make_scaler_simmap: Make stochastic map with rate scalers

In Caetanods/buddPhy: Trait Evolution and Budding Speciation

Description

Plot the rate scalers used in the simulation to the phylogenetic tree. Also return a vector of colors to be used for visualization of the gradient paired with the breaking points for the rate scaler values.
Use 'low_cut' or 'high_cut' to focus the rate categories into the slow or fast rate categories. This can be used to provide a more informative plot of rates along the branches of the phylogeny.

Usage

make_scaler_simmap(sims, ncat = 10, low_cut, high_cut)

Arguments

sims	the simulation object output from 'sim_Mk_budding_exp'.
ncat	number of categories to make the legend for the scalers plot.
low_cut	break for the first category (slow rate scalers). Rate scaler values above 'low_cut' value will be divided into 'ncat'-1 categories.
high_cut	break for the last category (fast rate scalers). Rate scaler values below 'high_cut' value will be divided into 'ncat'-1 categories.

Value

a list with a simmap object and a matrix with legend information

Caetanods/buddPhy documentation built on Oct. 12, 2021, 12:14 p.m.