skelesim: an extensible, general framework for population genetic simulation in R.

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dc.citation.issue1
dc.citation.volume17
dc.contributor.authorParobek CM
dc.contributor.authorArcher FI
dc.contributor.authorDePrenger-Levin ME
dc.contributor.authorHoban SM
dc.contributor.authorLiggins L
dc.contributor.authorStrand AE
dc.date.available2017-01
dc.date.available2016-09-26
dc.date.issued2017-01
dc.descriptionCAUL read and publish agreement
dc.description.abstractSimulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods. Due to growing computational power and a diversity of software with different capabilities, simulations are becoming increasingly powerful and useful. However, the widespread use of simulations by geneticists and ecologists is hindered by difficulties in understanding these softwares' complex capabilities, composing code and input files, a daunting bioinformatics barrier and a steep conceptual learning curve. skelesim (an R package) guides users in choosing appropriate simulations, setting parameters, calculating genetic summary statistics and organizing data output, in a reproducible pipeline within the R environment. skelesim is designed to be an extensible framework that can 'wrap' around any simulation software (inside or outside the R environment) and be extended to calculate and graph any genetic summary statistics. Currently, skelesim implements coalescent and forward-time models available in the fastsimcoal2 and rmetasim simulation engines to produce null distributions for multiple population genetic statistics and marker types, under a variety of demographic conditions. skelesim is intended to make simulations easier while still allowing full model complexity to ensure that simulations play a fundamental role in molecular ecology investigations. skelesim can also serve as a teaching tool: demonstrating the outcomes of stochastic population genetic processes; teaching general concepts of simulations; and providing an introduction to the R environment with a user-friendly graphical user interface (using shiny).
dc.description.publication-statusPublished
dc.format.extent101 - 109
dc.identifierhttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000390413500013&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=c5bb3b2499afac691c2e3c1a83ef6fef
dc.identifier.citationMOLECULAR ECOLOGY RESOURCES, 2017, 17 (1), pp. 101 - 109
dc.identifier.doi10.1111/1755-0998.12607
dc.identifier.eissn1755-0998
dc.identifier.elements-id282433
dc.identifier.harvestedMassey_Dark
dc.identifier.issn1755-098X
dc.relation.isPartOfMOLECULAR ECOLOGY RESOURCES
dc.rights(c) The Author/s
dc.subjectconservation genetics
dc.subjectforward-time
dc.subjectnull model
dc.subjectopen-source
dc.subjectpopulation genetics
dc.subjectpower analysis
dc.subjectsimulations
dc.subjectthe coalescent
dc.subject.anzsrc06 Biological Sciences
dc.titleskelesim: an extensible, general framework for population genetic simulation in R.
dc.typeJournal article
pubs.notesNot known
pubs.organisational-group/Massey University
pubs.organisational-group/Massey University/College of Sciences
pubs.organisational-group/Massey University/College of Sciences/School of Natural Sciences
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