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1 files changed, 112 insertions, 131 deletions
diff --git a/vignettes/web_only/benchmarks.html b/vignettes/web_only/benchmarks.html
index 054b4afc..c80a7e44 100644
--- a/vignettes/web_only/benchmarks.html
+++ b/vignettes/web_only/benchmarks.html
@@ -1,17 +1,17 @@
<!DOCTYPE html>
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
<head>
<meta charset="utf-8" />
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
+<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<meta name="author" content="Johannes Ranke" />
-<meta name="date" content="2019-05-02" />
+<meta name="date" content="2020-05-10" />
<title>Benchmark timings for mkin on various systems</title>
@@ -69,8 +69,6 @@ overflow: auto;
margin-left: 2%;
position: fixed;
border: 1px solid #ccc;
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@@ -98,10 +96,15 @@ font-size: 12px;
.tocify-subheader .tocify-subheader {
text-indent: 30px;
}
-
.tocify-subheader .tocify-subheader .tocify-subheader {
text-indent: 40px;
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+.tocify-subheader .tocify-subheader .tocify-subheader .tocify-subheader {
+text-indent: 50px;
+}
+.tocify-subheader .tocify-subheader .tocify-subheader .tocify-subheader .tocify-subheader {
+text-indent: 60px;
+}
.tocify .tocify-item > a, .tocify .nav-list .nav-header {
margin: 0px;
@@ -504,13 +507,13 @@ float: none;
item.append($("<a/>", {
- "text": self.text()
+ "html": self.html()
}));
} else {
- item.text(self.text());
+ item.html(self.html());
}
@@ -1285,7 +1288,7 @@ window.initializeCodeFolding = function(show) {
// create a collapsable div to wrap the code in
var div = $('<div class="collapse r-code-collapse"></div>');
- if (show)
+ if (show || $(this)[0].classList.contains('fold-show'))
div.addClass('in');
var id = 'rcode-643E0F36' + currentIndex++;
div.attr('id', id);
@@ -1401,7 +1404,6 @@ code {
}
img {
max-width:100%;
- height: auto;
}
.tabbed-pane {
padding-top: 12px;
@@ -1463,6 +1465,7 @@ summary {
border: none;
display: inline-block;
border-radius: 4px;
+ background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
@@ -1475,56 +1478,12 @@ summary {
}
</style>
-<script>
-$(document).ready(function () {
- window.buildTabsets("TOC");
-});
-
-$(document).ready(function () {
- $('.tabset-dropdown > .nav-tabs > li').click(function () {
- $(this).parent().toggleClass('nav-tabs-open')
- });
-});
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-
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<style type="text/css">
.code-folding-btn { margin-bottom: 4px; }
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- window.initializeCodeFolding("show" === "show");
-});
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-
-
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-$(document).ready(function () {
- // move toc-ignore selectors from section div to header
- $('div.section.toc-ignore')
- .removeClass('toc-ignore')
- .children('h1,h2,h3,h4,h5').addClass('toc-ignore');
- // establish options
- var options = {
- selectors: "h1,h2,h3",
- theme: "bootstrap3",
- context: '.toc-content',
- hashGenerator: function (text) {
- return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase();
- },
- ignoreSelector: ".toc-ignore",
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-});
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<style type="text/css">
@@ -1538,6 +1497,12 @@ $(document).ready(function () {
}
}
+@media print {
+.toc-content {
+ /* see https://github.com/w3c/csswg-drafts/issues/4434 */
+ float: right;
+}
+}
.toc-content {
padding-left: 30px;
@@ -1573,8 +1538,6 @@ div.tocify {
.tocify-subheader .tocify-item {
font-size: 0.90em;
- padding-left: 25px;
- text-indent: 0;
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.tocify .list-group-item {
@@ -1620,7 +1583,7 @@ div.tocify {
<h1 class="title toc-ignore">Benchmark timings for mkin on various systems</h1>
<h4 class="author">Johannes Ranke</h4>
-<h4 class="date">2019-05-02</h4>
+<h4 class="date">2020-05-10</h4>
</div>
@@ -1640,11 +1603,16 @@ if (mkin_version &gt; &quot;0.9.48.1&quot;) {
} else {
mmkin_bench &lt;- function(models, datasets, error_model = NULL) mmkin(models, datasets, reweight.method = error_model, cores = 1, quiet = TRUE)
}</code></pre>
-<pre class="r"><code># Parent only
-t1 &lt;- system.time(mmkin_bench(c(&quot;SFO&quot;, &quot;FOMC&quot;, &quot;DFOP&quot;, &quot;HS&quot;), list(FOCUS_2006_C, FOCUS_2006_D)))[[&quot;elapsed&quot;]]
-t2 &lt;- system.time(mmkin_bench(c(&quot;SFO&quot;, &quot;FOMC&quot;, &quot;DFOP&quot;, &quot;HS&quot;), list(FOCUS_2006_C, FOCUS_2006_D), error_model = &quot;tc&quot;))[[&quot;elapsed&quot;]]</code></pre>
+<pre class="r"><code>FOCUS_C &lt;- FOCUS_2006_C
+FOCUS_D &lt;- subset(FOCUS_2006_D, value != 0)
+# Parent only
+t1 &lt;- system.time(mmkin_bench(c(&quot;SFO&quot;, &quot;FOMC&quot;, &quot;DFOP&quot;, &quot;HS&quot;), list(FOCUS_C, FOCUS_D)))[[&quot;elapsed&quot;]]
+t2 &lt;- system.time(mmkin_bench(c(&quot;SFO&quot;, &quot;FOMC&quot;, &quot;DFOP&quot;, &quot;HS&quot;), list(FOCUS_C, FOCUS_D), error_model = &quot;tc&quot;))[[&quot;elapsed&quot;]]</code></pre>
<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
-## false convergence (8)</code></pre>
+## iteration limit reached without convergence (10)
+
+## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
+## iteration limit reached without convergence (10)</code></pre>
<pre class="r"><code># One metabolite
SFO_SFO &lt;- mkinmod(
parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;),
@@ -1658,25 +1626,11 @@ SFO_SFO &lt;- mkinmod(
parent = mkinsub(&quot;FOMC&quot;, &quot;m1&quot;),
m1 = mkinsub(&quot;SFO&quot;))</code></pre>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<pre class="r"><code>t3 &lt;- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D)))[[&quot;elapsed&quot;]]</code></pre>
-<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
-## Observations with value of zero were removed from the data</code></pre>
-<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
-## Observations with value of zero were removed from the data
-
-## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
-## Observations with value of zero were removed from the data</code></pre>
-<pre class="r"><code>t4 &lt;- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(subset(FOCUS_2006_D, value != 0)), error_model = &quot;tc&quot;))[[&quot;elapsed&quot;]]
-t5 &lt;- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D), error_model = &quot;obs&quot;))[[&quot;elapsed&quot;]]</code></pre>
-<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
-## Observations with value of zero were removed from the data
-
-## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
-## Observations with value of zero were removed from the data
-
-## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
-## Observations with value of zero were removed from the data</code></pre>
-<pre class="r"><code># Two metabolites, synthetic data
+<pre class="r"><code>t3 &lt;- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[[&quot;elapsed&quot;]]
+t4 &lt;- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D), error_model = &quot;tc&quot;))[[&quot;elapsed&quot;]]
+t5 &lt;- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D), error_model = &quot;obs&quot;))[[&quot;elapsed&quot;]]
+
+# Two metabolites, synthetic data
m_synth_SFO_lin &lt;- mkinmod(parent = mkinsub(&quot;SFO&quot;, &quot;M1&quot;),
M1 = mkinsub(&quot;SFO&quot;, &quot;M2&quot;),
M2 = mkinsub(&quot;SFO&quot;),
@@ -1701,91 +1655,70 @@ t10 &lt;- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_
t11 &lt;- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = &quot;obs&quot;))[&quot;elapsed&quot;]
mkin_benchmarks[system_string, paste0(&quot;t&quot;, 1:11)] &lt;- c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
-mkin_benchmarks</code></pre>
-<pre><code>## CPU
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 AMD Ryzen 7 1700 Eight-Core Processor
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 AMD Ryzen 7 1700 Eight-Core Processor
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 AMD Ryzen 7 1700 Eight-Core Processor
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 AMD Ryzen 7 1700 Eight-Core Processor
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 AMD Ryzen 7 1700 Eight-Core Processor
-## OS
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 Linux
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 Linux
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 Linux
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 Linux
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 Linux
-## mkin
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 0.9.48.1
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 0.9.49.1
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 0.9.49.2
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 0.9.49.3
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 0.9.49.4
-## t1
+mkin_benchmarks[, -c(1:3)]</code></pre>
+<pre><code>## t1
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.610
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.023
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 1.658
## t2
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.409
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 3.820
## t3
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.283
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 3.424
## t4
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 8.461
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 14.531
-## t5
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.744
-## t6
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.518
-## t7
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.211
-## t8
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.02
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.557
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 18.375
+## t5 t6
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 2.623
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 2.542
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 2.723
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 2.643
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002 2.635
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 7.480 2.188
+## t7 t8
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 7.525
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 4.632
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 4.862
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374 7.02
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259 4.737
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 3.69 3.87
## t9
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.171
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.618
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.739
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.763
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 8.872
## t10
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.413
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 6.257
## t11
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 5.636
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.574
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.365
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.588</code></pre>
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.626
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 9.289</code></pre>
<pre class="r"><code>save(mkin_benchmarks, file = &quot;~/git/mkin/vignettes/mkin_benchmarks.rda&quot;)</code></pre>
</div>
@@ -1809,6 +1742,54 @@ $(document).ready(function () {
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+<!-- tabsets -->
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+ window.buildTabsets("TOC");
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+ $('.tabset-dropdown > .nav-tabs > li').click(function () {
+ $(this).parent().toggleClass('nav-tabs-open')
+ });
+});
+</script>
+
+<!-- code folding -->
+<script>
+$(document).ready(function () {
+ window.initializeCodeFolding("show" === "show");
+});
+</script>
+
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+$(document).ready(function () {
+
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+ $('div.section.toc-ignore')
+ .removeClass('toc-ignore')
+ .children('h1,h2,h3,h4,h5').addClass('toc-ignore');
+
+ // establish options
+ var options = {
+ selectors: "h1,h2,h3",
+ theme: "bootstrap3",
+ context: '.toc-content',
+ hashGenerator: function (text) {
+ return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase();
+ },
+ ignoreSelector: ".toc-ignore",
+ scrollTo: 0
+ };
+ options.showAndHide = true;
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