ade4: palm – R documentation

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palm

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

Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release