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mattfidler committed Jul 5, 2023
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46 changes: 23 additions & 23 deletions docs/advanced-miscellaneous-topics.html
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Expand Up @@ -1200,11 +1200,11 @@ <h4><span class="header-section-number">13.4.1.5</span> Compare the times betwee
<div class="sourceCode" id="cb319"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb319-1"><a href="advanced-miscellaneous-topics.html#cb319-1" aria-hidden="true"></a>bench &lt;-<span class="st"> </span><span class="kw">microbenchmark</span>(<span class="kw">runFor</span>(), <span class="kw">runSapply</span>(), <span class="kw">runSingleThread</span>(),<span class="kw">run2Thread</span>())</span>
<span id="cb319-2"><a href="advanced-miscellaneous-topics.html#cb319-2" aria-hidden="true"></a><span class="kw">print</span>(bench)</span>
<span id="cb319-3"><a href="advanced-miscellaneous-topics.html#cb319-3" aria-hidden="true"></a><span class="co">#&gt; Unit: milliseconds</span></span>
<span id="cb319-4"><a href="advanced-miscellaneous-topics.html#cb319-4" aria-hidden="true"></a><span class="co">#&gt; expr min lq mean median uq max</span></span>
<span id="cb319-5"><a href="advanced-miscellaneous-topics.html#cb319-5" aria-hidden="true"></a><span class="co">#&gt; runFor() 226.15820 230.7579 243.22972 237.99745 242.83007 526.66555</span></span>
<span id="cb319-6"><a href="advanced-miscellaneous-topics.html#cb319-6" aria-hidden="true"></a><span class="co">#&gt; runSapply() 227.60148 233.3769 239.82478 241.06274 242.72300 295.61188</span></span>
<span id="cb319-7"><a href="advanced-miscellaneous-topics.html#cb319-7" aria-hidden="true"></a><span class="co">#&gt; runSingleThread() 21.67092 23.0014 23.46411 23.47942 23.87948 30.52206</span></span>
<span id="cb319-8"><a href="advanced-miscellaneous-topics.html#cb319-8" aria-hidden="true"></a><span class="co">#&gt; run2Thread() 12.84359 13.6482 13.99618 14.09172 14.27220 16.54704</span></span>
<span id="cb319-4"><a href="advanced-miscellaneous-topics.html#cb319-4" aria-hidden="true"></a><span class="co">#&gt; expr min lq mean median uq max</span></span>
<span id="cb319-5"><a href="advanced-miscellaneous-topics.html#cb319-5" aria-hidden="true"></a><span class="co">#&gt; runFor() 221.52904 224.53362 230.50298 226.55532 229.52575 499.55070</span></span>
<span id="cb319-6"><a href="advanced-miscellaneous-topics.html#cb319-6" aria-hidden="true"></a><span class="co">#&gt; runSapply() 220.90154 225.60848 231.40003 226.88348 229.59026 492.54267</span></span>
<span id="cb319-7"><a href="advanced-miscellaneous-topics.html#cb319-7" aria-hidden="true"></a><span class="co">#&gt; runSingleThread() 21.00395 21.68517 22.64487 22.29470 22.66506 33.93919</span></span>
<span id="cb319-8"><a href="advanced-miscellaneous-topics.html#cb319-8" aria-hidden="true"></a><span class="co">#&gt; run2Thread() 12.62902 13.03897 13.54841 13.41709 13.56646 24.87075</span></span>
<span id="cb319-9"><a href="advanced-miscellaneous-topics.html#cb319-9" aria-hidden="true"></a><span class="co">#&gt; neval</span></span>
<span id="cb319-10"><a href="advanced-miscellaneous-topics.html#cb319-10" aria-hidden="true"></a><span class="co">#&gt; 100</span></span>
<span id="cb319-11"><a href="advanced-miscellaneous-topics.html#cb319-11" aria-hidden="true"></a><span class="co">#&gt; 100</span></span>
Expand All @@ -1228,22 +1228,22 @@ <h4><span class="header-section-number">13.4.1.5</span> Compare the times betwee
<span id="cb320-8"><a href="advanced-miscellaneous-topics.html#cb320-8" aria-hidden="true"></a><span class="kw">print</span>(bench)</span>
<span id="cb320-9"><a href="advanced-miscellaneous-topics.html#cb320-9" aria-hidden="true"></a><span class="co">#&gt; Unit: milliseconds</span></span>
<span id="cb320-10"><a href="advanced-miscellaneous-topics.html#cb320-10" aria-hidden="true"></a><span class="co">#&gt; expr min lq mean median uq max neval</span></span>
<span id="cb320-11"><a href="advanced-miscellaneous-topics.html#cb320-11" aria-hidden="true"></a><span class="co">#&gt; runThread(1) 21.217093 22.603772 27.77254 23.976837 28.87527 70.02361 100</span></span>
<span id="cb320-12"><a href="advanced-miscellaneous-topics.html#cb320-12" aria-hidden="true"></a><span class="co">#&gt; runThread(2) 12.647233 14.029550 16.82615 14.708023 17.75534 33.80651 100</span></span>
<span id="cb320-13"><a href="advanced-miscellaneous-topics.html#cb320-13" aria-hidden="true"></a><span class="co">#&gt; runThread(3) 9.892849 10.957928 14.73565 11.726385 15.54481 30.18948 100</span></span>
<span id="cb320-14"><a href="advanced-miscellaneous-topics.html#cb320-14" aria-hidden="true"></a><span class="co">#&gt; runThread(4) 8.390000 9.344577 12.71494 9.855669 14.46360 36.42976 100</span></span>
<span id="cb320-15"><a href="advanced-miscellaneous-topics.html#cb320-15" aria-hidden="true"></a><span class="co">#&gt; runThread(5) 7.743284 8.525385 12.01956 10.095110 13.32747 33.56991 100</span></span>
<span id="cb320-16"><a href="advanced-miscellaneous-topics.html#cb320-16" aria-hidden="true"></a><span class="co">#&gt; runThread(6) 7.237351 8.058066 11.45158 8.898332 11.16910 41.71598 100</span></span>
<span id="cb320-17"><a href="advanced-miscellaneous-topics.html#cb320-17" aria-hidden="true"></a><span class="co">#&gt; runThread(7) 7.147392 7.801658 12.64134 9.426020 15.24159 43.21039 100</span></span>
<span id="cb320-18"><a href="advanced-miscellaneous-topics.html#cb320-18" aria-hidden="true"></a><span class="co">#&gt; runThread(8) 6.721420 7.542280 11.73857 9.032715 12.25422 31.74301 100</span></span>
<span id="cb320-19"><a href="advanced-miscellaneous-topics.html#cb320-19" aria-hidden="true"></a><span class="co">#&gt; runThread(9) 8.169215 9.164979 14.30070 9.960441 14.85892 39.81410 100</span></span>
<span id="cb320-20"><a href="advanced-miscellaneous-topics.html#cb320-20" aria-hidden="true"></a><span class="co">#&gt; runThread(10) 7.834896 9.214598 16.42769 11.906840 20.09549 39.07519 100</span></span>
<span id="cb320-21"><a href="advanced-miscellaneous-topics.html#cb320-21" aria-hidden="true"></a><span class="co">#&gt; runThread(11) 7.910969 8.837327 15.26403 9.976056 16.47040 43.97615 100</span></span>
<span id="cb320-22"><a href="advanced-miscellaneous-topics.html#cb320-22" aria-hidden="true"></a><span class="co">#&gt; runThread(12) 8.095937 8.524579 14.64636 9.975169 15.94399 34.84128 100</span></span>
<span id="cb320-23"><a href="advanced-miscellaneous-topics.html#cb320-23" aria-hidden="true"></a><span class="co">#&gt; runThread(13) 7.713107 8.582307 15.86284 12.621961 19.97018 34.43492 100</span></span>
<span id="cb320-24"><a href="advanced-miscellaneous-topics.html#cb320-24" aria-hidden="true"></a><span class="co">#&gt; runThread(14) 7.541924 8.420599 16.65419 11.219531 26.18666 39.54343 100</span></span>
<span id="cb320-25"><a href="advanced-miscellaneous-topics.html#cb320-25" aria-hidden="true"></a><span class="co">#&gt; runThread(15) 7.896863 8.376005 15.42602 11.019405 20.21669 43.64940 100</span></span>
<span id="cb320-26"><a href="advanced-miscellaneous-topics.html#cb320-26" aria-hidden="true"></a><span class="co">#&gt; runThread(16) 7.593061 9.427874 18.12144 14.903820 29.99918 37.54062 100</span></span>
<span id="cb320-11"><a href="advanced-miscellaneous-topics.html#cb320-11" aria-hidden="true"></a><span class="co">#&gt; runThread(1) 20.478632 21.238959 27.76242 23.806887 32.67021 61.74166 100</span></span>
<span id="cb320-12"><a href="advanced-miscellaneous-topics.html#cb320-12" aria-hidden="true"></a><span class="co">#&gt; runThread(2) 12.382024 13.296515 18.63013 15.698400 21.20031 48.97627 100</span></span>
<span id="cb320-13"><a href="advanced-miscellaneous-topics.html#cb320-13" aria-hidden="true"></a><span class="co">#&gt; runThread(3) 9.758075 10.551780 14.68611 12.750122 15.72262 27.19474 100</span></span>
<span id="cb320-14"><a href="advanced-miscellaneous-topics.html#cb320-14" aria-hidden="true"></a><span class="co">#&gt; runThread(4) 8.302496 9.188338 12.29240 10.429770 13.91077 25.11170 100</span></span>
<span id="cb320-15"><a href="advanced-miscellaneous-topics.html#cb320-15" aria-hidden="true"></a><span class="co">#&gt; runThread(5) 7.570208 8.403296 11.98074 10.073218 13.40568 33.56223 100</span></span>
<span id="cb320-16"><a href="advanced-miscellaneous-topics.html#cb320-16" aria-hidden="true"></a><span class="co">#&gt; runThread(6) 7.197837 8.040814 10.37280 8.962774 11.86176 21.34960 100</span></span>
<span id="cb320-17"><a href="advanced-miscellaneous-topics.html#cb320-17" aria-hidden="true"></a><span class="co">#&gt; runThread(7) 7.019912 8.176984 13.29175 10.411661 17.10394 33.58193 100</span></span>
<span id="cb320-18"><a href="advanced-miscellaneous-topics.html#cb320-18" aria-hidden="true"></a><span class="co">#&gt; runThread(8) 6.814645 8.462036 15.66626 11.357105 20.79003 37.21024 100</span></span>
<span id="cb320-19"><a href="advanced-miscellaneous-topics.html#cb320-19" aria-hidden="true"></a><span class="co">#&gt; runThread(9) 7.897544 9.981732 17.75131 13.465383 22.35634 44.87879 100</span></span>
<span id="cb320-20"><a href="advanced-miscellaneous-topics.html#cb320-20" aria-hidden="true"></a><span class="co">#&gt; runThread(10) 7.875182 9.151114 16.99347 12.023134 20.34318 39.12266 100</span></span>
<span id="cb320-21"><a href="advanced-miscellaneous-topics.html#cb320-21" aria-hidden="true"></a><span class="co">#&gt; runThread(11) 7.824056 8.911672 15.19120 12.085762 19.58844 40.93842 100</span></span>
<span id="cb320-22"><a href="advanced-miscellaneous-topics.html#cb320-22" aria-hidden="true"></a><span class="co">#&gt; runThread(12) 7.750037 8.936590 16.06225 11.450040 19.73431 45.88040 100</span></span>
<span id="cb320-23"><a href="advanced-miscellaneous-topics.html#cb320-23" aria-hidden="true"></a><span class="co">#&gt; runThread(13) 7.784521 9.299858 16.33838 13.143767 19.42095 38.70954 100</span></span>
<span id="cb320-24"><a href="advanced-miscellaneous-topics.html#cb320-24" aria-hidden="true"></a><span class="co">#&gt; runThread(14) 7.225379 9.376242 17.94548 13.285951 31.00986 38.27920 100</span></span>
<span id="cb320-25"><a href="advanced-miscellaneous-topics.html#cb320-25" aria-hidden="true"></a><span class="co">#&gt; runThread(15) 7.386251 8.896935 16.68194 11.767271 28.35965 33.54668 100</span></span>
<span id="cb320-26"><a href="advanced-miscellaneous-topics.html#cb320-26" aria-hidden="true"></a><span class="co">#&gt; runThread(16) 7.597419 9.869726 19.29197 18.183483 30.53563 35.07168 100</span></span>
<span id="cb320-27"><a href="advanced-miscellaneous-topics.html#cb320-27" aria-hidden="true"></a><span class="kw">autoplot</span>(bench)</span></code></pre></div>
<p><img src="rxode2-manual_files/figure-html/unnamed-chunk-180-1.png" width="100%" /></p>
<p>There can be a suite spot in speed vs number or cores. The system type
Expand Down Expand Up @@ -1329,7 +1329,7 @@ <h3><span class="header-section-number">13.4.2</span> A real life example<a href
<span id="cb321-67"><a href="advanced-miscellaneous-topics.html#cb321-67" aria-hidden="true"></a>Stoplapply &lt;-<span class="st"> </span><span class="kw">Sys.time</span>()</span>
<span id="cb321-68"><a href="advanced-miscellaneous-topics.html#cb321-68" aria-hidden="true"></a> </span>
<span id="cb321-69"><a href="advanced-miscellaneous-topics.html#cb321-69" aria-hidden="true"></a><span class="kw">print</span>(Stoplapply <span class="op">-</span><span class="st"> </span>Startlapply)</span>
<span id="cb321-70"><a href="advanced-miscellaneous-topics.html#cb321-70" aria-hidden="true"></a><span class="co">#&gt; Time difference of 13.68241 secs</span></span></code></pre></div>
<span id="cb321-70"><a href="advanced-miscellaneous-topics.html#cb321-70" aria-hidden="true"></a><span class="co">#&gt; Time difference of 14.80478 secs</span></span></code></pre></div>
<p>By applying some of the new parallel solving concepts you can simply
run the same simulation both with less code and faster:</p>
<div class="sourceCode" id="cb322"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb322-1"><a href="advanced-miscellaneous-topics.html#cb322-1" aria-hidden="true"></a>rx &lt;-<span class="st"> </span><span class="kw">rxode2</span>({</span>
Expand Down Expand Up @@ -1368,7 +1368,7 @@ <h3><span class="header-section-number">13.4.2</span> A real life example<a href
<span id="cb322-34"><a href="advanced-miscellaneous-topics.html#cb322-34" aria-hidden="true"></a>res &lt;-<span class="st"> </span><span class="kw">rxSolve</span>(rx, ev, <span class="dt">omega=</span>omega, <span class="dt">returnType=</span><span class="st">&quot;data.table&quot;</span>)</span>
<span id="cb322-35"><a href="advanced-miscellaneous-topics.html#cb322-35" aria-hidden="true"></a>endParallel &lt;-<span class="st"> </span><span class="kw">Sys.time</span>()</span>
<span id="cb322-36"><a href="advanced-miscellaneous-topics.html#cb322-36" aria-hidden="true"></a><span class="kw">print</span>(endParallel <span class="op">-</span><span class="st"> </span>startParallel)</span>
<span id="cb322-37"><a href="advanced-miscellaneous-topics.html#cb322-37" aria-hidden="true"></a><span class="co">#&gt; Time difference of 0.1143248 secs</span></span></code></pre></div>
<span id="cb322-37"><a href="advanced-miscellaneous-topics.html#cb322-37" aria-hidden="true"></a><span class="co">#&gt; Time difference of 0.1319878 secs</span></span></code></pre></div>
<p>You can see a striking time difference between the two methods; A few
things to keep in mind:</p>
<ul>
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Expand Up @@ -528,7 +528,7 @@ <h1><span class="header-section-number">Chapter 1</span> Introduction<a href="in
Yongchao</a> which was translated
based on the manual dated June 9, 2023.</p></li>
</ul>
<p>This book was assembled on Wed Jul 5 18:10:25 2023 with rxode2 version
<p>This book was assembled on Wed Jul 5 18:19:20 2023 with rxode2 version
2.0.13.9000 automatically by github actions.</p>
</div>
</section>
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Expand Up @@ -831,7 +831,7 @@ <h3><span class="header-section-number">6.4.1</span> How rxode2 numbers compartm
<p>If you look at the summary, you can see where rxode2 assigned the compartment number(s)</p>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb26-1"><a href="syntax.html#cb26-1" aria-hidden="true"></a><span class="kw">summary</span>(pbpk)</span></code></pre></div>
<pre><code>#&gt; rxode2 2.0.13.9000 model named rx_0d8d3c8f765b9ace54057fc27aa07891 model (✔ ready).
#&gt; DLL: /tmp/RtmpOvvReS/rxode2/rx_0d8d3c8f765b9ace54057fc27aa07891__.rxd/rx_0d8d3c8f765b9ace54057fc27aa07891_.so
#&gt; DLL: /tmp/RtmpC1rwH4/rxode2/rx_0d8d3c8f765b9ace54057fc27aa07891__.rxd/rx_0d8d3c8f765b9ace54057fc27aa07891_.so
#&gt; NULL
#&gt;
#&gt; Calculated Variables:
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This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.7.4) 5 JUL 2023 18:15
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.7.4) 5 JUL 2023 18:24
entering extended mode
restricted \write18 enabled.
%&-line parsing enabled.
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Overfull \hbox (242.99829pt too wide) in paragraph at lines 1326--1326
[]\T1/lmtt/m/n/10 #> DLL: /tmp/RtmpVVOFLL/rxode2/rx_0d8d3c8f765b9ace54057fc27aa
[]\T1/lmtt/m/n/10 #> DLL: /tmp/RtmpIJS9aW/rxode2/rx_0d8d3c8f765b9ace54057fc27aa
07891__.rxd/rx_0d8d3c8f765b9ace54057fc27aa07891_.so[]
[]

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Output written on rxode2-manual.pdf (243 pages, 1805349 bytes).
Output written on rxode2-manual.pdf (243 pages, 1808100 bytes).
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