ecomor {ade4} | R Documentation |
This data set gives ecomorphological informations about 129 bird species.
data(ecomor)
ecomor
is a list of 7 components.
'taxo'
: the variables are factors giving nested classifications.Blondel, J., Vuilleumier, F., Marcus, L.F., and Terouanne, E. (1984). Is there ecomorphological convergence among mediterranean bird communities of Chile, California, and France. In Evolutionary Biology (eds M.K. Hecht, B. Wallace and R.J. MacIntyre), 141–213, 18. Plenum Press, New York.
See a data description at http://pbil.univ-lyon1.fr/R/pps/pps023.pdf (in French).
data(ecomor) ric <- apply(ecomor$habitat, 2, sum) s.corcircle(dudi.pca(log(ecomor$morpho), scan = FALSE)$co) forsub <- data.frame(t(apply(ecomor$forsub, 1, function (x) x/sum(x)))) pca1 <- dudi.pca(forsub, scan = FALSE, scale = FALSE) s.arrow(pca1$c1) w <- as.matrix(forsub) s.label(w, clab = 0, add.p = TRUE, cpoi = 2) diet <- data.frame(t(apply(ecomor$diet, 1, function (x) x/sum(x)))) pca2 <- dudi.pca(diet, scan = FALSE, scale = FALSE) s.arrow(pca2$c1) w <- as.matrix(diet) s.label(w, clab = 0, add.p = TRUE, cpoi = 2) ## Not run: dmorpho <- dist.quant(log(ecomor$morpho), 3) dhabitat <- dist.binary(ecomor$habitat, 1) mantel.randtest(dmorpho, dhabitat) RV.rtest(pcoscaled(dmorpho), pcoscaled(dhabitat), 999) procuste.randtest(pcoscaled(dmorpho), pcoscaled(dhabitat)) ecophy <- taxo2phylog(ecomor$taxo) table.phylog(ecomor$habitat, ecophy, clabel.n = 0.5, f = 0.6, clabel.c = 0.75, clabel.r = 0.5, csi = 0.75, cleg = 0) plot.phylog(ecophy, clabel.n = 0.75, clabel.l = 0.75, labels.l = ecomor$labels[,"latin"]) dtaxo <- ecophy$Wdist mantel.randtest(dmorpho, dtaxo) mantel.randtest(dhabitat, dtaxo) ## End(Not run)