R: Phylogenetic and quantitative traits of amazonian palm trees

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.

### Examples

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

    if (requireNamespace("adephylo", quietly = TRUE) & requireNamespace("ape", quietly = TRUE)) {
      tre <- ape::read.tree(text = palm$tre)
      adephylo::orthogram(palm$traits[, 4], tre)
    }
    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)

[Package ade4 version 1.7-17 Index]