R interface for contrast
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.
object of class
a matrix of continuous valued traits (in columns) with rownames containing species names. For one trait,
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).
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.
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.VarA.Correlations, estimates obtained when
VarA is not included in the model;
nonVa.logLik, log-likelihood when
VarA is included (or not) in the model;
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@example.com>
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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