getCladeSuccess: Clade success through time

In DomBennett/MoreTreeTools: Tools for manipulating phylogenetic trees

Description

Return a dataframe of clade tip number from a list of trees.

Usage

getCladeSuccess(trees, ind = FALSE, count.extincts = FALSE,
  time.intervals = 1:length(trees))

Arguments

ind	boolean, use independent counting? Deafult FALSE
count.extincts	boolean, count extinct and extant tips? Default FALSE
time.intervals	vector of time represented by each tree in trees
tree	phylogenetic tree (ape class)

Details

The function takes a list of trees and counts the success of each clade, returning a dataframe of number of tips for each tree for each named clade. It requires nodes to be labeled in the 'node.label' slot of the Phylo class.

Takes list of trees generated from runEDBMM(record=TRUE).

Setting 'ind' (or independent) as TRUE will implement a counting method that attempts to count descendents unique to the clade by preventing double counting in decsendent clades. Independent counting works by limiting the maximum clade count to the minimum of the descendant counts of the two daughter clades. If one of the daughter clades continues to speciate while the other goes extinct then the parent clade of the two will be limited to 0 rather than the size of a single daughter clade.

'time.intervals' is a vector of time steps represented by each tree. Default is 1 to length of number of trees.

Setting 'count.extincts' to TRUE will count both extinct and extant tips through time.

References

No references yet! https://github.com/DomBennett/MoreTreeTools.

Examples

#library (MoreTreeTools)

DomBennett/MoreTreeTools documentation built on May 6, 2019, 2:51 p.m.