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

Description Usage Arguments Details Value Author(s) See Also

View source: R/utilities-misc.R


converting MCMC samples between auteur and coda


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



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


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


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.


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.


JM Eastman

See Also


geiger documentation built on May 29, 2017, 10:40 a.m.

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