summary.by.elements: Calculate Taxonomic Disparity For All Taxa

In andrew-hipp/morton: Tools for manipulation of phylogenetic, genetic, and other biodiversity data

Calculate Taxonomic Disparity For All Taxa

Description

Calculate taxonomic disparity for all taxa represented in a tree, assuming that tip labels are pipe-delimited and the first part of the label is the taxon.

Usage

summary.by.elements(tr, returnEffectOnTreeLength = TRUE, minSizeForEffect = 3, ...)

Arguments

tr	The tree to be analyzed, of class phylo
returnEffectOnTreeLength	A boolean determining whether each taxon's effect on tree length should be calculated and returned. Increases calculation time.
minSizeForEffect	The minimum number of individuals in a taxon to calculate its effect on tree length.
...	Arguments which can be passed to the function label.elements.

Details

The default for returnEffectOnTreeLength is TRUE. The default for minSizeForEffect is 3, and any taxa with less than 3 individuals is automatically assigned an effect size of 0.

Value

disparity.mat	A matrix with taxa as rows and the number of individuals in each taxon, the expected number of tips from the taxon's most recent common ancestor, and the taxonomic disparity of the taxon as columns.
effectSize	A vector of the effects of each taxon on the tree length. Names of each effect size are the taxa with which they are associated.

Author(s)

Andrew Hipp and Kasey Pham

See Also

label.elements, tips.expected

andrew-hipp/morton documentation built on April 7, 2024, 12:15 p.m.