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benchmarks.html
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benchmarks.html
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<h1>Benchmarks</h1>
</div>
<div id="benchmarks" class="section level1">
<ul>
<li><a href="#setup">Setup</a></li>
<li>
<a href="#spreadgather_draws"><code>spread/gather_draws</code></a>
<ul>
<li><a href="#spreading-with-indices">Spreading with indices</a></li>
<li><a href="#array-columns">Array columns</a></li>
</ul>
</li>
</ul>
<p>Some rough benchmarks for testing how long things take…</p>
<div id="setup" class="section level2">
<h2 class="hasAnchor">
<a href="#setup" class="anchor"></a>Setup</h2>
<div class="sourceCode" id="cb1"><html><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">tidyverse</span>)</pre></html></div>
<div class="sourceCode" id="cb2"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a><span class="co">## -- Attaching packages ------------------------------------------------------------ tidyverse 1.2.1 --</span></span>
<span id="cb2-2"><a href="#cb2-2"></a></span>
<span id="cb2-3"><a href="#cb2-3"></a><span class="co">## v ggplot2 3.2.1 v purrr 0.3.2</span></span>
<span id="cb2-4"><a href="#cb2-4"></a><span class="co">## v tibble 2.1.3 v dplyr 0.8.3</span></span>
<span id="cb2-5"><a href="#cb2-5"></a><span class="co">## v tidyr 1.0.0 v stringr 1.4.0</span></span>
<span id="cb2-6"><a href="#cb2-6"></a><span class="co">## v readr 1.3.1 v forcats 0.4.0</span></span>
<span id="cb2-7"><a href="#cb2-7"></a></span>
<span id="cb2-8"><a href="#cb2-8"></a><span class="co">## -- Conflicts --------------------------------------------------------------- tidyverse_conflicts() --</span></span>
<span id="cb2-9"><a href="#cb2-9"></a><span class="co">## x dplyr::filter() masks stats::filter()</span></span>
<span id="cb2-10"><a href="#cb2-10"></a><span class="co">## x dplyr::lag() masks stats::lag()</span></span></code></pre></div>
<div class="sourceCode" id="cb3"><html><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">tidybayes</span>)</pre></html></div>
</div>
<div id="spreadgather_draws" class="section level2">
<h2 class="hasAnchor">
<a href="#spreadgather_draws" class="anchor"></a><code>spread/gather_draws</code>
</h2>
<div class="sourceCode" id="cb4"><html><pre class="r"><span class="no">k</span> <span class="kw">=</span> <span class="fl">50000</span>
<span class="fu"><a href="https://rdrr.io/r/base/Random.html">set.seed</a></span>(<span class="fl">1234</span>)
<span class="no">df</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(
<span class="kw">.chain</span> <span class="kw">=</span> <span class="fl">NA</span>,
<span class="kw">.iteration</span> <span class="kw">=</span> <span class="fl">NA</span>,
<span class="kw">.draw</span> <span class="kw">=</span> <span class="fl">1</span>:<span class="no">k</span>,
<span class="kw">`a[2]`</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="no">k</span>),
<span class="kw">`b[2]`</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="no">k</span>),
<span class="kw">`c[2]`</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="no">k</span>),
<span class="kw">`d[2]`</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="no">k</span>),
<span class="kw">`e[2]`</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="no">k</span>),
<span class="kw">`f[2]`</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="no">k</span>),
<span class="kw">`g[2]`</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="no">k</span>),
<span class="kw">`h[2]`</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="no">k</span>),
<span class="kw">`i[2]`</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="no">k</span>),
<span class="kw">`j[2]`</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="no">k</span>),
<span class="kw">`k[2]`</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="no">k</span>),
<span class="kw">`l[2]`</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="no">k</span>),
<span class="kw">stringsAsFactors</span> <span class="kw">=</span> <span class="fl">FALSE</span>,
<span class="kw">check.names</span> <span class="kw">=</span> <span class="fl">FALSE</span>
) <span class="kw">%>%</span>
<span class="fu">as_tibble</span>()
<span class="no">df</span></pre></html></div>
<div class="sourceCode" id="cb5"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a><span class="co">## # A tibble: 50,000 x 15</span></span>
<span id="cb5-2"><a href="#cb5-2"></a><span class="co">## .chain .iteration .draw `a[2]` `b[2]` `c[2]` `d[2]` `e[2]` `f[2]`</span></span>
<span id="cb5-3"><a href="#cb5-3"></a><span class="co">## <lgl> <lgl> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl></span></span>
<span id="cb5-4"><a href="#cb5-4"></a><span class="co">## 1 NA NA 1 -1.21 0.491 -1.42 0.892 -0.553 -0.276</span></span>
<span id="cb5-5"><a href="#cb5-5"></a><span class="co">## 2 NA NA 2 0.277 0.0250 0.317 -0.573 -1.13 0.919</span></span>
<span id="cb5-6"><a href="#cb5-6"></a><span class="co">## 3 NA NA 3 1.08 1.30 0.728 0.0640 0.0360 -1.02 </span></span>
<span id="cb5-7"><a href="#cb5-7"></a><span class="co">## 4 NA NA 4 -2.35 -0.235 -1.90 0.0434 -1.17 -1.42 </span></span>
<span id="cb5-8"><a href="#cb5-8"></a><span class="co">## 5 NA NA 5 0.429 -0.453 -1.14 1.80 0.0443 -0.660</span></span>
<span id="cb5-9"><a href="#cb5-9"></a><span class="co">## 6 NA NA 6 0.506 -0.0111 0.577 -2.58 0.269 0.296</span></span>
<span id="cb5-10"><a href="#cb5-10"></a><span class="co">## 7 NA NA 7 -0.575 0.933 0.198 -0.218 -0.182 -0.906</span></span>
<span id="cb5-11"><a href="#cb5-11"></a><span class="co">## 8 NA NA 8 -0.547 -0.729 1.07 2.15 -1.27 -1.05 </span></span>
<span id="cb5-12"><a href="#cb5-12"></a><span class="co">## 9 NA NA 9 -0.564 1.40 0.626 1.11 0.738 -0.778</span></span>
<span id="cb5-13"><a href="#cb5-13"></a><span class="co">## 10 NA NA 10 -0.890 -0.0584 -0.700 -0.956 -2.27 1.02 </span></span>
<span id="cb5-14"><a href="#cb5-14"></a><span class="co">## # ... with 49,990 more rows, and 6 more variables: `g[2]` <dbl>,</span></span>
<span id="cb5-15"><a href="#cb5-15"></a><span class="co">## # `h[2]` <dbl>, `i[2]` <dbl>, `j[2]` <dbl>, `k[2]` <dbl>, `l[2]` <dbl></span></span></code></pre></div>
<div id="spreading-with-indices" class="section level3">
<h3 class="hasAnchor">
<a href="#spreading-with-indices" class="anchor"></a>Spreading with indices</h3>
<p>This should be fairly fast. Last test was ~= 0.03 seconds on <code>monarch</code>.</p>
<div class="sourceCode" id="cb6"><html><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu"><a href="reference/spread_draws.html">spread_draws</a></span>(<span class="no">df</span>, <span class="no">`.`</span>[<span class="no">index</span>], <span class="kw">regex</span> <span class="kw">=</span> <span class="fl">TRUE</span>))</pre></html></div>
<div class="sourceCode" id="cb7"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a><span class="co">## user system elapsed </span></span>
<span id="cb7-2"><a href="#cb7-2"></a><span class="co">## 0.05 0.00 0.04</span></span></code></pre></div>
<div id="separate-spec-version" class="section level4">
<h4 class="hasAnchor">
<a href="#separate-spec-version" class="anchor"></a>Separate-spec version</h4>
<p>This is definitely slower than it could be, likely due to use of joins with chain information involved. This could almost definitely be made faster if nesting was used all the way up the spread_draws pipeline and chain information added at the last possible moment. Last test was ~= 0.35 seconds on <code>monarch</code>.</p>
<div class="sourceCode" id="cb8"><html><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu"><a href="reference/spread_draws.html">spread_draws</a></span>(<span class="no">df</span>,
<span class="no">a</span>[<span class="no">index</span>], <span class="no">b</span>[<span class="no">index</span>], <span class="no">c</span>[<span class="no">index</span>], <span class="no">d</span>[<span class="no">index</span>], <span class="no">e</span>[<span class="no">index</span>], <span class="no">f</span>[<span class="no">index</span>],
<span class="no">g</span>[<span class="no">index</span>], <span class="no">h</span>[<span class="no">index</span>], <span class="no">i</span>[<span class="no">index</span>], <span class="no">j</span>[<span class="no">index</span>], <span class="no">k</span>[<span class="no">index</span>], <span class="no">l</span>[<span class="no">index</span>]
))</pre></html></div>
<div class="sourceCode" id="cb9"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1"></a><span class="co">## user system elapsed </span></span>
<span id="cb9-2"><a href="#cb9-2"></a><span class="co">## 0.33 0.05 0.37</span></span></code></pre></div>
</div>
<div id="using-gather_draws" class="section level4">
<h4 class="hasAnchor">
<a href="#using-gather_draws" class="anchor"></a>Using gather_draws</h4>
<p>This is slower than the spread_draws version even though it shouldn’t really have to be. This is a result of spread_draws_long_ doing a spread that is later undone by gather_draws. Could either use a flag to skip this (although that is a little complicated as the <code><a href="https://rdrr.io/r/base/Logic.html">|</a></code> syntax might need the spread anyway) or rely on switching to nesting throughout the entire pipeline to just make the spread/gather round trip not so costly. Last test was ~= 0.13 seconds on <code>monarch</code>.</p>
<div class="sourceCode" id="cb10"><html><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu"><a href="reference/spread_draws.html">gather_draws</a></span>(<span class="no">df</span>, <span class="no">`.`</span>[<span class="no">index</span>], <span class="kw">regex</span> <span class="kw">=</span> <span class="fl">TRUE</span>))</pre></html></div>
<div class="sourceCode" id="cb11"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1"></a><span class="co">## user system elapsed </span></span>
<span id="cb11-2"><a href="#cb11-2"></a><span class="co">## 0.13 0.03 0.16</span></span></code></pre></div>
</div>
</div>
<div id="array-columns" class="section level3">
<h3 class="hasAnchor">
<a href="#array-columns" class="anchor"></a>Array columns</h3>
<p>This tends to be slower than spreading without array columns. Last test was ~0.08 seconds on <code>monarch</code>.</p>
<div class="sourceCode" id="cb12"><html><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/data.html">data</a></span>(<span class="no">RankCorr</span>, <span class="kw">package</span> <span class="kw">=</span> <span class="st">"ggdist"</span>)
<span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu"><a href="reference/spread_draws.html">spread_draws</a></span>(<span class="no">RankCorr</span>, <span class="no">b</span>[<span class="no">.</span>,<span class="no">.</span>]))</pre></html></div>
<div class="sourceCode" id="cb13"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1"></a><span class="co">## user system elapsed </span></span>
<span id="cb13-2"><a href="#cb13-2"></a><span class="co">## 0.07 0.00 0.06</span></span></code></pre></div>
<p>And this is currently very slow. Last test was ~0.5 seconds on <code>monarch</code>.</p>
<div class="sourceCode" id="cb14"><html><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu"><a href="reference/spread_draws.html">spread_draws</a></span>(<span class="no">df</span>, <span class="no">a</span>[<span class="no">.</span>]))</pre></html></div>
<div class="sourceCode" id="cb15"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1"></a><span class="co">## user system elapsed </span></span>
<span id="cb15-2"><a href="#cb15-2"></a><span class="co">## 0.47 0.06 0.53</span></span></code></pre></div>
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