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.
1 |
tree |
object of class |
X |
a matrix of continuous valued traits (in columns) with rownames containing species names. For one trait, |
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 <liam.revell@umb.edu>
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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