Description Usage Format Note Source Examples
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.
1 |
carni70
is a list containing the 2 following objects:
is a character string giving the phylogenetic tree in Newick format. Branch lengths are expressed as divergence times (millions of years)
is a data frame with 70 species and two traits: size (body size (kg)) ; range (geographic range size (km)).
This dataset replaces the former version in ade4.
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | ## 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)
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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
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