ade4: carni70 – R documentation

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carni70

Phylogeny and quantitative traits of carnivora

Description

This data set describes the phylogeny of 70 carnivora as reported by Diniz-Filho and Torres (2002). It also gives the geographic range size and body size corresponding to these 70 species.

Usage

data(carni70)

Format

carni70 is a list containing the 2 following objects:

tre: is a character string giving the phylogenetic tree in Newick format. Branch lengths are expressed as divergence times (millions of years)
tab: is a data frame with 70 species and two traits: size (body size (kg)) ; range (geographic range size (km)).

Source

Diniz-Filho, J. A. F., and N. M. Tôrres. (2002) Phylogenetic comparative methods and the geographic range size-body size relationship in new world terrestrial carnivora. Evolutionary Ecology, 16, 351–367.

Examples

## Not run: 
if (requireNamespace("adephylo", quietly = TRUE) & requireNamespace("ape", quietly = TRUE)) {
  data(carni70)
  carni70.phy <- newick2phylog(carni70$tre)
  plot(carni70.phy)
  
  size <- scalewt(log(carni70$tab))[,1]
  names(size) <- row.names(carni70$tab)
  symbols.phylog(carni70.phy,size)
  
  tre <- ape::read.tree(text = carni70$tre)
  adephylo::orthogram(size, tre = tre)
  
  yrange <- scalewt(carni70$tab[,2])
  names(yrange) <- row.names(carni70$tab)
  symbols.phylog(carni70.phy,yrange)
  adephylo::orthogram(as.vector(yrange), tre = tre)
  
  if(adegraphicsLoaded()) {
    g1 <- s.label(cbind.data.frame(size, yrange), plabel.cex = 0)
    g2 <- addhist(g1)
  } else {
    s.hist(cbind.data.frame(size, yrange), clabel = 0)
  }
}
## End(Not run)

ade4

Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release