get.phylo.stats {mmodely}

Get tree statistics for a trait

Description

This function uses Pagel's lambda, Blombergs k, and Ancestral Character Estimation [ACE] to calculate statistics on a tree given a specified trait.

Usage

get.phylo.stats(phylo, data, trait.clmn, gs.clmn='gn_sp', 
                ace.method='REML',ace.scaled=TRUE, ace.kappa=1)

Arguments

phylo

PARAMDESCRIPTION

data

PARAMDESCRIPTION

trait.clmn

PARAMDESCRIPTION

gs.clmn

PARAMDESCRIPTION

ace.method

PARAMDESCRIPTION

ace.scaled

PARAMDESCRIPTION

ace.kappa

PARAMDESCRIPTION

Value

statistics on a particular trait within a tree (Pagel's lambda, Blomberg's k, and the most ancestral ACE estimate)

Examples

data.path <- system.file("extdata","primate-example.data.csv", package="mmodely")
data <- read.csv(data.path, row.names=1)

data$gn_sp <- rownames(data)

tree.path <- system.file("extdata","primate-springer.2012.tre", package="mmodely")
phyl <- ape::read.tree(tree.path)[[5]]

get.phylo.stats(phylo=phyl, data=data, trait.clmn='OC', 
        gs.clmn='gn_sp', ace.method='REML',ace.scaled=TRUE, ace.kappa=1)