shiftSummaries: A function for summarizing the state of a model after a shift

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

A function for summarizing the state of a model after a shift

Description

A function for summarizing the state of a model after a shift

Usage

shiftSummaries(chain, mcmc, pp.cutoff = 0.3, branches = NULL)

Arguments

chain	A bayouMCMC chain
mcmc	A bayou mcmc object
pp.cutoff	The threshold posterior probability for shifts to summarize, if 'branches' specified than this is ignored.
branches	The specific branches with shifts to summarize, assuming postordered tree

Details

shiftSummaries summarizes the immediate parameter values after a shift on a particular branch. Parameters are summarized only for the duration that the particular shift exists. Thus, even global parameters will be different for particular shifts.

Value

A list with elements: pars = a bayoupars list giving the location of shifts specified; tree = The tree; pred = Predictor variable matrix; dat = A vector of the data; SE = A vector of standard errors; PP = Posterior probabilities of the specified shifts; model = A list specifying the model used; variables = The variables summarized; cladesummaries = A list providing the medians and densities of the distributions of regression variables for each shift; descendents = A list providing the taxa that belong to each regime regressions = A matrix providing the regression coefficients for each regime.

bayou documentation built on June 10, 2025, 5:13 p.m.