sortTraitData: Sort data and remove missing entries for tree and trait data

In motmot.2.0: Models of Trait Macroevolution on Trees

Description

Plots a phylogeny with lines representing the value of a continuous trait

Usage

sortTraitData(phy, y, log.trait = TRUE)

Arguments

phy	An object of class "phylo" or "multiPhylo" (see ape package).
y	A matrix of trait values with taxon names as rownames. Missing values should be NA
log.trait	Logical. If TRUE, data are log-transformed

Value

phy Tree with missing data pruned

trait Rearranged data with missing species removed

Author(s)

Mark Puttick

Examples

data(anolis.tree)
data(anolis.data)
attach(anolis.data)
male.length <- matrix(Male_SVL, dimnames=list(rownames(anolis.data)))
any(is.na(male.length[,1]))
data.sorted <- sortTraitData(anolis.tree, male.length)
phy <- data.sorted[[1]]
male.length <- data.sorted[[2]]

motmot.2.0 documentation built on May 1, 2019, 9:22 p.m.