Methods for lfJSDM Object

Methods for extracting information from a fitted latent factor joint species distribution model (lfJSDM).

Usage

# S3 method for lfJSDM
summary(object, level = 'both', quantiles = c(0.025, 0.5, 0.975), 
        digits = max(3L, getOption("digits") - 3L), ...)
# S3 method for lfJSDM
print(x, ...)
# S3 method for lfJSDM
plot(x, param, density = TRUE, ...)

Arguments

object, x

object of class lfJSDM.

level

a quoted keyword that indicates the level to summarize the model results. Valid key words are: "community", "species", or "both".

quantiles

for summary, posterior distribution quantiles to compute.

digits

for summary, number of digits to report.

param

parameter name for which to generate a traceplot. Valid names are "beta", "beta.star", "sigma.sq.psi", "beta.comm", "tau.sq.beta", "lambda".

density

logical value indicating whether to also generate a density plot for each parameter in addition to the MCMC traceplot.

...

currently no additional arguments

Details

A set of standard extractor functions for fitted model objects of class lfJSDM, including methods to the generic functions print, summary, and plot.

Value

No return value, called to display summary information of a lfJSDM object.