converting MCMC samples between auteur and coda
to.auteur(obj, phy = NULL, ...)
to.coda(obj)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.
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
JM Eastman
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.
load.rjmcmc