priorPosterior: priorPosterior

In MCMCtreeR: Prepare MCMCtree Analyses and Plot Bayesian Divergence Time Analyses Estimates on Trees

Description

Analyse prior and posterior node distributions from MCMCtree analysis

Usage

priorPosterior(MCMCPrior, MCMCPosterior = NULL, inputTree,
  return.density = FALSE, rootCalibration = NULL)

Arguments

MCMCPrior	prior of MCMC file from MCMCtree analysis using data=0
MCMCPosterior	posterior of MCMC file from MCMCtree analysis using data
inputTree	phylogeny in MCMCtree format used in MCMCtree analysis
return.density	Logical. Whether to return the density or original values for the effective prior and posterior.
rootCalibration	= NULL If NULL, then behaves as by default. Alternatively, if a user has specified a root prior in the MCMCtreeR control file it can be added here as a vector in the form it would appear tree.

Value

list containing node estimates for each distribution

• "prior" distribution of effective prior

• "posterior" distribution of posterior

• "specifiedPrior" distribution of specified prior

Author(s)

Mark Puttick, Pascal Title

Examples

data(MCMCtree.output)
# priorPosterior(MCMCPrior, 
# MCMCPosterior=MCMCtree.output$MCMCtree.posterior, 
# path.to.input.tree)

Example output

Loading required package: ape
Loading required package: sn
Loading required package: stats4

Attaching package: ‘sn’

The following object is masked from ‘package:stats’:

    sd

Loading required package: coda

MCMCtreeR documentation built on May 22, 2019, 1:03 a.m.