scrm is a coalescence simulator for the evolution of biological sequences. It is available as a command line program at scrm.github.io.
This R package contains a copy scrm, packaged for convenient usage in R.
It is recommended to use the current CRAN version. It can be installed from within R using
install.packages('scrm')
Use the function scrm::scrm()
to call scrm:
library('scrm')
sum_stats <- scrm('5 1 -r 10 100 -t 5 -oSFS')
scrm::scrm()
is explained in its R help page help('scrm')
.vignette('scrm-Arguments')
.Please cite the following article when using scrm in a publication:
Paul R. Staab, Sha Zhu, Dirk Metzler and Gerton Lunter. scrm: efficiently simulating long sequences using the approximated coalescent with recombination. Bioinformatics (2015) 31 (10): 1680-1682. doi:10.1093/bioinformatics/btu861.
Please report any problems via the issue tracker
or via email to develop (at) paulstaab (dot) de
.
Please include the version you are using and the exact command that causes the problem including seed (if applicable) in the report. Also, feel free to suggest features there.
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