Lposterior: Return a posterior of shift locations

In uyedaj/bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Return a posterior of shift locations

Description

Return a posterior of shift locations

Usage

Lposterior(chain, tree, burnin = 0, simpar = NULL, mag = TRUE)

Arguments

chain	A bayouMCMC chain
tree	A tree of class 'phylo'
burnin	A value giving the burnin proportion of the chain to be discarded
simpar	An optional bayou formatted parameter list giving the true values (if data were simulated)
mag	A logical indicating whether the average magnitude of the shifts should be returned

Value

A data frame with rows corresponding to postordered branches. pp indicates the posterior probability of the branch containing a shift. magnitude of theta2 gives the average value of the new optima after a shift. naive SE of theta2 gives the standard error of the new optima not accounting for autocorrelation in the MCMC and rel location gives the average relative location of the shift on the branch (between 0 and 1 for each branch).

uyedaj/bayou documentation built on Jan. 28, 2024, 5:09 a.m.