carni70 {ade4}R Documentation

Phylogeny and quantitative traits of carnivora

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)).

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: 
data(carni70)
carni70.phy <- newick2phylog(carni70$tre)
plot.phylog(carni70.phy)

size <- scalewt(log(carni70$tab))[,1]
names(size) <- row.names(carni70$tab)
symbols.phylog(carni70.phy,size)
orthogram(size, phylog = carni70.phy)

yrange <- scalewt(carni70$tab[,2])
names(yrange) <- row.names(carni70$tab)
symbols.phylog(carni70.phy,yrange)
orthogram(yrange, phylog = carni70.phy)

s.hist(cbind.data.frame(size, yrange), clabel = 0)

## End(Not run)

Worked out examples


> library(ade4)
> ### Name: carni70
> ### Title: Phylogeny and quantitative traits of carnivora
> ### Aliases: carni70
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(carni70)
> carni70.phy <- newick2phylog(carni70$tre)
> plot.phylog(carni70.phy)
> 
> size <- scalewt(log(carni70$tab))[,1]
> names(size) <- row.names(carni70$tab)
> symbols.phylog(carni70.phy,size)
> orthogram(size, phylog = carni70.phy)
class: krandtest 
Monte-Carlo tests
Call: orthogram(x = size, phylog = carni70.phy)

Test number:   4 
Permutation number:   999 
   Test        Obs   Std.Obs     Alter Pvalue
1 R2Max  0.3349344  6.686213   greater  0.001
2 SkR2k 12.9009893 -5.993492      less  0.001
3  Dmax  0.5312404  7.270751 two-sided  0.001
4   SCE  9.0528513 24.877405   greater  0.001

other elements: NULL
> 
> yrange <- scalewt(carni70$tab[,2])
> names(yrange) <- row.names(carni70$tab)
> symbols.phylog(carni70.phy,yrange)
> orthogram(yrange, phylog = carni70.phy)
class: krandtest 
Monte-Carlo tests
Call: orthogram(x = yrange, phylog = carni70.phy)

Test number:   4 
Permutation number:   999 
   Test        Obs    Std.Obs     Alter Pvalue
1 R2Max  0.0984368  0.1678610   greater  0.416
2 SkR2k 25.0758827 -3.0906725      less  0.004
3  Dmax  0.2806335  3.6609053 two-sided  0.003
4   SCE  1.9700654  6.3872838   greater  0.003

other elements: NULL
> 
> s.hist(cbind.data.frame(size, yrange), clabel = 0)
[1]  5 10 15
> 
> 
> 
> 

[Package ade4 Index]