Correlogram {ape}R Documentation

Compute a correlogram

Description

Compute a correlogram from taxonomic variables or from a phylogenetic tree with branch lengths. The first method relies on the dist.taxo function, and the second relies on the discrete.dist function. Both methods send an object of class correlogram to be plotted by the plot.correlogram method. For the correlogram.formula function, if several y are specified, an object of class correlogramList (a list of correlogram objects) is sent.

Usage

  correlogram.formula(formula, data = NULL, use="all.obs")
  correlogram.phylo(x, phy, nclass = NULL, breaks = NULL)

Arguments

x a vector containing the data to plot
formula a formula of the kind y1+..+yn ~ g1/../gn, where y are the data to plot and all g are the nested levels.
data a dataframe containing all variables in the formula. If NULL, variables are taken from the environment.
use an optional character string giving a method for computing Moran's indices in the presence of missing values. This must be one of the strings '"all.obs"', '"complete.obs"' or '"pairwise.complete.obs"'. In the first case, 'NA' values produce an error. If the seond option is used, all lines including 'NA' will be ignored. In the later case, 'NA' will be removed separately for each correlogram. If only one 'y' is given in the formula, the two last options will send the same result. Finally, unless 'use' is set to '"all.obs'", lines width 'NA' values in grouping variables will be removed.
phy an object of class "phylo" width edge lengths
breaks,nclass The class bounds or the number of classes to use. If both are NULL, compute Moran's I on the whole distance matrix.

Details

See example of the Moran.I function to see how the correlogram.formula function works. To deal with phylogenies, the correlogram.phylo function creates classes according to distances intervals. Such intervals may be specified using the breaks argument or by giving a number of classes (nclass argument).

Value

An object of class correlogram, containing:

obs all measured Moran's I
p.values the p-values of each I
labels the names of each level

or an object of class correlogramList containing a list of correlogram objects.

Warning

correlogram.phylo will return NAs if void classes are used. This may happen if breaks if not properly defined, or sometimes with the nclass=argument, depending on the tree used. Usually, you'll have to pull classes.

Author(s)

Julien Dutheil julien.dutheil@univ-montp2.fr

See Also

plot.correlogram, plot.correlogramList

Examples

  library(ape)
  data(carnivora)
  ### Using the formula interface:
  co <- correlogram.formula(
                        log10(SW) ~ Order/SuperFamily/Family/Genus,
                        data=carnivora)
  co
  plot(co)
        ### Several correlograms on the same plot:
  cos <- correlogram.formula(
                        log10(SW) + log10(FW) ~ Order/SuperFamily/Family/Genus,
                        data=carnivora)
  names(cos)
  plot(cos)

  ### Using the phylo interface:
  ### (the same analysis than in help(pic)...)

  cat("((((Homo:0.21,Pongo:0.21):0.28,",
     "Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);",
     file = "ex.tre", sep = "\n")
  tree.primates <- read.tree("ex.tre")
  X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
  Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
  ### Since this is a small tree, 2 classes is a reasonable number:
  coX <- correlogram.phylo(X, tree.primates, nclass=2)
  coY <- correlogram.phylo(Y, tree.primates, nclass=2)
  plot(coX)
  plot(coY)
  ### Nothing significant...
  ### Computing Moran's I on the whole matrix:
  coX2 <- correlogram.phylo(X, tree.primates); coX2
  ### Significant at the 5
  coY2 <- correlogram.phylo(Y, tree.primates); coY2
  ### Not significant
  unlink("ex.tre") # delete the file "ex.tre"   

[Package ape version 1.7 Index]