shiftSummaries: A function for summarizing the state of a model after a shift
In uyedaj/bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

shiftSummaries

R Documentation

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.