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Part I
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<a href="Population_Strata.html">Population strata and clone correction</a>
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<a href="Locus_Stats.html">Locus-based statistics and missing data</a>
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<a href="Genotypic_EvenRichDiv.html">Genotypic evenness, richness, and diversity</a>
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<div id="population-genetics-and-genomics-in-r" class="section level1">
<h1>Population genetics and genomics in R</h1>
<p><a href="https://zenodo.org/badge/latestdoi/20031384"><img src="https://zenodo.org/badge/20031384.svg" alt="DOI" /></a></p>
<p><em>Niklaus J. Grünwald, Zhian N. Kamvar, Sydney E. Everhart, Brian J. Knaus, and Javier F. Tabima</em></p>
<p>Welcome! This primer provides a concise introduction to conducting applied analyses of population genetic data in R, with a special emphasis on non-model populations including clonal or partially clonal organisms. It provides a valuable resource for tackling the nitty-gritty analysis of populations that do not necessarily conform to textbook genetics and might or might not be in Hardy-Weinberg equilibrium. While this primer does not require extensive knowledge of programming in R, the user is expected to install R and all packages required for this primer.</p>
<p>We recently revised the primer substantially to include population genomic data, that is VCF data resulting from high-throughput sequencing of populations of either whole or reduced representation genomes.</p>
<p>Please note that this primer is still being written and will be changing as we continue writing it. Please provide us feedback on any errors you might find or suggestions for improvement. The primer is currently published <a href="http://grunwaldlab.github.io/Population_Genetics_in_R/">here</a>.</p>
<p>© 2017, Corvallis, Oregon, USA</p>
<blockquote>
<p><em>I was really impressed with what you’ve accomplished with [poppr], it is very thoughtful and addressed a number of things I never considered but which many pop gen folks that I know deal with all the time and complain about. I think it is going to be very well received by the community.</em></p>
</blockquote>
<p>– Andy Jones, Assistant Professor, Oregon State University, Corvallis, OR, 2014.</p>
</div>
<div id="citation" class="section level1">
<h1>Citation</h1>
<p>If you use this primer in your work, please cite as:</p>
<p>Niklaus Grunwald, Zhian N. Kamvar, & Sydney E. Everhart. (2016). grunwaldlab/Population_Genetics_in_R: First release [Data set]. Zenodo. <a href="http://doi.org/10.5281/zenodo.160588" class="uri">http://doi.org/10.5281/zenodo.160588</a></p>
<p>If you use BibTeX:</p>
<div class="sourceCode"><pre class="sourceCode tex"><code class="sourceCode latex">@misc{zhian_n_kamvar_2016_160588,
author = {Niklaus J. Grunwald and Zhian N. Kamvar and Sydney E. Everhart},
title = {{grunwaldlab/Population_Genetics_in_R: First release}},
month = oct,
year = 2016,
doi = {10.5281/zenodo.160588},
url = {https://doi.org/10.5281/zenodo.160588}
}</code></pre></div>
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