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| # Variance component estimation with AIREMLF90 for Single Trait Analysis | ||
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| In the previous post, I tried to show how to solve MME to derive BLUP values with **assumed** variance components. We need to estimate actual variance components of the animals under study in practical application. Especially, if: | ||
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| - we are interested in a new trait, from which no parameters are available | ||
| - variances and covariances might have changed over time | ||
| - considerable changes have occurred in a population e.g. due to recent | ||
| importations. | ||
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| Here is a brief overview of the methods used in VCE. We use AI-REML method as default in BLUPF90. We can use EM-REML and Gibbs Sampling also, depending on individual use cases. A good explanation of which method to use, can be found here. https://doi.org/10.1111/j.1439-0388.2008.00774.x | ||
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| {{< figure src="/posts/airemlf90_vce/aireml.jpeg" title="Evolution of methods used for VCE" >}} | ||
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| In this example, we use simulated data and corresponding pedigree file to estimate the variance components. The model contains animals as random effect, farm, sex, year as fixed effects, and a single trait (observation). The following video explains the process in detail. | ||
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| {{< youtube YvXRJq6Tqq8 >}} | ||
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| This exmpale has also been taken from Y. Masuda's awesome tutorial for BLUPF90 suite of programs. You can find the details here. https://masuday.github.io/blupf90_tutorial/vc_aireml.html |
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@@ -101,6 +101,21 @@ | |
| alt="https://www.gravatar.com/avatar/81e89bdcd46adae9c20fff13fdd00839?s=240&d=mp" | ||
| title="https://www.gravatar.com/avatar/81e89bdcd46adae9c20fff13fdd00839?s=240&d=mp" /></a></div><h1 class="home-title">Md. Shamim Aktar</h1><div class="home-subtitle"><div id="id-1" class="typeit"></div></div><div class="links"><a href="https://github.com/shamimaktar" title="GitHub" target="_blank" rel="noopener noreffer me"><i class="fab fa-github-alt fa-fw" aria-hidden="true"></i></a><a href="https://linkedin.com/in/mdshamimaktar" title="LinkedIn" target="_blank" rel="noopener noreffer me"><i class="fab fa-linkedin fa-fw" aria-hidden="true"></i></a><a href="https://facebook.com/ShamimAktarShovon" title="facebook" target="_blank" rel="noopener noreffer me"><i class="fab fa-facebook fa-fw" aria-hidden="true"></i></a><a href="mailto:[email protected]" title="Email" rel=" me"><i class="far fa-envelope fa-fw" aria-hidden="true"></i></a><a href="/index.xml" title="RSS" target="_blank" rel="noopener noreffer me"><i class="fas fa-rss fa-fw" aria-hidden="true"></i></a></div></div> | ||
| <article class="single summary" itemscope itemtype="http://schema.org/Article"><div class="featured-image-preview"> | ||
| <a href="/airemlf90_vce/"><img | ||
| class="lazyload" | ||
| src="/svg/loading.min.svg" | ||
| data-src="/airemlf90.jpg" | ||
| data-srcset="/airemlf90.jpg, /airemlf90.jpg 1.5x, /airemlf90.jpg 2x" | ||
| data-sizes="auto" | ||
| alt="/airemlf90.jpg" | ||
| title="Variance component estimation with AIREMLF90 for Single Trait Analysis" width="384" height="134" /></a> | ||
| </div><h1 class="single-title" itemprop="name headline"> | ||
| <a href="/airemlf90_vce/">Variance component estimation with AIREMLF90 for Single Trait Analysis</a> | ||
| </h1><div class="post-meta"><span class="post-author"><a href="/" title="Author" rel=" author" class="author"><i class="fas fa-user-circle fa-fw" aria-hidden="true"></i>Md. Shamim Aktar</a></span> <span class="post-publish">published on <time datetime="2023-02-05">2023-02-05</time></span> <span class="post-category">included in <a href="/categories/abg/"><i class="far fa-folder fa-fw" aria-hidden="true"></i>ABG</a></span></div><div class="content">In the previous post, I tried to show how to solve MME to derive BLUP values with assumed variance components. We need to estimate actual variance components of the animals under study in practical application. Especially, if: | ||
| we are interested in a new trait, from which no parameters are available variances and covariances might have changed over time considerable changes have occurred in a population e.g. due to recent importations.</div><div class="post-footer"> | ||
| <a href="/airemlf90_vce/">Read More</a><div class="post-tags"> | ||
| <i class="fas fa-tags fa-fw" aria-hidden="true"></i> <a href="/tags/vce/">VCE</a>, <a href="/tags/variance-component-estimation/">Variance component estimation</a>, <a href="/tags/blupf90+/">BLUPF90+</a>, <a href="/tags/quantitative-genetics/">Quantitative genetics</a></div></div> | ||
| </article><article class="single summary" itemscope itemtype="http://schema.org/Article"><div class="featured-image-preview"> | ||
| <a href="/blupf90_single_trait_mme_solver/"><img | ||
| class="lazyload" | ||
| src="/svg/loading.min.svg" | ||
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@@ -142,7 +157,7 @@ | |
| <a href="/vc6/">How to install VCE 6.0.2 on a Windows x86 64-bit machine</a> | ||
| </h1><div class="post-meta"><span class="post-author"><a href="/" title="Author" rel=" author" class="author"><i class="fas fa-user-circle fa-fw" aria-hidden="true"></i>Md. Shamim Aktar</a></span> <span class="post-publish">published on <time datetime="2022-10-26">2022-10-26</time></span> <span class="post-category">included in <a href="/categories/abg/"><i class="far fa-folder fa-fw" aria-hidden="true"></i>ABG</a></span></div><div class="content">**This is the version6 of VCE a package for estimating (co)variance components by REML and Gibbs Sampling The vce6 directory contains 3 subdirectories: bin - contains executables for a number of computing platforms doc - contains the documentation in A4 and US Letter format examples - contains just that: data and parameter files that should run out of the box after installation** 1. First, go to this link and download the 53.</div><div class="post-footer"> | ||
| <a href="/vc6/">Read More</a><div class="post-tags"> | ||
| <i class="fas fa-tags fa-fw" aria-hidden="true"></i> <a href="/tags/variance-component-estimation/">Variance Component Estimation</a>, <a href="/tags/vce/">VCE</a></div></div> | ||
| <i class="fas fa-tags fa-fw" aria-hidden="true"></i> <a href="/tags/variance-component-estimation/">Variance component estimation</a>, <a href="/tags/vce/">VCE</a></div></div> | ||
| </article><article class="single summary" itemscope itemtype="http://schema.org/Article"><div class="featured-image-preview"> | ||
| <a href="/first_post/"><img | ||
| class="lazyload" | ||
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