ecomor {ade4} | R Documentation

## Ecomorphological Convergence

### Description

This data set gives ecomorphological informations about 129 bird species.

### Usage

    data(ecomor)

### Format

`ecomor` is a list of 7 components.

forsub
  is a data frame with 129 species, 6 variables (the feeding place classes): foliage, ground , twig , bush, trunk and aerial feeders. These dummy variables indicate the use (1) or no use (0) of a given feeding place by a species.
diet
  is a data frame with 129 species and 8 variables (diet types): Gr (granivorous: seeds), Fr (frugivorous: berries, acorns, drupes), Ne (frugivorous: nectar), Fo (folivorous: leaves), In (invertebrate feeder: insects, spiders, myriapods, isopods, snails, worms), Ca (carnivorous: flesh of small vertebrates), Li (limnivorous: invertebrates in fresh water), and Ch (carrion feeder). These dummy variables indicate the use (1) or no use (0) of a given diet type by a species.
habitat
  is a data frame with 129 species, 16 dummy variables (the habitats). These variables indicate the species presence (1) or the species absence (0) in a given habitat.
morpho
  is a data frame with 129 species abd 8 morphological variables: wingl (Wing length, mm), taill (Tail length, mm), culml (Culmen length, mm), bilh (Bill height, mm), bilw (Bill width, mm), tarsl (Tarsus length, mm), midtl (Middle toe length, mm) and weig (Weight, g).
taxo
  is a data frame with 129 species and 3 factors: Genus, Family and Order. It is a data frame of class `'taxo'`: the variables are factors giving nested classifications.
labels
  is a data frame with vectors of the names of species (complete and in abbreviated form.
categ
  is a data frame with 129 species, 2 factors : 'forsub' summarizing the feeding place and 'diet' the diet type.

### 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.

### 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$forsub, 1,
         function (x) x/sum(x))))
    pca1 <- dudi.pca(forsub, scan = FALSE, scale = FALSE)
    s.arrow(pca1$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)

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