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P op G en R eport : simplifying basic population genetic analyses in R
Author(s) -
Adamack Aaron T.,
Gruber Bernd
Publication year - 2014
Publication title -
methods in ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.425
H-Index - 105
ISSN - 2041-210X
DOI - 10.1111/2041-210x.12158
Subject(s) - computer science , population , pairwise comparison , scripting language , modular design , function (biology) , r package , operating system , programming language , biology , genetics , artificial intelligence , demography , sociology
Summary 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 op G en R eport is a new R package that simplifies performing population genetics analyses in R, through the use of a new report‐generating function. The function popgenreport 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 pdf report and are also made available as individual files (figures are provided in multiple formats, table contents are provided as csv files). 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 ([Smouse, P.E., 1999]) and Kosman and Leonard ([Kosman, E., 2005]), respectively, detect the presence of null alleles, calculate allelic richness, and test for spatial autocorrelation in genotypes using the methods of Smouse and Peakall ([Smouse, P.E., 1999]). 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 pdf report. To support users not experienced in R, the website ( www.popgenreport.org ) has a tutorial for the package and a downloadable, portable version of the package with LaTeX pre‐configured for the Windows operating system.