pg_mvgp_univariate: Bayesian Polya-gamma regression
In jtipton25/pgR: Bayesian Polya-Gamma Regression

pg_mvgp_univariate

R Documentation

Bayesian Polya-gamma regression

Description

this function runs the Bayesian multinomial regression using Polya-gamma data augmentation

Usage

pg_mvgp_univariate(
  Y,
  X,
  Z0,
  locs,
  params,
  priors,
  corr_fun = "exponential",
  model = "iid error",
  n_cores = 1L,
  inits = NULL,
  config = NULL,
  verbose = FALSE,
  n_chain = 1
)

Arguments

`Y`	is a n x J matrix of compositional count data.
`X`	is a n x p matrix of fixed effects (like latitude, elevation, etc)
`Z0`	is a n x Q matrix of observed climate variables
`locs`	is a n x 2 matrix of observation locations.
`params`	is a list of parameter settings. The list `params` must contain the following values: `n_adapt`: A positive integer number of adaptive MCMC iterations. `n_mcmc`: A positive integer number of total MCMC iterations post adaptation. `n_thin`: A positive integer number of MCMC iterations per saved sample. `n_message`: A positive integer number of frequency of iterations to output a progress message. For example, `n_message = 50` outputs progress messages every 50 iterations.
`priors`	is the list of prior settings.
`corr_fun`	is a character that denotes the correlation function form. Current options include "matern" and "exponential".
`model`	is the form of the polya-gamma model. Currently, this option is not active the only model is the "iid error" model. This option allows for independent species-specific overdispersion variance terms.
`n_cores`	is the number of cores for parallel computation using openMP.
`inits`	is the list of initial values if the user wishes to specify initial values. If these values are not specified, then the initial values will be randomly sampled from the prior.
`config`	is the list of configuration values if the user wishes to specify initial values. If these values are not specified, then default a configuration will be used.
`verbose`	is a logicial input that determines whether to print more detailed messages.
`n_chain`	is the MCMC chain id. The default is 1.