convertToCodaObject function

convertToCodaObject

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

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

Returns

A named list that can be analysed with list("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)