make.simmap2: Modified stochastic mapping which is resistant to model...

In coleoguy/evobir: Evolutionary Biology in R

Modified stochastic mapping which is resistant to model failure

Description

This function is an extension of the make.simmap function of phytools which allows users to monitor rejections at specific edges during the simulation proces and set an upper limit on the number of rejections permitted per edge.

Usage

make.simmap2(tree, x, model="SYM", nsim=1 ,
             monitor = FALSE, rejmax = NULL, rejint = 1000000, 
             ...)

Arguments

tree	see make.simmap
x	see make.simmap
model	see make.simmap
nsim	see make.simmap
monitor	boolean describing whether or not to print number of rejections per edge to console. Defaults to FALSE
rejmax	int greater than one giving the maximum number of rejections permitted before an edge is skipped. Defaults to NULL (no upper limit on rejections)
rejint	int giving the interval after which rejection number is to be printed to console
...	optional arguments. see make.simmap

Value

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

In addition to the states present in the model, an additional state fail in the maps and mapped.edge elements is assigned to edges which are skipped due to exceeding the rejection limit.

Author(s)

Matthew Marano, Maximos Chin, and Heath Blackmon

References

http://coleoguy.github.io/

See Also

make.simmap

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