stan_gllvm: Alias for 'stan_jsdm' with 'method = "gllvm"'

In fseaton/jsdmstan: Fitting jSDMs in Stan

Alias for stan_jsdm with method = "gllvm"

Description

Alias for stan_jsdm with method = "gllvm"

Usage

stan_gllvm(X, ...)

## Default S3 method:
stan_gllvm(
  X = NULL,
  Y = NULL,
  D = NULL,
  species_intercept = TRUE,
  dat_list = NULL,
  family,
  site_intercept = "none",
  prior = jsdm_prior(),
  save_data = TRUE,
  iter = 4000,
  ...
)

## S3 method for class 'formula'
stan_gllvm(formula, data = list(), ...)

Arguments

X	The covariates matrix, with rows being site and columns being covariates. Ignored in favour of data when formula approach is used to specify model.
...	Arguments passed to rstan::sampling()
Y	Matrix of species by sites. Rows are assumed to be sites, columns are assumed to be species
D	The number of latent variables within a GLLVM model
species_intercept	Whether the model should be fit with an intercept by species, by default TRUE
dat_list	Alternatively, data can be given to the model as a list containing Y, X, N, S, K, and site_intercept. See output of jsdm_sim_data() for an example of how this can be formatted.
family	is the response family, must be one of "gaussian", "neg_binomial", "poisson", "binomial", "bernoulli", or "zi_poisson". Regular expression matching is supported.
site_intercept	Whether a site intercept should be included, potential values "none" (no site intercept), "grouped" (a site intercept with hierarchical grouping) or "ungrouped" (site intercept with no grouping)
prior	Set of prior specifications from call to jsdm_prior()
save_data	If the data used to fit the model should be saved in the model object, by default TRUE.
iter	A positive integer specifying the number of iterations for each chain, default 4000.
formula	The formula of covariates that the species means are modelled from
data	Dataframe or list of covariates.

Methods (by class)

• stan_gllvm(default): Default

• stan_gllvm(formula): Formula interface

fseaton/jsdmstan documentation built on Sept. 29, 2024, 6:40 p.m.