convertToCodaObject: convertToCodaObject

In Hmsc: Hierarchical Model of Species Communities

convertToCodaObject

Description

Converts the Hmsc posterior into a named list of mcmc.list objects

Usage

convertToCodaObject(
  hM,
  start = 1,
  spNamesNumbers = c(TRUE, TRUE),
  covNamesNumbers = c(TRUE, TRUE),
  trNamesNumbers = c(TRUE, TRUE),
  Beta = TRUE,
  Gamma = TRUE,
  V = TRUE,
  Sigma = TRUE,
  Rho = TRUE,
  Eta = TRUE,
  Lambda = TRUE,
  Alpha = TRUE,
  Omega = TRUE,
  Psi = TRUE,
  Delta = TRUE
)

Arguments

hM	a fitted Hmsc model object
start	index of first MCMC sample included
spNamesNumbers	logical of length 2, where first entry controls whether species names are printed, and second entry controls whether species numbers are printed
covNamesNumbers	Logical of length 2, where first entry controls whether covariate names are printed, and second entry controls whether covariate numbers are printed
trNamesNumbers	Logical of length 2, where first entry controls whether trait names are printed, and second entry controls whether traits numbers are printed
Beta	logical indicating whether posterior of Beta is included
Gamma	logical indicating whether posterior of Gamma is included
V	logical indicating whether posterior of V is included
Sigma	logical indicating whether posterior of Sigma is included
Rho	logical indicating whether posterior of Rho is included
Eta	logical indicating whether posterior of Eta is included
Lambda	logical indicating whether posterior of Lambda is included
Alpha	logical indicating whether posterior of Alpha is included
Omega	logical indicating whether posterior of Omega is included
Psi	logical indicating whether posterior of Psi is included
Delta	logical indicating whether posterior of Delta is included

Value

A named list that can be analysed with coda functions.

Examples

# Convert recorded posterior samples in \code{Hmsc} object to coda object
codaObject = convertToCodaObject(TD$m)

# Convert recorded posterior samples, starting from sample 100, in m object to coda object
codaObject = convertToCodaObject(TD$m, start=100)

Hmsc documentation built on Aug. 11, 2022, 5:11 p.m.