R: Variance Components with Orthonormal Contrasts

varCompPhylip {ape} | R Documentation

## Variance Components with Orthonormal Contrasts

### Description

This function calls Phylip's contrast program and returns the phylogenetic and phenotypic variance-covariance components for one or several traits. There can be several observations per species.

### Usage

    varCompPhylip(x, phy, exec = NULL)

### Arguments

`x` | a numeric vector, a matrix (or data frame), or a list.
`phy` | an object of class `"phylo"`.
`exec` | a character string giving the name of the executable contrast program (see details).

### Details

The data `x` can be in several forms: (i) a numeric vector if there is single trait and one observation per species; (ii) a matrix or data frame if there are several traits (as columns) and a single observation of each trait for each species; (iii) a list of vectors if there is a single trait and several observations per species; (iv) a list of matrices or data frames: same than (ii) but with several traits and the rows are individuals.

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`.

Phylip (version 3.68 or higher) must be accessible on your computer. If you have a Unix-like operating system, the executable name is assumed to be `"phylip contrast"` (as in Debian); otherwise it is set to `"contrast"`. If this doesn't suit your system, use the option `exec` accordingly. If the executable is not in the path, you may need to specify it, e.g., `exec = "C:/Program Files/Phylip/contrast"`.

### Value

a list with elements `varA` and `varE` with the phylogenetic (additive) and phenotypic (environmental) variance-covariance matrices. If a single trait is analyzed, these contains its variances.

### Author(s)

Emmanuel Paradis

### References

Felsenstein, J. (2004) Phylip (Phylogeny Inference Package) version 3.68. Department of Genetics, University of Washington, Seattle, USA. http://evolution.genetics.washington.edu/phylip/phylip.html.

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

### See Also

`pic`, `pic.ortho`, `compar.lynch`

### Examples

    ## Not run:
    tr <- rcoal(30)
    ### Five traits, one observation per species:
    x <- replicate(5, rTraitCont(tr, sigma = 1))
    varCompPhylip(x, tr) # varE is small
    x <- replicate(5, rnorm(30))
    varCompPhylip(x, tr) # varE is large
    ### Five traits, ten observations per species:
    x <- replicate(30, replicate(5, rnorm(10)), simplify = FALSE)
    varCompPhylip(x, tr)

    ## End(Not run)

[Package ape version 4.1 Index]