From 6211f3ef4995657798686d8d4ab43ed9406e8a08 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 12 May 2020 16:34:00 +0200
Subject: Update vignettes and docs

---
 vignettes/web_only/benchmarks.html | 179 +++++++++++++++++--------------------
 1 file changed, 82 insertions(+), 97 deletions(-)

(limited to 'vignettes/web_only/benchmarks.html')

diff --git a/vignettes/web_only/benchmarks.html b/vignettes/web_only/benchmarks.html
index 337ccbb3..5c9cc67e 100644
--- a/vignettes/web_only/benchmarks.html
+++ b/vignettes/web_only/benchmarks.html
@@ -11,9 +11,9 @@
 
 <meta name="author" content="Johannes Ranke" />
 
-<meta name="date" content="2020-05-11" />
+<meta name="date" content="2020-05-12" />
 
-<title>Benchmark timings for mkin on various systems</title>
+<title>Benchmark timings for mkin</title>
 
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@@ -1581,40 +1581,43 @@ div.tocify {
 
 
 
-<h1 class="title toc-ignore">Benchmark timings for mkin on various systems</h1>
+<h1 class="title toc-ignore">Benchmark timings for mkin</h1>
 <h4 class="author">Johannes Ranke</h4>
-<h4 class="date">2020-05-11</h4>
+<h4 class="date">2020-05-12</h4>
 
 </div>
 
 
-<div id="systems" class="section level2">
-<h2>Systems</h2>
-<p>Each system is characterized by its CPU type, the operating system type and the mkin version.</p>
+<p>Each system is characterized by its CPU type, the operating system type and the mkin version. Currently only values for one system are available.</p>
 <pre class="r"><code>cpu_model &lt;- benchmarkme::get_cpu()$model_name
 operating_system &lt;- Sys.info()[[&quot;sysname&quot;]]
 mkin_version &lt;- as.character(packageVersion(&quot;mkin&quot;))
 system_string &lt;- paste0(operating_system, &quot;, &quot;, cpu_model, &quot;, mkin version &quot;, mkin_version)
 load(&quot;~/git/mkin/vignettes/web_only/mkin_benchmarks.rda&quot;)
-mkin_benchmarks[system_string, c(&quot;CPU&quot;, &quot;OS&quot;, &quot;mkin&quot;)] &lt;- c(cpu_model, operating_system, mkin_version)
+mkin_benchmarks[system_string, c(&quot;CPU&quot;, &quot;OS&quot;, &quot;mkin&quot;)] &lt;-
+  c(cpu_model, operating_system, mkin_version)
 
 if (mkin_version &gt; &quot;0.9.48.1&quot;) {
-  mmkin_bench &lt;- function(models, datasets, error_model = &quot;const&quot;) mmkin(models, datasets, error_model = error_model, cores = 1, quiet = TRUE)
+  mmkin_bench &lt;- function(models, datasets, error_model = &quot;const&quot;) {
+    mmkin(models, datasets, error_model = error_model, cores = 1, quiet = TRUE)
+  }
 } else {
-  mmkin_bench &lt;- function(models, datasets, error_model = NULL) mmkin(models, datasets, reweight.method = error_model, cores = 1, quiet = TRUE)
+  mmkin_bench &lt;- function(models, datasets, error_model = NULL) {
+    mmkin(models, datasets, reweight.method = error_model, cores = 1, quiet = TRUE)
+  }
 }</code></pre>
+<div id="test-cases" class="section level2">
+<h2>Test cases</h2>
+<p>Parent only:</p>
 <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:
-## 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_datasets &lt;- list(FOCUS_C, FOCUS_D)
+
+t1 &lt;- system.time(mmkin_bench(c(&quot;SFO&quot;, &quot;FOMC&quot;, &quot;DFOP&quot;, &quot;HS&quot;), parent_datasets))[[&quot;elapsed&quot;]]
+t2 &lt;- system.time(mmkin_bench(c(&quot;SFO&quot;, &quot;FOMC&quot;, &quot;DFOP&quot;, &quot;HS&quot;), parent_datasets,
+    error_model = &quot;tc&quot;))[[&quot;elapsed&quot;]]</code></pre>
+<p>One metabolite:</p>
+<pre class="r"><code>SFO_SFO &lt;- mkinmod(
   parent = mkinsub(&quot;SFO&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>
@@ -1627,11 +1630,12 @@ SFO_SFO &lt;- mkinmod(
   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_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;),
+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;]]</code></pre>
+<p>Two metabolites, synthetic data:</p>
+<pre class="r"><code>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;),
                            use_of_ff = &quot;max&quot;, quiet = TRUE)
@@ -1648,78 +1652,59 @@ DFOP_par_c &lt;- synthetic_data_for_UBA_2014[[12]]$data
 t6 &lt;- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))[&quot;elapsed&quot;]
 t7 &lt;- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))[&quot;elapsed&quot;]
 
-t8 &lt;- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = &quot;tc&quot;))[&quot;elapsed&quot;]
-t9 &lt;- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = &quot;tc&quot;))[&quot;elapsed&quot;]
-
-t10 &lt;- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = &quot;obs&quot;))[&quot;elapsed&quot;]
-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[, -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 5.936
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50   1.678
-##                                                                         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 20.545
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50    3.837
-##                                                                        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 4.446
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50   1.372
-##                                                                         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 15.335
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50    6.071
-##                                                                        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   2.709 0.746
-##                                                                        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   1.208 1.268
-##                                                                         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  7.763
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50    2.836
-##                                                                       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 3.427
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50   2.019
-##                                                                        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  5.626
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50    2.951</code></pre>
-<pre class="r"><code>save(mkin_benchmarks, file = &quot;~/git/mkin/vignettes/mkin_benchmarks.rda&quot;)</code></pre>
+t8 &lt;- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
+    error_model = &quot;tc&quot;))[&quot;elapsed&quot;]
+t9 &lt;- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
+    error_model = &quot;tc&quot;))[&quot;elapsed&quot;]
+
+t10 &lt;- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
+    error_model = &quot;obs&quot;))[&quot;elapsed&quot;]
+t11 &lt;- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
+    error_model = &quot;obs&quot;))[&quot;elapsed&quot;]</code></pre>
+<pre class="r"><code>mkin_benchmarks[system_string, paste0(&quot;t&quot;, 1:11)] &lt;-
+  c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
+save(mkin_benchmarks, file = &quot;~/git/mkin/vignettes/web_only/mkin_benchmarks.rda&quot;)</code></pre>
+</div>
+<div id="results" class="section level2">
+<h2>Results</h2>
+<p>Currently, we only have benchmark information on one system, therefore only the mkin version is shown with the results below. Timings are in seconds, shorter is better.</p>
+<p>Benchmarks for all available error models are shown.</p>
+<div id="parent-only" class="section level3">
+<h3>Parent only</h3>
+<p>Constant variance and two-component error model:</p>
+<pre class="r"><code>print(mkin_benchmarks[, c(&quot;mkin&quot;, &quot;t1&quot;, &quot;t2&quot;)], row.names = FALSE)</code></pre>
+<pre><code>##      mkin    t1     t2
+##  0.9.48.1 3.610 11.019
+##  0.9.49.1 8.184 22.889
+##  0.9.49.2 7.064 12.558
+##  0.9.49.3 7.296 21.239
+##  0.9.49.4 5.936 20.545
+##  0.9.50.2 1.547  3.955</code></pre>
+</div>
+<div id="one-metabolite" class="section level3">
+<h3>One metabolite</h3>
+<p>Constant variance, variance by variable and two-component error model:</p>
+<pre class="r"><code>print(mkin_benchmarks[, c(&quot;mkin&quot;, &quot;t3&quot;, &quot;t4&quot;, &quot;t5&quot;)], row.names = FALSE)</code></pre>
+<pre><code>##      mkin    t3     t4    t5
+##  0.9.48.1 3.764 14.347 9.495
+##  0.9.49.1 4.649 13.789 6.395
+##  0.9.49.2 4.786  8.461 5.675
+##  0.9.49.3 4.510 13.805 7.386
+##  0.9.49.4 4.446 15.335 6.002
+##  0.9.50.2 1.379  6.176 2.713</code></pre>
+</div>
+<div id="two-metabolites" class="section level3">
+<h3>Two metabolites</h3>
+<p>Two different datasets, for each constant variance, variance by variable and two-component error model are shown:</p>
+<pre class="r"><code>print(mkin_benchmarks[, c(&quot;mkin&quot;, paste0(&quot;t&quot;, 6:11))], row.names = FALSE)</code></pre>
+<pre><code>##      mkin    t6    t7    t8     t9   t10    t11
+##  0.9.48.1 2.623 4.587 7.525 16.621 8.576 31.267
+##  0.9.49.1 2.542 4.128 4.632  8.171 3.676  5.636
+##  0.9.49.2 2.723 4.478 4.862  7.618 3.579  5.574
+##  0.9.49.3 2.643 4.374  7.02 11.124 5.388  7.365
+##  0.9.49.4 2.635 4.259 4.737  7.763 3.427  5.626
+##  0.9.50.2 0.742 1.202 1.269   2.97 2.028  2.959</code></pre>
+</div>
 </div>
 
 
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