PopGenReport: simplifying basic population genetic analyses in R. Issue 4 (2nd March 2014)

• Record Type: Journal Article
• Authors: Adamack, Aaron T.; Gruber, Bernd; Dray, Stephane
• Is Part Of: Methods in ecology and evolution. Volume 5:Issue 4(2014:Apr.)
• Page Start: 384
• Page End: 387
• Publication Date: 2014-03-02
• Subjects: Ecology -- Periodicals; Evolution -- Periodicals; 577
• DOI: 10.1111/2041-210X.12158
• Languages: English
• ISSNs: 2041-210X

Abstract

<abstract abstract-type="main" id="mee312158-abs-0001"> <title>Summary</title> <p> <list id="mee312158-list-0001" list-type="order"> <list-item> <p>Using scripting languages such as R to perform population genetic analyses can improve the reproducibility of research, but using R can be challenging for many researchers due to its steep learning curve.</p> </list-item> <list-item> <p>P<sc>op</sc>G<sc>en</sc>R<sc>eport</sc> is a new R package that simplifies performing population genetics analyses in R, through the use of a new report‐generating function. The function <sc>popgenreport</sc> allows users to perform up to 13 pre‐defined and 1 user‐defined analyses through the use of a single command line. Each analysis generates figures and tables that are incorporated into a <sc>pdf</sc> report and are also made available as individual files (figures are provided in multiple formats, table contents are provided as <sc>csv</sc> files).</p> </list-item> <list-item> <p>The package includes new R functions that simplify the importation of data from a spreadsheet file, examine allele distributions across populations and loci and identify private alleles, determine pairwise individual genetic distances using the methods of Smouse and Peakall (<xref ref-type="link" rid="mee312158-bib-0028">1999</xref>) and Kosman and Leonard (<xref ref-type="link" rid="mee312158-bib-0017">2005</xref>), respectively, detect the presence of null alleles, calculate allelic richness, and test for spatial autocorrelation in genotypes using the methods of Smouse and Peakall (<xref ref-type="link" rid="mee312158-bib-0028">1999</xref>).</p> </list-item> <list-item> <p>The package has a modular structure that makes the process of adding new functionality straightforward. To facilitate the addition of user‐designed functions, the package includes a fully customizable module that can be automatically included in the <sc>pdf</sc> report.</p> </list-item> <list-item> <p>To support users not experienced in R, the website (<ext-link ext-link-type="uri" xlink:href="http://www.popgenreport.org" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">www.popgenreport.org</ext-link>) has a tutorial for the package and a downloadable, portable version of the package with LaTeX pre‐configured for the Windows operating system.</p> </list-item> </list> </p> </abstract>