Built site for gh-pages

.nojekyll

@@ -1 +1 @@
-c1bfc7bd
+270c34f1

about.html

@@ -8566,7 +8566,7 @@ <h2 class="anchored" data-anchor-id="nbis">NBIS</h2>
     <div class="nav-footer-right">Published with <a href="https://quarto.org/">Quarto</a> v<!--?quarto.version?--></div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"loop":true,"selector":".lightbox","descPosition":"bottom","closeEffect":"zoom","openEffect":"zoom"});</script>
+<script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","descPosition":"bottom","loop":true,"openEffect":"zoom","selector":".lightbox"});</script>
 
 
 

exercises/data.html

@@ -8599,7 +8599,7 @@ <h1 class="title">Data</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">20-Aug-2023</p>
+      <p class="date">22-Aug-2023</p>
     </div>
   </div>
 
@@ -8993,7 +8993,7 @@ <h3 class="anchored" data-anchor-id="sec-data-simulated-ooa-outgroups">Out of Af
     <div class="nav-footer-right">Published with <a href="https://quarto.org/">Quarto</a> v<!--?quarto.version?--></div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"openEffect":"zoom","closeEffect":"zoom","loop":true,"selector":".lightbox","descPosition":"bottom"});</script>
+<script>var lightboxQuarto = GLightbox({"openEffect":"zoom","descPosition":"bottom","selector":".lightbox","closeEffect":"zoom","loop":true});</script>
 
 
 

exercises/demopy/index.html

@@ -4859,7 +4859,7 @@ <h1 class="title">Exercise example using pgip jupyter kernel (WIP)</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">20-Aug-2023</p>
+      <p class="date">22-Aug-2023</p>
     </div>
   </div>
 
@@ -4888,7 +4888,7 @@ <h2 class="anchored" data-anchor-id="python-code">Python code</h2>
 <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> os</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>os.listdir()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div id="test" class="cell-output cell-output-display" data-execution_count="1">
-<pre><code>[&#39;.jupyter_cache&#39;, &#39;index.qmd&#39;, &#39;index.ipynb&#39;]</code></pre>
+<pre><code>[&#39;index.qmd&#39;, &#39;index.ipynb&#39;, &#39;.jupyter_cache&#39;]</code></pre>
 </div>
 </div>
 <div class="cell" data-execution_count="2">

exercises/ld_and_phasing/index.html

@@ -4886,7 +4886,7 @@ <h1 class="title">Principal component analysis</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">20-Aug-2023</p>
+      <p class="date">22-Aug-2023</p>
     </div>
   </div>
 

exercises/ld_pruning/index.html

@@ -4886,7 +4886,7 @@ <h1 class="title">Linkage disequilibrium pruning</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">20-Aug-2023</p>
+      <p class="date">22-Aug-2023</p>
     </div>
   </div>
 

index.html

@@ -8539,7 +8539,7 @@ <h5 class="anchored" data-anchor-id="november-2023-uppsala-sweden">6-10 November
     <div class="nav-footer-right">Published with <a href="https://quarto.org/">Quarto</a> v<!--?quarto.version?--></div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","loop":true,"descPosition":"bottom","openEffect":"zoom","selector":".lightbox"});</script>
+<script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","loop":true,"selector":".lightbox","openEffect":"zoom","descPosition":"bottom"});</script>
 
 
 

lectures/genetic_diversity/index.html

@@ -4958,7 +4958,7 @@ <h1 class="title">Genetic diversity</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">20-Aug-2023</p>
+      <p class="date">22-Aug-2023</p>
     </div>
   </div>
 

references.html

@@ -4869,6 +4869,9 @@ <h1>References</h1>
 <div id="ref-charlesworth_EffectsOfSelection_2021" class="csl-entry" role="listitem">
 Charlesworth, B., &amp; Jensen, J. D. (2021). Effects of selection at linked sites on patterns of genetic variability. <em>Annual Review of Ecology, Evolution, and Systematics</em>, <em>52</em>(1), 177–197. <a href="https://doi.org/10.1146/annurev-ecolsys-010621-044528">https://doi.org/10.1146/annurev-ecolsys-010621-044528</a>
 </div>
+<div id="ref-cooplab_PopulationGeneticsCourse_2011" class="csl-entry" role="listitem">
+cooplab. (2011). Population genetics course resources: <span>Hardy-Weinberg Eq</span>. In <em>gcbias</em>. <a href="https://gcbias.org/2011/10/13/population-genetics-course-resources-hardy-weinberg-eq/">https://gcbias.org/2011/10/13/population-genetics-course-resources-hardy-weinberg-eq/</a>
+</div>
 <div id="ref-corbett-detig_NaturalSelectionConstrains_2015" class="csl-entry" role="listitem">
 Corbett-Detig, R. B., Hartl, D. L., &amp; Sackton, T. B. (2015). Natural <span>Selection Constrains Neutral Diversity</span> across <span>A Wide Range</span> of <span>Species</span>. <em>PLOS Biology</em>, <em>13</em>(4), e1002112. <a href="https://doi.org/10.1371/journal.pbio.1002112">https://doi.org/10.1371/journal.pbio.1002112</a>
 </div>
@@ -5025,6 +5028,9 @@ <h1>References</h1>
 <div id="ref-_VertebrateGenomesProject_" class="csl-entry" role="listitem">
 <em>Vertebrate <span>Genomes Project</span></em>. (n.d.). https://vertebrategenomesproject.org. Retrieved November 3, 2022, from <a href="https://vertebrategenomesproject.org">https://vertebrategenomesproject.org</a>
 </div>
+<div id="ref-waples_WhatNeAnyway_2022" class="csl-entry" role="listitem">
+Waples, R. S. (2022). What <span>Is Ne</span>, <span>Anyway</span>? <em>Journal of Heredity</em>, <em>113</em>(4), 371–379. <a href="https://doi.org/10.1093/jhered/esac023">https://doi.org/10.1093/jhered/esac023</a>
+</div>
 <div id="ref-webstermatthew_GeneticVariationMountain_2022" class="csl-entry" role="listitem">
 Webster, Matthew, &amp; Yuanzhen Liu. (2022). <em>Genetic <span>Variation</span> in <span>Mountain Bumblebees</span></em>.
 </div>

sitemap.xml

@@ -2,186 +2,186 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/simulation/index.html</loc>
-    <lastmod>2023-08-20T16:31:26.998Z</lastmod>
+    <lastmod>2023-08-22T23:02:49.335Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/recap_day3/index.html</loc>
-    <lastmod>2023-08-20T16:30:59.052Z</lastmod>
+    <lastmod>2023-08-22T23:02:26.971Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/recap_day1/index.html</loc>
-    <lastmod>2023-08-20T16:30:53.724Z</lastmod>
+    <lastmod>2023-08-22T23:02:22.999Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/pgip/index.html</loc>
-    <lastmod>2023-08-20T16:30:47.043Z</lastmod>
+    <lastmod>2023-08-22T23:02:17.935Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/ld_and_recombination/index.html</loc>
-    <lastmod>2023-08-20T16:29:12.926Z</lastmod>
+    <lastmod>2023-08-22T23:01:03.727Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/index.html</loc>
-    <lastmod>2023-08-20T16:29:07.594Z</lastmod>
+    <lastmod>2023-08-22T23:00:59.807Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/foundations/index.html</loc>
-    <lastmod>2023-08-20T16:29:02.325Z</lastmod>
+    <lastmod>2023-08-22T23:00:55.671Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/demography/index.html</loc>
-    <lastmod>2023-08-20T16:26:00.679Z</lastmod>
+    <lastmod>2023-08-22T22:58:27.220Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/datageneration/index.html</loc>
-    <lastmod>2023-08-20T16:25:42.586Z</lastmod>
+    <lastmod>2023-08-22T22:58:13.536Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/admixture/index.html</loc>
-    <lastmod>2023-08-20T16:25:11.036Z</lastmod>
+    <lastmod>2023-08-22T22:57:49.812Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/references.html</loc>
-    <lastmod>2023-08-20T16:25:07.156Z</lastmod>
+    <lastmod>2023-08-22T22:57:46.824Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/program.html</loc>
-    <lastmod>2023-08-20T16:25:03.764Z</lastmod>
+    <lastmod>2023-08-22T22:57:44.264Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/lectures/datageneration/index.html</loc>
-    <lastmod>2023-08-20T16:25:01.363Z</lastmod>
+    <lastmod>2023-08-22T22:57:42.636Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/variant_calling/index.html</loc>
-    <lastmod>2023-08-20T16:24:59.119Z</lastmod>
+    <lastmod>2023-08-22T22:57:41.036Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/popgen_primer/index.html</loc>
-    <lastmod>2023-08-20T16:24:57.151Z</lastmod>
+    <lastmod>2023-08-22T22:57:39.536Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/linked_selection/index.html</loc>
-    <lastmod>2023-08-20T16:24:47.067Z</lastmod>
+    <lastmod>2023-08-22T22:57:31.592Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/ld_and_phasing/index.html</loc>
-    <lastmod>2023-08-20T16:24:32.098Z</lastmod>
+    <lastmod>2023-08-22T22:57:19.932Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/gl/index.html</loc>
-    <lastmod>2023-08-20T16:24:13.869Z</lastmod>
+    <lastmod>2023-08-22T22:57:06.640Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/fstatistics/index.html</loc>
-    <lastmod>2023-08-20T16:24:09.244Z</lastmod>
+    <lastmod>2023-08-22T22:57:03.072Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/direct_selection/index.html</loc>
-    <lastmod>2023-08-20T16:23:59.032Z</lastmod>
+    <lastmod>2023-08-22T22:56:55.081Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/demo/index.html</loc>
-    <lastmod>2023-08-20T16:23:53.331Z</lastmod>
+    <lastmod>2023-08-22T22:56:50.409Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/data.html</loc>
-    <lastmod>2023-08-20T16:23:01.512Z</lastmod>
+    <lastmod>2023-08-22T22:56:08.645Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/contents.html</loc>
-    <lastmod>2023-08-20T16:22:52.300Z</lastmod>
+    <lastmod>2023-08-22T22:56:01.333Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/about.html</loc>
-    <lastmod>2023-08-20T16:22:51.048Z</lastmod>
+    <lastmod>2023-08-22T22:56:00.281Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/admixture/index.html</loc>
-    <lastmod>2023-08-20T16:22:53.292Z</lastmod>
+    <lastmod>2023-08-22T22:56:02.125Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/data_filtering/index.html</loc>
-    <lastmod>2023-08-20T16:23:52.407Z</lastmod>
+    <lastmod>2023-08-22T22:56:49.653Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/demopy/index.html</loc>
-    <lastmod>2023-08-20T16:23:58.104Z</lastmod>
+    <lastmod>2023-08-22T22:56:54.305Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/fst_divergence/index.html</loc>
-    <lastmod>2023-08-20T16:24:00.028Z</lastmod>
+    <lastmod>2023-08-22T22:56:55.809Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/genetic_diversity/index.html</loc>
-    <lastmod>2023-08-20T16:24:12.237Z</lastmod>
+    <lastmod>2023-08-22T22:57:05.364Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/index.html</loc>
-    <lastmod>2023-08-20T16:24:15.505Z</lastmod>
+    <lastmod>2023-08-22T22:57:07.940Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/ld_pruning/index.html</loc>
-    <lastmod>2023-08-20T16:24:46.095Z</lastmod>
+    <lastmod>2023-08-22T22:57:30.848Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/msmc/index.html</loc>
-    <lastmod>2023-08-20T16:24:56.227Z</lastmod>
+    <lastmod>2023-08-22T22:57:38.808Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/exercises/preparation.html</loc>
-    <lastmod>2023-08-20T16:24:58.151Z</lastmod>
+    <lastmod>2023-08-22T22:57:40.296Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/index.html</loc>
-    <lastmod>2023-08-20T16:25:00.071Z</lastmod>
+    <lastmod>2023-08-22T22:57:41.772Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/lectures/genetic_diversity/index.html</loc>
-    <lastmod>2023-08-20T16:25:02.668Z</lastmod>
+    <lastmod>2023-08-22T22:57:43.512Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/recipes/index.html</loc>
-    <lastmod>2023-08-20T16:25:05.968Z</lastmod>
+    <lastmod>2023-08-22T22:57:45.928Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/schedule.html</loc>
-    <lastmod>2023-08-20T16:25:08.312Z</lastmod>
+    <lastmod>2023-08-22T22:57:47.732Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/applications_selection/index.html</loc>
-    <lastmod>2023-08-20T16:25:13.852Z</lastmod>
+    <lastmod>2023-08-22T22:57:51.940Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/demo/index.html</loc>
-    <lastmod>2023-08-20T16:25:58.179Z</lastmod>
+    <lastmod>2023-08-22T22:58:25.348Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/direct_selection/index.html</loc>
-    <lastmod>2023-08-20T16:26:03.287Z</lastmod>
+    <lastmod>2023-08-22T22:58:29.184Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/genetic_diversity/index.html</loc>
-    <lastmod>2023-08-20T16:29:05.314Z</lastmod>
+    <lastmod>2023-08-22T23:00:57.979Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/introduction/index.html</loc>
-    <lastmod>2023-08-20T16:29:10.374Z</lastmod>
+    <lastmod>2023-08-22T23:01:01.851Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/linked_selection/index.html</loc>
-    <lastmod>2023-08-20T16:30:42.363Z</lastmod>
+    <lastmod>2023-08-22T23:02:14.619Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/population_structure/index.html</loc>
-    <lastmod>2023-08-20T16:30:51.096Z</lastmod>
+    <lastmod>2023-08-22T23:02:21.027Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/recap_day2/index.html</loc>
-    <lastmod>2023-08-20T16:30:56.360Z</lastmod>
+    <lastmod>2023-08-22T23:02:24.979Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/NBISweden/workshop-pgip/slides/recap_day4/index.html</loc>
-    <lastmod>2023-08-20T16:31:01.816Z</lastmod>
+    <lastmod>2023-08-22T23:02:28.935Z</lastmod>
   </url>
 </urlset>

slides/admixture/index.html

@@ -351,7 +351,7 @@ <h1 class="title">Population admixture</h1>
   <h3 class="subtitle">Admixture</h3>
   <h4 class="author">Per Unneberg</h4>
   <h4 class="institute">NBIS</h4>
-  <h4 class="date">20-Aug-2023</h4>
+  <h4 class="date">22-Aug-2023</h4>
 </section><section id="TOC">
 <nav role="doc-toc"> 
 <h2 id="toc-title">Table of contents</h2>

slides/applications_selection/index.html

@@ -351,7 +351,7 @@ <h1 class="title">Genome scans to detect selection</h1>
   <h3 class="subtitle">Genome scans</h3>
   <h4 class="author">Per Unneberg</h4>
   <h4 class="institute">NBIS</h4>
-  <h4 class="date">20-Aug-2023</h4>
+  <h4 class="date">22-Aug-2023</h4>
 </section><section id="TOC">
 <nav role="doc-toc"> 
 <h2 id="toc-title">Table of contents</h2>

slides/datageneration/index.html

@@ -351,7 +351,7 @@ <h1 class="title">Data generation and processing</h1>
   <h3 class="subtitle">Sequencing protocols, best practice variant calling and filtering</h3>
   <h4 class="author">Per Unneberg</h4>
   <h4 class="institute">NBIS</h4>
-  <h4 class="date">20-Aug-2023</h4>
+  <h4 class="date">22-Aug-2023</h4>
 </section><section id="TOC">
 <nav role="doc-toc"> 
 <h2 id="toc-title">Table of contents</h2>