palm: Phylogenetic and quantitative traits of amazonian palm trees

In adephylo: adephylo: exploratory analyses for the phylogenetic comparative method.

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)

Note

This dataset replaces the former version in ade4.

Source

This data set was obtained by Clémentine Gimaret-Carpentier
[e-mail].

Examples

## Not run: 
if(require(ape) && require(phylobase)){

## load data, make a tree and a phylo4d object
data(palm)
tre <- read.tree(text=palm$tre)
rord <- as.integer(palm$traits$rord) # just use this for plotting purpose
traits <- data.frame(rord, palm$traits[,-1])
x <- phylo4d(tre, traits)

## plot data
par(mar=rep(.1,4))
table.phylo4d(x, cex.lab=.6)

## test phylogenetic autocorrelation
if(require(ade4)){
prox <- proxTips(x, method="sumDD")
phylAutoTests <- gearymoran(prox, traits[,-3], nrep=499)
plot(phylAutoTests)
}
}

## End(Not run)

Example output

Loading required package: ade4
Registered S3 method overwritten by 'spdep':
  method   from
  plot.mst ape 
Loading required package: ape
Loading required package: phylobase

Attaching package: ‘phylobase’

The following object is masked from ‘package:ape’:

    edges

adephylo documentation built on May 2, 2019, 4:54 p.m.