summariseTrees: summariseTrees

In hferg/BTprocessR: A set of tools to help with the interpretation and analysis of the output of BayesTraits MCMC analyses.

Description

Summarise a posterior sample of trees from a rate-varible or RJ local transformation BayesTraits MCMC analysis.

Usage

summariseTrees(reftree, trees, burnin = 0, thinning = 1,
  verbose = TRUE)

Arguments

reftree	A tree that provides the reference topology (in most cases this is time-tree the analysis was run on). Can be a filename of a tree in the working directory or an object of class "phylo"
trees	The posterior sample of trees from a rate-variable or RJlocaltransformation MCMC BayesTraits analysis. Typically will have the .Output.trees extension. Either the filename of the posterior, or an object of class "multiPhylo".
burnin	Number of trees to discard as burnin (if, for example, the MCMC chain had not converged until later in the run).
thinning	If >1 then every nth tree will be sampled - useful if the sampling interval of the original MCMC analysis was too small. Note that is it preferable to ensure proper chain convergence prior to analysis of the results, in which case the default settings of burnin and thinning will be appropriate.
verbose	If TRUE a progress bar will be shown when ladderizing the posterior trees (this step can be time consuming).

hferg/BTprocessR documentation built on March 8, 2020, 11:45 a.m.