mrf_penalty.phylo: MRF penalty from a phylogeny

In eric-pedersen/MRFtools: Tools for Constructing and Plotting Markov Random Fields in R for Graphical Data

MRF penalty from a phylogeny

Description

MRF penalty from a phylogeny

Usage

## S3 method for class 'phylo'
mrf_penalty(object, node_labels = NULL, add_delta = FALSE, eps = 0, ...)

Arguments

object	an R object to create the MRF penalty from.
node_labels	character; a vector of alternative labels for the levels of the factor.
add_delta	numeric or logical; either the numeric value to add to the diagonal of the MRF penalty matrix, or a logical value indicating if such an adjustment should be made. The default is to not alter the diagonal of the penalty matrix.
eps	A value to add to the variance-covariance matrix diagonal to make it positive definite
...	arguments passed to other methods.

eric-pedersen/MRFtools documentation built on Jan. 28, 2024, 2:13 a.m.