lizards {ade4}R Documentation

Phylogeny and quantitative traits of lizards

Description

This data set describes the phylogeny of 18 lizards as reported by Bauwens and D\'iaz-Uriarte (1997). It also gives life-history traits corresponding to these 18 species.

Usage

data(lizards)

Format

lizards is a list containing the 3 following objects :

traits
is a data frame with 18 species and 8 traits.
hprA
is a character string giving the phylogenetic tree (hypothesized phylogenetic relationships based on immunological distances) in Newick format.
hprB
is a character string giving the phylogenetic tree (hypothesized phylogenetic relationships based on morphological characteristics) in Newick format.

Details

Variables of lizards$traits are the following ones : mean.L (mean length (mm)), matur.L (length at maturity (mm)), max.L (maximum length (mm)), hatch.L (hatchling length (mm)), hatch.m (hatchling mass (g)), clutch.S (Clutch size), age.mat (age at maturity (number of months of activity)), clutch.F (clutch frequency).

References

Bauwens, D., and D\'iaz-Uriarte, R. (1997) Covariation of life-history traits in lacertid lizards: a comparative study. American Naturalist, 149, 91–111.

See a data description at http://pbil.univ-lyon1.fr/R/pps/pps063.pdf (in French).

Examples

data(lizards)
w <- data.frame(scalewt(log(lizards$traits)))
par(mfrow = c(1,2))
wphy <- newick2phylog(lizards$hprA)
table.phylog(w, wphy, csi = 3)
wphy <- newick2phylog(lizards$hprB)
table.phylog(w, wphy, csi = 3)
par(mfrow = c(1,1))

Worked out examples


> library(ade4)
> ### Name: lizards
> ### Title: Phylogeny and quantitative traits of lizards
> ### Aliases: lizards
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(lizards)
> w <- data.frame(scalewt(log(lizards$traits)))
> par(mfrow = c(1,2))
> wphy <- newick2phylog(lizards$hprA)
> table.phylog(w, wphy, csi = 3)
> wphy <- newick2phylog(lizards$hprB)
> table.phylog(w, wphy, csi = 3)
> par(mfrow = c(1,1))
> 
> 
> 
> 

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