R interface for seqboot
This function is an R interface for seqboot in the PHYLIP package (Felsenstein 2013). seqboot can be to perform the non-parametric bootstrap following Felsenstein (1985).
either: (a) an object of class
path to the executable containing seqboot. If
optional arguments to be passed to seqboot. See details for more information.
Optional arguments include the following:
quiet suppress some output to R console (defaults to
quiet = FALSE);
type the data type (options are
method analysis method (options are
percentage a bootstrap or jacknife percentage (can be
block.size block size in number of characters for the bootstrap, jacknife, or permutation (defaults to
1, the regular bootstrap);
replicates number of replicates (defaults to
weights a vector of weights that must be
1 - characters with weight of
0 are excluded from the resampling procedure;
rate.categories vector of integers between
9 indicating the rate category for each character - this is supplied so that resampled rate categories can be output by the method;
mixture vector of
cleanup remove PHYLIP input & output files after the analysis is completed (defaults to
cleanup = TRUE).
More information about the seqboot program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/seqboot.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.
This function returns a list of objects of class
"rest.data" depending on the input data type. If
rate.categories are supplied, then each element of the list contains an object
data (containing the data), and vectors
categories, containing the resampled input vectors.
Liam J. Revell, Scott A. Chamberlain
Maintainer: Liam J. Revell <firstname.lastname@example.org>
Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
Felsenstein, J. (1989) PHYLIP–Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164-166.
Felsenstein, J. (2013) PHYLIP (Phylogeny Inference Package) version 3.695. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.