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<h1 class="title toc-ignore">SMASH companion source code repository</h1>
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<p><strong>Last updated:</strong> 2018-11-09</p>
<strong>workflowr checks:</strong> <small>(Click a bullet for more information)</small>
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<p><details> <summary> <strong style="color:blue;">✔</strong> <strong>R Markdown file:</strong> up-to-date </summary></p>
<p>Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.</p>
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<p><details> <summary> <strong style="color:blue;">✔</strong> <strong>Repository version:</strong> <a href="https://github.com/stephenslab/smash-paper/tree/9d9b934df4f64dc9ac872766d3c4ea2e8b97f7ef" target="_blank">9d9b934</a> </summary></p>
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated. <br><br> Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
<pre><code>
Ignored files:
Ignored: dsc/code/Wavelab850/MEXSource/CPAnalysis.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/DownDyadHi.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/DownDyadLo.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/FAIPT.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/FCPSynthesis.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/FMIPT.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/FWPSynthesis.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/FWT2_PO.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/FWT_PBS.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/FWT_PO.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/FWT_TI.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/IAIPT.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/IMIPT.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/IWT2_PO.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/IWT_PBS.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/IWT_PO.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/IWT_TI.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/LMIRefineSeq.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/MedRefineSeq.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/UpDyadHi.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/UpDyadLo.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/WPAnalysis.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/dct_ii.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/dct_iii.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/dct_iv.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/dst_ii.mexmac
Ignored: dsc/code/Wavelab850/MEXSource/dst_iii.mexmac
</code></pre>
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes. </details>
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Peter Carbonetto
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Re-built the home page after revamping it.
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Build site.
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Peter Carbonetto
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2018-08-23
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Start workflowr project with wflow_start().
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<p></details></p>
<hr />
<p>This repository contains data and R source code accompanying our manuscript,</p>
<blockquote>
<p>Zhengrong Xing and Matthew Stephens (2016). <em>Smoothing via Adaptive Shrinkage (smash): denoising Poisson and heteroskedastic Gaussian signals.</em> <a href="http://arxiv.org/abs/1605.07787">arXiv:1709.10066</a>.</p>
</blockquote>
<p>If you find any of the source code in this repository useful for your work, please cite our paper.</p>
<p>The new methods can be found in the <a href="https://github.com/stephenslab/smashr">smashr package</a>.</p>
<div id="contents" class="section level2">
<h2>Contents</h2>
<p>The following analyses generate some of the empirical results presented in <a href="http://arxiv.org/abs/1605.07787">Xing & Stephens (2016)</a>. If you encounter a problem running any of the R code in these examples, please post an <a href="https://github.com/stephenslab/smash-paper/issues">issue</a>.</p>
<div id="illustration" class="section level3">
<h3>Illustration</h3>
<ul>
<li><a href="spikesdemo.html">SMASH applied to the “Spikes” data set.</a></li>
</ul>
</div>
<div id="simulation-experiments" class="section level3">
<h3>Simulation experiments</h3>
<ol style="list-style-type: decimal">
<li><p><a href="gaussmeanest.html">Estimating the mean function from Gaussian-distributed data.</a></p></li>
<li><p><a href="gaussvarest.html">Estimating the variance function from Gaussian-distributed data</a>.</p></li>
<li><p>Poisson-distributed data.</p></li>
</ol>
</div>
<div id="illustrative-applications" class="section level3">
<h3>Illustrative applications</h3>
<ol style="list-style-type: decimal">
<li><p><a href="motorcycle.html">Motorcycle acceleration data.</a></p></li>
<li><p><a href="chipseq.html">ChIP-seq data.</a></p></li>
</ol>
</div>
</div>
<div id="whats-included-in-the-git-repository" class="section level2">
<h2>What’s included in the git repository</h2>
<p>See here for the source repository. This is what you will find in the repository:</p>
<p><em>Fill out this section.</em></p>
</div>
<div id="license" class="section level2">
<h2>License</h2>
<p>Copyright (c) 2016-2018, Zhengrong Xing, Peter Carbonetto & Matthew Stephens.</p>
<p>All source code and software in this repository are made available under the terms of the <a href="https://opensource.org/licenses/mit-license.html">MIT license</a>. See the <a href="LICENSE" class="uri">LICENSE</a> file for the full text of the license.</p>
</div>
<div id="credits" class="section level2">
<h2>Credits</h2>
<p>This project was developed by <a href="https://github.com/zrxing">Zhengrong Xing</a> at the University of Chicago, with support and contributions from <a href="http://pcarbo.github.io">Peter Carbonetto</a> and <a href="http://stephenslab.uchicago.edu">Matthew Stephens</a>.</p>
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