ade4 (version 1.7-5)

ecomor: Ecomorphological Convergence

Description

This data set gives ecomorphological informations about 129 bird species.

Usage

data(ecomor)

Format

ecomor is a list of 7 components.

Source

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.

References

See a data description at http://pbil.univ-lyon1.fr/R/pdf/pps023.pdf (in French).

Examples

data(ecomor)
ric <- apply(ecomor$habitat, 2, sum)
s.corcircle(dudi.pca(log(ecomor$morpho), scan = FALSE)$co)

forsub <- data.frame(t(apply(ecomor$forsub, 1, function (x) x / sum(x))))
pca1 <- dudi.pca(forsub, scan = FALSE, scale = FALSE)
w1 <- as.matrix(forsub)
if(adegraphicsLoaded()) {
  g1 <- s.arrow(pca1$c1, plot = FALSE)
  g2 <- s.label(w1, plab.cex = 0, ppoi.cex = 2, plot = FALSE)
  G1 <- superpose(g1, g2, plot = TRUE)
} else {
  s.arrow(pca1$c1)
  s.label(w1, clab = 0, add.p = TRUE, cpoi = 2)
}

diet <- data.frame(t(apply(ecomor$diet, 1, function (x) x / sum(x))))
pca2 <- dudi.pca(diet, scan = FALSE, scale = FALSE)
w2 <- as.matrix(diet)
if(adegraphicsLoaded()) {
  g3 <- s.arrow(pca2$c1, plot = FALSE)
  g4 <- s.label(w2, plab.cex = 0, ppoi.cex = 2, plot = FALSE)
  G2 <- superpose(g3, g4, plot = TRUE)
} else {
  s.arrow(pca2$c1)
  s.label(w2, clab = 0, add.p = TRUE, cpoi = 2)
}


## Not run: 
# dmorpho <- dist.quant(log(ecomor$morpho), 3)
# dhabitat <- dist.binary(ecomor$habitat, 1)
# dtaxo <- dist.taxo(ecomor$taxo)
# 
# mantel.randtest(dmorpho, dhabitat)
# RV.rtest(pcoscaled(dmorpho), pcoscaled(dhabitat), 999)
# procuste.randtest(pcoscaled(dmorpho), pcoscaled(dhabitat))
# 
# ecophy <- taxo2phylog(ecomor$taxo, add.tools=TRUE)
# table.phylog(ecomor$habitat, ecophy, clabel.n = 0.5, f = 0.6,
#      clabel.c = 0.75, clabel.r = 0.5, csi = 0.75, cleg = 0)
# plot(ecophy, clabel.n = 0.75, clabel.l = 0.75,
#      labels.l = ecomor$labels[,"latin"])
# mantel.randtest(dmorpho, dtaxo)
# mantel.randtest(dhabitat, dtaxo)
# ## End(Not run)