Allan Strand
2004-Jan-06 02:32 UTC
[R] rmetasim: a population genetic simulation environment
Hi all, My student, James Niehaus, and I have been working on an individual-based population genetic simulation package in R. Currently, the package is still rough, but useful enough that it may be of interest to population/ecological geneticists. The best description of the basic model (implemented in C++) can be found in: Allan E. Strand. Metasim 1.0: an individual-based environment for simulating population genetics of complex population dynamics. Mol. Ecol. Notes, 2:373-376, 2002. My idea was to produce an extremely flexible engine that could simulate genotypic data that result from most any demographic scenario. These data can be used as null distributions to compare to observed datasets. Results of simulations can be exported to a variety of canned population genetic analysis programs, and rmetasim implements a few rudimentary analyses (e.g Weir&Cockerhams theta, mismatch distributions, and assignment tests) as well. Several example sessions are included in pdf files found in the rmetasim/doc subdirectory. rmetasim is mostly a wrapper for the C++ engine described in the paper cited above. Because it simulates individuals directly, rmetasim is not terribly fast, even though the majority of the processing occurs in compiled code. Nevertheless, I have found it useful, and running multiple simulations from the same starting conditions seems to work in a cluster environment using Rmpi. We are actively working on this package, and would appreciate feedback so that we can improve its quality. The source distribution can be found at: http://linum.cofc.edu:/filedrop/rmetasim_0.0.3.tar.gz It should compile on linux boxes (that have R installed), though doing so takes a while. Binary distribution for Mac OS X: http://linum.cofc.edu:/filedrop/rmetasim_0.0.3_R_powerpc-apple-darwin6.8.tar.gz Binary distribution for Windows: http://linum.cofc.edu:/filedrop/rmetasim_0.0.3.zip cheers, a. -- Allan Strand, Biology http://linum.cofc.edu College of Charleston Ph. (843) 953-9189 Charleston, SC 29424 Fax (843) 953-9199
Thanks in advance Bernardo Rangel Tura, MD, MSc National Institute of Cardiology Laranjeiras Rio de Janeiro Brazil
Maybe you intended to supply a little more information in the body of your message, but without that, the best suggestion I can give with a similar degree of effort on my part is: ?nls At Thursday 08:04 PM 1/8/2004 -0200, Bernardo Rangel Tura wrote:>Thanks in advance > >Bernardo Rangel Tura, MD, MSc >National Institute of Cardiology Laranjeiras >Rio de Janeiro Brazil >______________________________________________ >R-help at stat.math.ethz.ch mailing list >https://www.stat.math.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide! http://www.R-project.org/posting-guide.htmlTony Plate tplate at acm.org