R interface for contrast

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Description

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.

Usage

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Rcontrast(tree, X, path=NULL, ...)

Arguments

tree

object of class "phylo".

X

a matrix of continuous valued traits (in columns) with rownames containing species names. For one trait, X can be a matrix with one column or a vector with names(X) containing species names matching tree$tip.label. For within-species contrasts analysis, the matrix should contain repeating (identical) row names for conspecifics.

path

path to the executable containing contrast. If path = NULL, the R will search several commonly used directories for the correct executable file.

...

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

Details

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).

Value

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.

Author(s)

Liam J. Revell, Scott A. Chamberlain

Maintainer: Liam J. Revell <liam.revell@umb.edu>

References

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.

See Also

pic, Rcontml, Rthreshml

Examples

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## Not run: 
data(cotton)
contrasts<-Rcontrast(tree = cotton$tree, X = cotton$data)

## End(Not run)

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