemis models — compile

This compiles the models needed for the artemis package. This must be done before using the eDNA_lm* functions. This function is called for its side-effects.

compile_models(
  model_names = c("eDNA_lm.stan", "eDNA_lmer.stan", "eDNA_lm_zinf.stan",
    "eDNA_lmer_zinf.stan", "eDNA_pois_lm.stan", "eDNA_pois_lmer.stan",
    "eDNA_sim_omni.stan"),
  models = system.file("stan", model_names, package = "artemis"),
  cache_dir = getOption("artemis_cache_dir", R_user_dir("artemis", "cache")),
  rewrite = FALSE,
  verbose = TRUE,
  ...
)

Arguments

model_names: the names of the models to compile
models: full file path to the location of models
cache_dir: a directory to store the Stan model code and compiled models. Can be set with the option "artemis_cache_dir", otherwise defaults to the directory returned by R_user_dir(). If the directory does not exist, it will be created.
rewrite: logical, whether to re-compile the models, overwriting previous versions.
verbose: logical, if TRUE messages will report steps being taken
...: additional arguments passed to cmdstanr::cmdstan_model()

Author

Matt Espe