to.auteur: conversion of MCMC samples between auteur and coda

In geiger: Analysis of Evolutionary Diversification

conversion of MCMC samples between auteur and coda

Description

converting MCMC samples between auteur and coda

Usage

to.auteur(obj, phy = NULL, ...)
to.coda(obj)

Arguments

obj	for to.auteur – an object of class codaMCMCMC, mcmc.list, or an object exported to an rda file by auteur; for to.coda – an object of class auteurMCMCMC or a list of objects individually of class auteurMCMC
phy	a phylogenetic tree of class 'phylo' against which to compile results; if NULL, the tree stored within the rda file is used
...	arguments (burnin and thin) to be passed to load.rjmcmc

Details

A coda format of run(s) is recommended for diagnostic purposes; for summarization, auteur formats are advised. For single chains, the format adopted by both auteur and coda is identical (an object of class mcmc). For a series of combined runs, formats differ between the auteur and coda packages: auteur requires an intercalated (single) matrix of values, whereas functions within coda expect the values to be concatenated into a list (of class mcmc.list). The function to.coda is used solely for pooling multiple runs into a format compatible with the coda package.

Value

For to.auteur, an object of class auteurMCMCMC (given multiple runs) or auteurMCMC (given a single run) is returned; for to.coda, an object of class codaMCMCMC is returned.

Author(s)

JM Eastman

See Also

load.rjmcmc

geiger documentation built on April 4, 2023, 1:07 a.m.