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<title>Time analysis</title>
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<h1 class="title toc-ignore">Time analysis</h1>
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<p>
<button type="button" class="btn btn-default btn-workflowr btn-workflowr-report" data-toggle="collapse" data-target="#workflowr-report">
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<span class="glyphicon glyphicon-list" aria-hidden="true"></span> workflowr <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span>
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<a data-toggle="tab" href="#summary">Summary</a>
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<a data-toggle="tab" href="#checks"> Checks <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> </a>
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<a data-toggle="tab" href="#versions">Past versions</a>
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<p>
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<strong>Last updated:</strong> 2022-05-02
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</p>
<p>
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<strong>Checks:</strong> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> 7 <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> 0
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</p>
<p>
<strong>Knit directory:</strong> <code>mage_2020_marker-gene-benchmarking/</code> <span class="glyphicon glyphicon-question-sign" aria-hidden="true" title="This is the local directory in which the code in this file was executed."> </span>
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<p>
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This reproducible <a href="https://rmarkdown.rstudio.com">R Markdown</a> analysis was created with <a
  href="https://github.com/workflowr/workflowr">workflowr</a> (version 1.7.0). The <em>Checks</em> tab describes the reproducibility checks that were applied when the results were created. The <em>Past versions</em> tab lists the development history.
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRMarkdownfilestronguptodate"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>R Markdown file:</strong> up-to-date </a>
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<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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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongEnvironmentstrongempty"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Environment:</strong> empty </a>
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<p>Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.</p>
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongSeedstrongcodesetseed20190102code"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Seed:</strong> <code>set.seed(20190102)</code> </a>
</p>
</div>
<div id="strongSeedstrongcodesetseed20190102code" class="panel-collapse collapse">
<div class="panel-body">
<p>The command <code>set.seed(20190102)</code> was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.</p>
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongSessioninformationstrongrecorded"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Session information:</strong> recorded </a>
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<p>Great job! Recording the operating system, R version, and package versions is critical for reproducibility.</p>
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongCachestrongnone"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Cache:</strong> none </a>
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<div id="strongCachestrongnone" class="panel-collapse collapse">
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<p>Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.</p>
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<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongFilepathsstrongrelative"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>File paths:</strong> relative </a>
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<div id="strongFilepathsstrongrelative" class="panel-collapse collapse">
<div class="panel-body">
<p>Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.</p>
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenprivatemage2020markergenebenchmarkingtree50bca7c1f36680d5fcb00fbe642d0cf576795269targetblank50bca7ca"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/tree/50bca7c1f36680d5fcb00fbe642d0cf576795269" target="_blank">50bca7c</a> </a>
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<p>
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
</p>
<p>
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The results in this page were generated with repository version <a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/tree/50bca7c1f36680d5fcb00fbe642d0cf576795269" target="_blank">50bca7c</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
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<p>
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:
</p>
<pre><code>
Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    .snakemake/
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    Ignored:    NSForest/.Rhistory
    Ignored:    NSForest/NS-Forest_v3_Extended_Binary_Markers_Supplmental.csv
    Ignored:    NSForest/NS-Forest_v3_Full_Results.csv
    Ignored:    NSForest/NSForest3_medianValues.csv
    Ignored:    NSForest/NSForest_v3_Final_Result.csv
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<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tibble)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(dplyr)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggplot2)</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyr)</span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(purrr)</span>
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<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(forcats)</span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(patchwork)</span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(stringr)</span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggrepel)</span>
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<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="fu">source</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;code&quot;</span>, <span class="st">&quot;analysis-utils.R&quot;</span>))</span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="fu">source</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;code&quot;</span>, <span class="st">&quot;plot-utils.R&quot;</span>))</span></code></pre></div>
<div id="aim" class="section level1">
<h1>Aim</h1>
<p>Measure the time different methods take to run.</p>
</div>
<div id="simulated-data" class="section level1">
<h1>Simulated data</h1>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>sim_pars <span class="ot">&lt;-</span> <span class="fu">retrive_simulation_parameters</span>()</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>num_cells_time_data <span class="ot">&lt;-</span> sim_pars <span class="sc">%&gt;%</span> </span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>  <span class="fu">filter</span>(sim_label <span class="sc">==</span> <span class="st">&quot;num_cells&quot;</span>) <span class="sc">%&gt;%</span> </span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>  <span class="fu">rowwise</span>() <span class="sc">%&gt;%</span> </span>