carniherbi49 {ade4}R Documentation

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

Description

This data set describes the taxonomic and phylogenetic relationships of 49 carnivora and herbivora species as reported by Garland and Janis (1993) and Garland et al. (1993). It also gives seven traits corresponding to these 49 species.

Usage

data(carniherbi49)

Format

carniherbi49 is a list containing the 5 following objects :

taxo
is a data frame with 49 species and 2 columns : 'fam', a factor family with 14 levels and 'ord', a factor order with 3 levels.
tre1
is a character string giving the phylogenetic tree in Newick format as reported by Garland et al. (1993).
tre2
is a character string giving the phylogenetic tree in Newick format as reported by Garland and Janis (1993).
tab1
is a data frame with 49 species and 2 traits: 'bodymass' (body mass (kg)) and 'homerange' (home range (km)).
tab2
is a data frame with 49 species and 5 traits: 'clade' (dietary with two levels Carnivore and Herbivore), 'runningspeed' (maximal sprint running speed (km/h)), 'bodymass' (body mass (kg)), 'hindlength' (hind limb length (cm)) and 'mtfratio' (metatarsal/femur ratio).

Source

Garland, T., Dickerman, A. W., Janis, C. M. and Jones, J. A. (1993) Phylogenetic analysis of covariance by computer simulation. Systematics Biology, 42, 265–292.

Garland, T. J. and Janis, C.M. (1993) Does metatarsal-femur ratio predict maximal running speed in cursorial mammals? Journal of Zoology, 229, 133–151.

Examples

## Not run: 
data(carniherbi49)
par(mfrow=c(1,3))
plot(newick2phylog(carniherbi49$tre1), clabel.leaves = 0,
 f.phylog = 2, sub ="article 1")
plot(newick2phylog(carniherbi49$tre2), clabel.leaves = 0,
 f.phylog = 2, sub = "article 2")
taxo <- as.taxo(carniherbi49$taxo)
plot(taxo2phylog(taxo), clabel.nodes = 1.2, clabel.leaves = 1.2)
par(mfrow = c(1,1))

## End(Not run)

Worked out examples


> library(ade4)
> ### Name: carniherbi49
> ### Title: Taxonomy, phylogenies and quantitative traits of carnivora and
> ###   herbivora
> ### Aliases: carniherbi49
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(carniherbi49)
> par(mfrow=c(1,3))
> plot(newick2phylog(carniherbi49$tre1), clabel.leaves = 0,
+  f.phylog = 2, sub ="article 1")
> plot(newick2phylog(carniherbi49$tre2), clabel.leaves = 0,
+  f.phylog = 2, sub = "article 2")
> taxo <- as.taxo(carniherbi49$taxo)
> plot(taxo2phylog(taxo), clabel.nodes = 1.2, clabel.leaves = 1.2)
> par(mfrow = c(1,1))
> 
> 
> 
> 

[Package ade4 Index]