palm {ade4}R Documentation

Phylogenetic and quantitative traits of amazonian palm trees

Description

This data set describes the phylogeny of 66 amazonian palm trees. It also gives 7 traits corresponding to these 66 species.

Usage

data(palm)

Format

palm is a list containing the 2 following objects:

tre
is a character string giving the phylogenetic tree in Newick format.
traits
is a data frame with 66 species (rows) and 7 traits (columns).

Details

Variables of palm$traits are the following ones:
rord: specific richness with five ordered levels
h: height in meter (squared transform)
dqual: diameter at breast height in centimeter with five levels sout : subterranean, d1(0, 5 cm), d2(5, 15 cm), d3(15, 30 cm) and d4(30, 100 cm)
vfruit: fruit volume in mm^3 (logged transform)
vgrain: seed volume in mm^3 (logged transform)
aire: spatial distribution area (km^2)
alti: maximum altitude in meter (logged transform)

Source

This data set was obtained by Clémentine Gimaret-Carpentier
gimaret@biomserv.univ-lyon1.fr.

Examples

## Not run: 
data(palm)
palm.phy <- newick2phylog(palm$tre)
radial.phylog(palm.phy,clabel.l=1.25)

orthogram(palm$traits[,4],palm.phy$Bscores)
dotchart.phylog(palm.phy,palm$traits[,4], clabel.l = 1,
 labels.n = palm.phy$Blabels, clabel.n = 0.75)
w <- cbind.data.frame(palm.phy$Bscores[,c(3,4,6,13,21)],
 scalewt((palm$traits[,4])))
names(w)[6] <- names(palm$traits[4])
table.phylog(w, palm.phy, clabel.r = 0.75, f = 0.5)

gearymoran(palm.phy$Amat, palm$traits[,-c(1,3)])

## End(Not run)

Worked out examples


> library(ade4)
> ### Name: palm
> ### Title: Phylogenetic and quantitative traits of amazonian palm trees
> ### Aliases: palm
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(palm)
> palm.phy <- newick2phylog(palm$tre)
> radial.phylog(palm.phy,clabel.l=1.25)
> 
> orthogram(palm$traits[,4],palm.phy$Bscores)
class: krandtest 
Monte-Carlo tests
Call: orthogram(x = palm$traits[, 4], orthobas = palm.phy$Bscores)

Test number:   4 
Permutation number:   999 
   Test        Obs   Std.Obs     Alter Pvalue
1 R2Max  0.1645069  2.735153   greater  0.016
2 SkR2k 18.6232494 -4.398535      less  0.001
3  Dmax  0.4063715  5.390459 two-sided  0.001
4   SCE  4.0384632 12.490428   greater  0.001

other elements: NULL
> dotchart.phylog(palm.phy,palm$traits[,4], clabel.l = 1,
+  labels.n = palm.phy$Blabels, clabel.n = 0.75)
> w <- cbind.data.frame(palm.phy$Bscores[,c(3,4,6,13,21)],
+  scalewt((palm$traits[,4])))
> names(w)[6] <- names(palm$traits[4])
> table.phylog(w, palm.phy, clabel.r = 0.75, f = 0.5)
> 
> gearymoran(palm.phy$Amat, palm$traits[,-c(1,3)])
class: krandtest 
Monte-Carlo tests
Call: as.krandtest(sim = matrix(res$result, ncol = nvar, byr = TRUE), 
    obs = res$obs, alter = alter, names = test.names)

Test number:   5 
Permutation number:   999 
    Test        Obs   Std.Obs   Alter Pvalue
1      h 0.02526036 0.3847817 greater  0.330
2 vfruit 0.39074523 5.3279187 greater  0.001
3 vgrain 0.29691940 4.0977853 greater  0.001
4   aire 0.23696157 3.2072108 greater  0.002
5   alti 0.10851706 1.4238875 greater  0.078

other elements: NULL
> 
> 
> 
> 

[Package ade4 Index]