fix.simmap: Fix a stochastic map with failed edges

In coleoguy/evobir: Evolutionary Biology in R

Fix a stochastic map with failed edges

Description

This function facilitates automated resolution of failed edges in a modified stochastic map produced by make.simmap2 through application of graph theory implemented in igraph.

Usage

fix.simmap(hists, tips, transition.matrix)

Arguments

hists	an object of class simmap or multiSimmap produced by make.simmap2
tips	two column dataframe with first column listing species name as shown in tree tips and second column listing model state for each species
transition.matrix	square matrix describing possible transitions between states

Value

A object of class simmap or multiSimmap, see make.simmap.

All edges which failed in the original stochastic maps should be resolved.

Author(s)

Maximos Chin, Matthew Marano, and Heath Blackmon

References

http://coleoguy.github.io/

See Also

make.simmap2

coleoguy/evobir documentation built on May 8, 2024, 6:57 p.m.