getPostEstimate function

getPostEstimate

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

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

Returns

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)