gibbs.SAM: Main function of the Species Archetype Model (SAM)

In drvalle1/EcoCluster: Bayesian Clustering using Truncated Stick-Breaking priors

Description

Runs the Gibbs sampler and returns samples from the posterior distribution

Usage

gibbs.SAM(y, xmat, ngroups, ngibbs, burnin)

Arguments

y	this matrix has L rows (locations) and S columns (species) and contains the presence-absence data
xmat	L X P design matrix containing the covariates (columns) for each location (rows). Notice that this matrix does not contain a column of 1's for the intercept
ngroups	maximum number of species groups (K)
ngibbs	number of Gibbs sampler iterations
burnin	number of iterations to discard as part of burn-in phase

Value

this function returns a list containing several matrices, all of which have ngibbs-burnin rows, containing samples from the posterior distribution of:

• logl: log-likelihood for each iteration

• theta: probability associated with each species group

• betas: slope parameters for each group

• cs: cluster assignment of each species

• alpha: intercept of each species

• gamma: TSB prior parameter

drvalle1/EcoCluster documentation built on Jan. 25, 2022, 12:46 a.m.