abouheif.eg {ade4}R Documentation

Phylogenies and quantitative traits from Abouheif

Description

This data set gathers three phylogenies with three sets of traits as reported by Abouheif (1999).

Usage

data(abouheif.eg)

Format

abouheif.eg is a list containing the 6 following objects :

tre1
is a character string giving the first phylogenetic tree made up of 8 leaves.
vec1
is a numeric vector with 8 values.
tre2
is a character string giving the second phylogenetic tree made up of 7 leaves.
vec2
is a numeric vector with 7 values.
tre3
is a character string giving the third phylogenetic tree made up of 15 leaves.
vec3
is a numeric vector with 15 values.

Source

Data taken from the phylogenetic independence program developped by Ehab Abouheif starting from http://ww2.mcgill.ca/biology/faculty/abouheif/programs.html.

References

Abouheif, E. (1999) A method for testing the assumption of phylogenetic independence in comparative data. Evolutionary Ecology Research, 1, 895–909.

Examples

data(abouheif.eg)
par(mfrow=c(2,2))
symbols.phylog(newick2phylog(abouheif.eg$tre1), abouheif.eg$vec1,
 sub = "Body Mass (kg)", csi = 2, csub = 2)
symbols.phylog(newick2phylog(abouheif.eg$tre2), abouheif.eg$vec2,
 sub = "Body Mass (kg)", csi = 2, csub = 2)
dotchart.phylog(newick2phylog(abouheif.eg$tre1), abouheif.eg$vec1,
 sub = "Body Mass (kg)", cdot = 2, cnod = 1, possub = "topleft",
  csub = 2, ceti = 1.5)
dotchart.phylog(newick2phylog(abouheif.eg$tre2), abouheif.eg$vec2,
 sub = "Body Mass (kg)", cdot = 2, cnod = 1, possub = "topleft",
  csub = 2, ceti = 1.5)
par(mfrow = c(1,1))

w.phy=newick2phylog(abouheif.eg$tre3)
dotchart.phylog(w.phy,abouheif.eg$vec3, clabel.n = 1)

Worked out examples


> library(ade4)
> ### Name: abouheif.eg
> ### Title: Phylogenies and quantitative traits from Abouheif
> ### Aliases: abouheif.eg
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(abouheif.eg)
> par(mfrow=c(2,2))
> symbols.phylog(newick2phylog(abouheif.eg$tre1), abouheif.eg$vec1,
+  sub = "Body Mass (kg)", csi = 2, csub = 2)
> symbols.phylog(newick2phylog(abouheif.eg$tre2), abouheif.eg$vec2,
+  sub = "Body Mass (kg)", csi = 2, csub = 2)
> dotchart.phylog(newick2phylog(abouheif.eg$tre1), abouheif.eg$vec1,
+  sub = "Body Mass (kg)", cdot = 2, cnod = 1, possub = "topleft",
+   csub = 2, ceti = 1.5)
> dotchart.phylog(newick2phylog(abouheif.eg$tre2), abouheif.eg$vec2,
+  sub = "Body Mass (kg)", cdot = 2, cnod = 1, possub = "topleft",
+   csub = 2, ceti = 1.5)
> par(mfrow = c(1,1))
> 
> w.phy=newick2phylog(abouheif.eg$tre3)
> dotchart.phylog(w.phy,abouheif.eg$vec3, clabel.n = 1)
> 
> 
> 
> 

[Package ade4 Index]