Description Usage Arguments Details Value Author(s) References
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).
1 |
X |
either: (a) an object of class |
path |
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 "sequence"
, "morph"
, "rest"
, or "gene.freq"
); method
analysis method (options are "bootstrap"
, "jacknife"
, and "permute"
); percentage
a bootstrap or jacknife percentage (can be >100
); 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 100
); weights
a vector of weights that must be 0
or 1
- characters with weight of 0
are excluded from the resampling procedure; rate.categories
vector of integers between 1
and 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 "W"
and "C"
(see Rmix
); and 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 "DNAbin"
, "proseq"
, "phylip.data"
, or "rest.data"
depending on the input data type. If ancestors
, mixture
, or rate.categories
are supplied, then each element of the list contains an object data
(containing the data), and vectors ancestors
, mixture
, and/or categories
, containing the resampled input vectors.
Liam J. Revell, Scott A. Chamberlain
Maintainer: Liam J. Revell <liam.revell@umb.edu>
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.
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