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)