carni70: Phylogeny and quantitative traits of carnivora

In adephylo: adephylo: exploratory analyses for the phylogenetic comparative method.

Description

This data set describes the phylogeny of 70 carnivora as reported by Diniz-Filho and Torres (2002). It also gives the geographic range size and body size corresponding to these 70 species.

Usage

data(carni70)

Format

carni70 is a list containing the 2 following objects:

tre

is a character string giving the phylogenetic tree in Newick format. Branch lengths are expressed as divergence times (millions of years)

tab

is a data frame with 70 species and two traits: size (body size (kg)) ; range (geographic range size (km)).

Note

This dataset replaces the former version in ade4.

Source

Diniz-Filho, J. A. F., and N. M. Tôrres. (2002) Phylogenetic comparative methods and the geographic range size-body size relationship in new world terrestrial carnivora. Evolutionary Ecology, 16, 351–367.

Examples

## Not run: 
if(require(ape) && require(phylobase)){

data(carni70)
rownames(carni70$tab) <- gsub("_", ".", rownames(carni70$tab))
tre <- read.tree(text=carni70$tre)
x <- phylo4d(tre, carni70$tab)
table.phylo4d(x)

par(mar=rep(.1,4))
table.phylo4d(x,cex.lab=.5, show.n=FALSE, ratio=.5)


## transform size in log and test for a phylogenetic signal
size <- log(carni70$tab)[,1]
names(size) <- row.names(carni70$tab)
orthogram(size, tre)

## transform range and test for a phylogenetic signal
yrange <- scale(carni70$tab)[,2]
names(yrange) <- row.names(carni70$tab)
orthogram(yrange, tre)
}

## End(Not run)

Example output

Loading required package: ade4
Loading required package: ape
Loading required package: phylobase

Attaching package: 'phylobase'

The following object is masked from 'package:ape':

    edges

class: krandtest lightkrandtest 
Monte-Carlo tests
Call: orthogram(x = yrange, tre = tre)

Number of tests:   4 

Adjustment method for multiple comparisons:   none 
Permutation number:   999 
   Test         Obs    Std.Obs   Alter Pvalue
1 R2Max  0.09843681  0.1955289 greater  0.409
2 SkR2k 24.18184019 -3.4623979 greater  1.000
3  Dmax  0.30607237  4.2289170 greater  0.001
4   SCE  2.31664284  8.6086208 greater  0.001

adephylo documentation built on May 2, 2019, 4:54 p.m.