R: Phylogenetically Independent Orthonormal Contrasts

pic.ortho {ape} | R Documentation

## Phylogenetically Independent Orthonormal Contrasts

### Description

This function computes the orthonormal contrasts using the method described by Felsenstein (2008). Only a single trait can be analyzed; there can be several observations per species.

### Usage

    pic.ortho(x, phy, var.contrasts = FALSE, intra = FALSE)

### Arguments

`x` | a numeric vector or a list of numeric vectors.
`phy` | an object of class `"phylo"`.
`var.contrasts` | logical, indicates whether the expected variances of the contrasts should be returned (default to `FALSE`).
`intra` | logical, whether to return the intraspecific contrasts.

### Details

The data `x` can be in two forms: a vector if there is a single observation for each species, or a list whose elements are vectors containing the individual observations for each species. These vectors may be of different lengths.

If `x` has names, its values are matched to the tip labels of `phy`, otherwise its values are taken to be in the same order than the tip labels of `phy`.

### Value

either a vector of contrasts, or a two-column matrix with the contrasts in the first column and their expected variances in the second column (if `var.contrasts = TRUE`). If the tree has node labels, these are used as labels of the returned object.

If `intra = TRUE`, the attribute `"intra"`, a list of vectors with the intraspecific contrasts or `NULL` for the species with a one observation, is attached to the returned object.

### Author(s)

Emmanuel Paradis

### References

Felsenstein, J. (2008) Comparative methods with sampling error and within-species variation: Contrasts revisited and revised. American Naturalist, 171, 713–725.

### See Also

`pic`, `varCompPhylip`

### Examples

    tr <- rcoal(30)
    ### a single observation per species:
    x <- rTraitCont(tr)
    pic.ortho(x, tr)
    pic.ortho(x, tr, TRUE)
    ### different number of observations per species:
    x <- lapply(sample(1:5, 30, TRUE), rnorm)
    pic.ortho(x, tr, intra = TRUE)

[Package ape version 5.4 Index]