getPostEstimate: getPostEstimate

In hmsc-r/HMSC: Hierarchical Model of Species Communities

getPostEstimate

Description

Calculates mean, support and other posterior quantities for a specified model parameter

Usage

getPostEstimate(
  hM,
  parName,
  r = 1,
  x = NULL,
  q = c(),
  chainIndex = 1:length(hM$postList),
  start = 1,
  thin = 1
)

Arguments

hM	a fitted Hmsc model object
parName	name of the parameter to be summarized. Can take value of model's baseline parameters, "Omega" or "OmegaCor".
r	the random level for which to calculate the parameter. Has effect only for Eta, Lambda, Omega and OmegaCor.
x	values of covariates for covariate dependent omega
q	vector of quantiles to calculate.
chainIndex	which posterior chains to use for summarization (defaults to all)
start	index of first MCMC sample included
thin	thinning interval of posterior distribution

Value

A named list of posterior quantities.

Examples

# Get posterior mean and support for species' responses to environmental covariates
postBeta = getPostEstimate(TD$m, parName='Beta')

# Get posterior mean and support for species' responses to latent factors for the first random level
postLambda = getPostEstimate(TD$m, parName='Lambda', r=1)

hmsc-r/HMSC documentation built on March 5, 2025, 10:52 p.m.