palm {adephylo} | R Documentation |
This data set describes the phylogeny of 66 amazonian palm trees. It also gives 7 traits corresponding to these 66 species.
data(palm)
palm
is a list containing the 2 following objects:
Variables of palm$traits
are the following ones:
- rord: specific richness with five ordered levels
- h: height in meter (squared transform)
- dqual: diameter at breast height in centimeter with five levels sout : subterranean
, d1(0, 5 cm)
, d2(5, 15 cm)
, d3(15, 30 cm)
and d4(30, 100 cm)
- vfruit: fruit volume in mm^3 (logged transform)
- vgrain: seed volume in mm^3 (logged transform)
- aire: spatial distribution area (km^2)
- alti: maximum altitude in meter (logged transform)
This dataset replaces the former version in ade4.
This data set was obtained by Clémentine Gimaret-Carpentier
gimaret@biomserv.univ-lyon1.fr.
## load data, make a tree and a phylo4d object data(palm) tre <- read.tree(text=palm$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) }