boral (version 1.7)

get.mcmcsamples: Extract MCMC samples from boral models

Description

Extract the MCMC samples from boral models, taking into account the burnin period and thinning.

Usage

get.mcmcsamples(object)

Arguments

object

An object for class "boral".

Value

A matrix containing the MCMC samples, with the number of rows equal to the number of MCMC samples after accounting the burnin period and thinning (i.e., number of rows = (n.iteration - n.burnin)/n.thin), and the number of columns equal to the number of parameters in the fitted boral model.

Details

For the function to work, the JAGS model file (containing the MCMC samples from the call to JAGS) has to have been saved when fitting the boral model, that is, save.model = TRUE. The function will throw an error if it cannot find the the JAGs model file.

Examples

# NOT RUN {
## NOTE: The values below MUST NOT be used in a real application;
## they are only used here to make the examples run quick!!!
example_mcmc_control <- list(n.burnin = 10, n.iteration = 100, 
     n.thin = 1)
     
library(mvabund) ## Load a dataset from the mvabund package
library(corrplot) ## For plotting correlations
data(spider)
y <- spider$abun
X <- scale(spider$x)
n <- nrow(y)
p <- ncol(y)
    
spiderfit_nb <- boral(y, X = X, family = "negative.binomial", 
     save.model = TRUE, mcmc.control = example_mcmc_control, 
     save.model = TRUE)

mcmcsamps <- get.mcmcsamples(spiderfit_nb)
# }
# NOT RUN {
# }