palm: Phylogenetic and quantitative traits of amazonian palm trees

palmR 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)

ade4 documentation built on Nov. 2, 2022, 1:07 a.m.

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