scrm: Simulating the Evolution of Biological Sequences

A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution. Different to other coalescent based simulations, it has an optional approximation parameter that allows for high accuracy while maintaining a linear run time cost for long sequences. It is optimized for simulating massive data sets as produced by Next- Generation Sequencing technologies for up to several thousand sequences.

Install the latest version of this package by entering the following in R:
install.packages("scrm")
AuthorPaul Staab [aut, cre, cph], Zhu Sha [aut, cph], Dirk Metzler [aut, cph, ths], Gerton Lunter [aut, cph, ths]
Date of publication2016-12-11 16:37:23
MaintainerPaul Staab <develop@paulstaab.de>
LicenseGPL (>= 3)
Version1.7.2-0
https://github.com/scrm/scrm-r

View on CRAN

Files

inst
inst/CITATION
inst/doc
inst/doc/scrm-TreesForApe.html
inst/doc/scrm-TreesForApe.Rmd
inst/doc/scrm-Arguments.html
inst/doc/scrm-Arguments.Rmd
inst/doc/scrm-TreesForApe.R
tests
tests/testthat.R
tests/testthat
tests/testthat/test-r_random-generator.R tests/testthat/test-scrm.R tests/testthat/test-summary-statistics.R
src
src/Makevars
src/summary_statistics.h
src/scrmr.cpp
src/scrm
src/scrm/event.h
src/scrm/random
src/scrm/random/fastfunc.h
src/scrm/random/random_generator.h
src/scrm/random/random_generator.cc
src/scrm/random/fastfunc.cc
src/scrm/tree_point.h
src/scrm/node.h
src/scrm/forest.h
src/scrm/param.cc
src/scrm/contemporaries_container.h
src/scrm/macros.h
src/scrm/model.h
src/scrm/model.cc
src/scrm/tree_point.cc
src/scrm/time_interval.cc
src/scrm/node_container.cc
src/scrm/node.cc
src/scrm/summary_statistics
src/scrm/summary_statistics/seg_sites.h
src/scrm/summary_statistics/seg_sites.cc
src/scrm/summary_statistics/oriented_forest.h
src/scrm/summary_statistics/tmrca.h
src/scrm/summary_statistics/tmrca.cc
src/scrm/summary_statistics/newick_tree.cc
src/scrm/summary_statistics/oriented_forest.cc
src/scrm/summary_statistics/summary_statistic.h
src/scrm/summary_statistics/frequency_spectrum.cc
src/scrm/summary_statistics/newick_tree.h
src/scrm/summary_statistics/frequency_spectrum.h
src/scrm/time_interval.h
src/scrm/forest.cc
src/scrm/node_container.h
src/scrm/param.h
src/r_random_generator.h
src/test_exports.cpp
src/Makevars.win
src/RcppExports.cpp
NAMESPACE
NEWS
R
R/scrm.R R/RcppExports.R
vignettes
vignettes/scrm-TreesForApe.Rmd
vignettes/scrm-Arguments.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/scrm.Rd man/scrm-package.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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