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<p><strong>Last updated:</strong> 2018-08-12</p>
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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/willwerscheid/FLASHvestigations/tree/6a9bf1c4cb55f106ec6bfa8279041df485958868" target="_blank">6a9bf1c</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>
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2018-07-27
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2018-07-17
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<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/e2e1286424015e8cbed280a8548f5e9b0d6a723b/docs/index.html" target="_blank">e2e1286</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-16
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/55f42cad6e56835471c8988e99ce73af56dedb8b/analysis/index.Rmd" target="_blank">55f42ca</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-16
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/de8f82306cc8bec7a369010bc572bc2e794b9544/docs/index.html" target="_blank">de8f823</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-16
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/f5379fab679055aa1fe5195856876bce376841e0/analysis/index.Rmd" target="_blank">f5379fa</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-16
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/7db12a1efed12474ff15a3cf6c111dbf946d7107/docs/index.html" target="_blank">7db12a1</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-16
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/873da40adfea91a43fd5eaa922c03ad24ab2d77e/docs/index.html" target="_blank">873da40</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-16
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/58e136aec27b1c1414626a3820ac4685c2252dc6/docs/index.html" target="_blank">58e136a</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-15
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/82c7cdd1d6fe660851f65975e7c1fff62ec60737/analysis/index.Rmd" target="_blank">82c7cdd</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-15
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/index.Rmd”, “analysis/about.Rmd”))
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/76eacb75d7f6a19857f7adfe769a3fd76643e3bb/docs/index.html" target="_blank">76eacb7</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-15
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/f6928cc38fc84fe9d0d5ddcf11d954fba36c6910/analysis/index.Rmd" target="_blank">f6928cc</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-15
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/index.Rmd”, “analysis/about.Rmd”))
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/56d7ded8c6138ce9a71293c5e31a2363fa6f0c75/analysis/index.Rmd" target="_blank">56d7ded</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-14
</td>
<td style="text-align:left;">
Start workflowr project.
</td>
</tr>
</tbody>
</table>
</ul>
<p></details></p>
<hr />
<div id="in-progress" class="section level2">
<h2>In Progress</h2>
<p><a href="init_fn.html">Investigation 5a.</a> We should change the default <code>init_fn</code> to <code>udv_si_svd</code> when there is missing data and <code>udv_svd</code> otherwise.</p>
<p><a href="init_fn2.html">Investigation 5b.</a> More evidence supporting a change to the default initialization function.</p>
<p><a href="parallel.html">Investigation 8.</a> Parallelizing backfitting updates shows promise.</p>
</div>
<div id="still-relevant" class="section level2">
<h2>Still Relevant</h2>
<p><a href="obj_notes.html">Note 1.</a> Notes on computing the FLASH objective function. I derive an explicit expression for the KL divergence between prior and posterior.</p>
<p><a href="flash_em.html">Note 2.</a> An alternate algorithm for optimizing the FLASH objective, using the explicit expression derived in the previous note.</p>
<p><a href="alt_alg.html">Investigation 4.</a> The alternate algorithm agrees with FLASH with respect to both the objective and fit obtained.</p>
</div>
<div id="archived" class="section level2">
<h2>Archived</h2>
<p>The bug causing the problem described in Investigations 1-3 was fixed in version 0.1-13 of package <code>ebnm</code>.</p>
<p><a href="objective.html">Investigation 1.</a> The FLASH objective function can behave very erratically.</p>
<p><a href="objective2.html">Investigation 2.</a> This problem only occurs when using <code>ebnm_pn</code>, not <code>ebnm_ash</code>.</p>
<p><a href="objective3.html">Investigation 3.</a> The objective can continue to get worse as loadings are repeatedly updated. Nonetheless, convergence takes place (from above!).</p>
<p>Investigations 6 and 7 are concerned with warmstarts, which were implemented in version 0.5-14 of <code>flashr</code>.</p>
<p><a href="warmstart.html">Investigation 6.</a> Poor <code>optim</code> results can produce large decreases in the objective function. We should use warmstarts when <code>ebnm_fn = ebnm_pn</code>.</p>
<p><a href="warmstart2.html">Investigation 7.</a> The advantages of warmstarts are not nearly as compelling when <code>ebnm_fn = ebnm_ash</code>.</p>
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