readMCMC: Read the MCMC output files

In Caetanods/ratematrix: Bayesian Estimation of the Evolutionary Rate Matrix

Read the MCMC output files

Description

Reads the output files from the MCMC with the posterior distribution of the chains.

Usage

readMCMC(handle, burn = 0, thin = 1, dir = NULL)

Arguments

handle	the output object from the 'ratematrixMCMC' function.
burn	the proportion of the burnin to be pruned from the MCMC chain. A number between 0 and 1 (default is 0).
thin	the thinning of the posterior distribution. A number with the interval between each MCMC step to be kept in the posterior distribution (default is 1).
dir	directory with the output files. If 'NULL' (default), then files are read from the directory chosen when running the MCMC chain using the argument 'dir' of the 'ratematrixMCMC' function (stored on handle). Otherwise function will read files from 'dir'.

Value

List with the MCMC chain for the phylogenetic mean (root value) and evolutionary rate matrices (R). *root* are the values for the phylogenetic mean in matrix format; *matrix* is a list of length equal to the number of rate regimes fitted to the tree, each of those are lists with the chain of respective R matrices.

Author(s)

Daniel S. Caetano and Luke J. Harmon

Examples

## Load data
data(centrarchidae)
## Run MCMC. This is just a very short chain.
handle <- ratematrixMCMC(data=centrarchidae$data, phy=centrarchidae$phy.map, gen=10000
                         , dir=tempdir())
## Load posterior distribution.
## We can set the burn-in value and the thinning.
posterior <- readMCMC(handle, burn=0.25, thin=1)

Caetanods/ratematrix documentation built on Jan. 4, 2023, 3:12 p.m.