R: Phylogenetic Correlogram

correlogram.formula {ape} | R Documentation

## Phylogenetic Correlogram

### Description

This function computes a correlogram from taxonomic levels.

### Usage

      correlogram.formula(formula, data = NULL, use = "all.obs")

### Arguments

`formula` | a formula of the type `y1+..+yn ~ g1/../gn`, where the `y`'s are the data to analyse and the `g`'s are the taxonomic levels.
`data` | a data frame containing the variables specified in the formula. If `NULL`, the variables are sought in the user's workspace.
`use` | a character string specifying how to handle missing values (i.e., `NA`). This must be one of "all.obs", "complete.obs", or "pairwise.complete.obs", or any unambiguous abbrevation of these. In the first case, the presence of missing values produces an error. In the second case, all rows with missing values will be removed before computation. In the last case, missing values are removed on a case-by-case basis.

### Details

See the vignette in R: `vignette("MoranI")`.

### Value

An object of class `correlogram` which is a data frame with three columns:

`obs` | the computed Moran's I
`p.values` | the corresponding P-values
`labels` | the names of each level

or an object of class `correlogramList` containing a list of objects of class `correlogram` if several variables are given as response in `formula`.

### Author(s)

Julien Dutheil dutheil@evolbio.mpg.de and Emmanuel Paradis

### See Also

`plot.correlogram, Moran.I`

### Examples

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

[Package ape version 5.6 Index]