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

In PuttickMacroevolution/motmot: Models of Trait Macroevolution on Trees

Description

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

Usage

sortTraitData(
  phy,
  y,
  data.name = NULL,
  log.trait = TRUE,
  pass.ultrametric = FALSE
)

Arguments

phy	An object of class phylo or multiPhylo (see ape)
y	A matrix of trait values with taxon names as rownames. Missing values should be NA
data.name	If null the first column of y is assummed as the trait, otherwise if y is a matrix with more than one column either the name of the column or the number of the column must be supplied by data.name
log.trait	Logical. If TRUE, data are log-transformed
pass.ultrametric	Although trees that are believed to be ultrametric to pass the function is.ultrametric in ape

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]]

PuttickMacroevolution/motmot documentation built on June 5, 2020, 7 p.m.