Description Usage Arguments Details Value Author(s) References See Also Examples

This function is an R interface for contrast in the PHYLIP package (Felsenstein 2013). contrast can be used to perform the among species phylogenetically independent contrasts method of Felsenstein (1985) and the within & among species method of Felsenstein (2008).

More information about the contrast program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/contrast.html.

Obviously, use of any of the functions of this package requires that PHYLIP (Felsenstein 1989, 2013) should first be installed. Instructions for installing PHYLIP can be found on the PHYLIP webpage: http://evolution.genetics.washington.edu/phylip.html.

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`tree` |
object of class |

`X` |
a |

`path` |
path to the executable containing contrast. If |

`...` |
optional arguments to be passed to contrast. See details for more information. |

Optional arguments include the following: `quiet`

suppress some output to R console (defaults to `quiet = FALSE`

); and `cleanup`

remove PHYLIP input/output files after the analysis is completed (defaults to `cleanup = TRUE`

).

If `X`

contains one observation per species (say, the species mean), then `Rcontrast`

returns a list with the following components: `Contrasts`

, a matrix with all phylogenetically independent contrats; `Covariance_matrix`

, a matrix containing the evolutionary variances (on diagonals) and covariances; `Regressions`

, a matrix containing the pair-wise bivariate regression coefficients (columns on rows); `Correlations`

, a correlation matrix of contrasts.

If `X`

contains more than one sample per species, then `Rcontrast`

returns a list with the following elements: `VarA`

, the estimated among-species variance-covariance matrix; `VarE`

, the estimated within-species (i.e., 'environmental') variance-covariance matrix; `VarA.Regression`

, a matrix containing the pair-wise bivariate among-species regression coefficients (columns on rows); `VarA.Correlations`

, a matrix with the among-species evolutionary correlations; `VarE.Regressions`

, the pair-wise bivariate within-species regression coefficients; `VarE.Correlations`

, the within-species correlations; `nonVa.VarE`

, `nonVa.VarE.Regressions`

, and `nonVa.VarA.Correlations`

, estimates obtained when `VarA`

is not included in the model; `logLik`

and `nonVa.logLik`

, log-likelihood when `VarA`

is included (or not) in the model; `k`

and `nonVa.k`

the number of parameters estimated in each model; and `P`

the p-value of a likelihood-ratio test of `VarA`

, in which `df = k - nonVa.k`

.

Liam J. Revell, Scott A. Chamberlain

Maintainer: Liam J. Revell <[email protected]>

Felsenstein, J. (1985) Phylogenies and the comparative method. *American Naturalist*, 125, 1-15.

Felsenstein, J. (1989) PHYLIP–Phylogeny Inference Package (Version 3.2). *Cladistics*, 5, 164-166.

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

Felsenstein, J. (2013) PHYLIP (Phylogeny Inference Package) version 3.695. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.

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