| Name : R-rSHAPE
| |
| Version : 0.3.2
| Vendor : obs://build_opensuse_org/devel:languages:R
|
| Release : lp153.12.4
| Date : 2024-06-14 11:49:55
|
| Group : Development/Libraries/Other
| Source RPM : R-rSHAPE-0.3.2-lp153.12.4.src.rpm
|
| Size : 0.36 MB
| |
| Packager : (none)
| |
| Summary : Simulated Haploid Asexual Population Evolution
|
Description :
In silico experimental evolution offers a cost-and-time effective means
to test evolutionary hypotheses. Existing evolutionary simulation
tools focus on simulations in a limited experimental framework, and
tend to report on only the results presumed of interest by the tools
designer. The R-package for Simulated Haploid Asexual Population
Evolution (\'rSHAPE\') addresses these concerns by implementing a robust
simulation framework that outputs complete population demographic and
genomic information for in silico evolving communities. Allowing more
than 60 parameters to be specified, \'rSHAPE\' simulates evolution across
discrete time-steps for an evolving community of haploid asexual
populations with binary state genomes. These settings are for the
current state of \'rSHAPE\' and future steps will be to increase the
breadth of evolutionary conditions permitted. At present, most effort
was placed into permitting varied growth models to be simulated (such
as constant size, exponential growth, and logistic growth) as well as
various fitness landscape models to reflect the evolutionary landscape
(e.g.: Additive, House of Cards - Stuart Kauffman and Simon Levin
(1987) < doi:10.1016/S0022-5193(87)80029-2>, NK - Stuart A. Kauffman and
Edward D. Weinberger (1989) < doi:10.1016/S0022-5193(89)80019-0>, Rough
Mount Fuji - Neidhart, Johannes and Szendro, Ivan G and Krug, Joachim
(2014) < doi:10.1534/genetics.114.167668>). This package includes
numerous functions though users will only need defineSHAPE(),
runSHAPE(), shapeExperiment() and summariseExperiment(). All other
functions are called by these main functions and are likely only to be
on interest for someone wishing to develop \'rSHAPE\'. Simulation
results will be stored in files which are exported to the directory
referenced by the shape_workDir option (defaults to tempdir() but do
change this by passing a folderpath argument for workDir when calling
defineSHAPE() if you plan to make use of your results beyond your
current session). \'rSHAPE\' will generate numerous replicate
simulations for your defined range of experimental parameters. The
experiment will be built under the experimental working directory
(i.e.: referenced by the option shape_workDir set using defineSHAPE() )
where individual replicate simulation results will be stored as well as
processed results which I have made in an effort to facilitate analyses
by automating collection and processing of the potentially thousands of
files which will be created. On that note, \'rSHAPE\' implements a robust
and flexible framework with highly detailed output at the cost of
computational efficiency and potentially requiring significant disk
space (generally gigabytes but up to tera-bytes for very large
simulation efforts). So, while \'rSHAPE\' offers a single framework in
which we can simulate evolution and directly compare the impacts of a
wide range of parameters, it is not as quick to run as other in silico
simulation tools which focus on a single scenario with limited output.
There you have it, \'rSHAPE\' offers you a less restrictive in silico
evolutionary playground than other tools and I hope you enjoy testing
your hypotheses.
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RPM found in directory: /packages/linux-pbone/ftp5.gwdg.de/pub/opensuse/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Leap_15.3/x86_64 |
