edgeVars: maps a vector of traits onto a reference tree

In nclark-lab/RERconverge: Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences

maps a vector of traits onto a reference tree

Description

maps a vector of traits onto a reference tree

Usage

edgeVars(mastertree, tip.vals, metric = "diff", se.filter = -1, return.var = F)

Arguments

mastertree	the tree species the topology of the output tree and the branch lengths are used to infer ancestral states
tip.vals	the trait/phenotype/character value at the tip, names(tip.vals) should match some of the mastertree$tip.label, though a perfect match is not required
metric	The metric used to translate node values into branch values. "Diff" takes the difference and makes the result phylogenetically independent. Other possible values are "mean" (the mean of the two values) and "last" the value of the most recent species on the branch. The last two options are not phylogenetically independent and downstream computations for those are not yet implemented
se.filter	Will remove branch values that are not at least se.filter*edge.se away from 0 (where edge.se is the standard error in the estimate for the edge value). Only implemented for metric="diff". Set se.filter to a positive value to filter. By default no filtering is done.
return.var	Returns the variance instead of the mean. Useful for seeing which estimates have high confidence.

Value

A phylo tree with branch values computed from the input tip.values

nclark-lab/RERconverge documentation built on March 2, 2024, 8:51 a.m.