break_vcv: Break the variance-covariance matrix

In suryakevin/drugcandy: Detecting Punctuated Evolution in Dinosaurs and Viruses

Break the variance-covariance matrix

Description

This function breaks the phylogenetic variance-covariance matrix into its correlation (off-diagonal) and variance components (on-diagonal). The output from break_vcv is necessary for using the est_node_density and fit_punc_model functions.

Usage

break_vcv(tree, lambda = 1, est_lambda = FALSE)

Arguments

tree	An object of class phylo
lambda	Pagel's λ, a measure of phylogenetic signal
est_lambda	If TRUE, the downstream function(s) estimate Pagel's λ

Value

This function returns a list comprising a correlation matrix (a corPagel object) and a variance weight vector.

Author(s)

Kevin Surya

References

Pagel (1999); Paradis and Schliep (2019)

suryakevin/drugcandy documentation built on May 6, 2022, 6:37 p.m.