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-rw-r--r--.Rbuildignore1
-rw-r--r--build.log4
-rw-r--r--docs/articles/FOCUS_D.html6
-rw-r--r--docs/articles/FOCUS_L.html42
-rw-r--r--docs/articles/web_only/benchmarks.html26
-rw-r--r--docs/articles/web_only/compiled_models.html10
-rw-r--r--docs/reference/add_err.html6
-rw-r--r--docs/reference/mkinfit.html26
-rw-r--r--docs/reference/mkinmod.html2
-rw-r--r--docs/reference/mkinpredict.html2
-rw-r--r--docs/reference/mmkin.html4
-rw-r--r--docs/reference/summary.mkinfit.html4
-rw-r--r--man/add_err.Rd3
-rw-r--r--tests/testthat/test_error_models.R1
-rw-r--r--vignettes/mkin_benchmarks.rdabin0 -> 801 bytes
-rw-r--r--vignettes/web_only/benchmarks.Rmd4
-rw-r--r--vignettes/web_only/benchmarks.html60
-rw-r--r--vignettes/web_only/mkin_benchmarks.rda (renamed from inst/benchmark_data/mkin_benchmarks.rda)bin797 -> 797 bytes
18 files changed, 103 insertions, 98 deletions
diff --git a/.Rbuildignore b/.Rbuildignore
index 934dc188..822bafab 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -22,6 +22,7 @@
^vignettes/figure
^vignettes/FOCUS_Z.tex$
^vignettes/mkin.tex$
+^vignettes/web_only/mkin_benchmarks.rda$
^mkin_.*\.tar\.gz
^mkin.tar$
^docs$
diff --git a/build.log b/build.log
index 7a0899cc..9728241a 100644
--- a/build.log
+++ b/build.log
@@ -6,7 +6,5 @@
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
- NB: this package now depends on R (>= 3.5.0)
- WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: 'mkin/inst/benchmark_data/mkin_benchmarks.rda'
-* building 'mkin_0.9.49.4.tar.gz'
+* building ‘mkin_0.9.49.4.tar.gz’
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 0ae6a391..4b82dd03 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -168,8 +168,8 @@
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.4
## R version used for fitting: 3.6.0
-## Date of fit: Thu May 2 12:40:29 2019
-## Date of summary: Thu May 2 12:40:29 2019
+## Date of fit: Thu May 2 17:42:41 2019
+## Date of summary: Thu May 2 17:42:41 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -177,7 +177,7 @@
##
## Model predictions using solution type deSolve
##
-## Fitted using 396 model solutions performed in 1.048 s
+## Fitted using 396 model solutions performed in 1.055 s
##
## Error model:
## Constant variance
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index b05963ae..05980b97 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -114,15 +114,15 @@
<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.4
## R version used for fitting: 3.6.0
-## Date of fit: Thu May 2 12:40:31 2019
-## Date of summary: Thu May 2 12:40:31 2019
+## Date of fit: Thu May 2 17:42:43 2019
+## Date of summary: Thu May 2 17:42:43 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 133 model solutions performed in 0.289 s
+## Fitted using 133 model solutions performed in 0.286 s
##
## Error model:
## Constant variance
@@ -215,8 +215,8 @@
## finite result is doubtful</code></pre>
<pre><code>## mkin version used for fitting: 0.9.49.4
## R version used for fitting: 3.6.0
-## Date of fit: Thu May 2 12:40:33 2019
-## Date of summary: Thu May 2 12:40:33 2019
+## Date of fit: Thu May 2 17:42:45 2019
+## Date of summary: Thu May 2 17:42:45 2019
##
##
## Warning: Optimisation did not converge:
@@ -228,7 +228,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 599 model solutions performed in 1.277 s
+## Fitted using 599 model solutions performed in 1.253 s
##
## Error model:
## Constant variance
@@ -319,15 +319,15 @@
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.4
## R version used for fitting: 3.6.0
-## Date of fit: Thu May 2 12:40:34 2019
-## Date of summary: Thu May 2 12:40:34 2019
+## Date of fit: Thu May 2 17:42:46 2019
+## Date of summary: Thu May 2 17:42:46 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 240 model solutions performed in 0.506 s
+## Fitted using 240 model solutions performed in 0.485 s
##
## Error model:
## Constant variance
@@ -394,8 +394,8 @@
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.4
## R version used for fitting: 3.6.0
-## Date of fit: Thu May 2 12:40:35 2019
-## Date of summary: Thu May 2 12:40:35 2019
+## Date of fit: Thu May 2 17:42:47 2019
+## Date of summary: Thu May 2 17:42:47 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -404,7 +404,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 587 model solutions performed in 1.273 s
+## Fitted using 587 model solutions performed in 1.22 s
##
## Error model:
## Constant variance
@@ -493,8 +493,8 @@
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.4
## R version used for fitting: 3.6.0
-## Date of fit: Thu May 2 12:40:37 2019
-## Date of summary: Thu May 2 12:40:37 2019
+## Date of fit: Thu May 2 17:42:49 2019
+## Date of summary: Thu May 2 17:42:49 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -503,7 +503,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 372 model solutions performed in 0.777 s
+## Fitted using 372 model solutions performed in 0.769 s
##
## Error model:
## Constant variance
@@ -598,15 +598,15 @@
<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.4
## R version used for fitting: 3.6.0
-## Date of fit: Thu May 2 12:40:38 2019
-## Date of summary: Thu May 2 12:40:38 2019
+## Date of fit: Thu May 2 17:42:50 2019
+## Date of summary: Thu May 2 17:42:50 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 146 model solutions performed in 0.298 s
+## Fitted using 146 model solutions performed in 0.293 s
##
## Error model:
## Constant variance
@@ -662,15 +662,15 @@
<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.4
## R version used for fitting: 3.6.0
-## Date of fit: Thu May 2 12:40:38 2019
-## Date of summary: Thu May 2 12:40:38 2019
+## Date of fit: Thu May 2 17:42:50 2019
+## Date of summary: Thu May 2 17:42:50 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 224 model solutions performed in 0.458 s
+## Fitted using 224 model solutions performed in 0.453 s
##
## Error model:
## Constant variance
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 2cafe5c9..0653517a 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -105,7 +105,7 @@
<a class="sourceLine" id="cb1-2" title="2">operating_system &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Sys.info">Sys.info</a></span>()[[<span class="st">"sysname"</span>]]</a>
<a class="sourceLine" id="cb1-3" title="3">mkin_version &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/character">as.character</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/packageDescription">packageVersion</a></span>(<span class="st">"mkin"</span>))</a>
<a class="sourceLine" id="cb1-4" title="4">system_string &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste0</a></span>(operating_system, <span class="st">", "</span>, cpu_model, <span class="st">", mkin version "</span>, mkin_version)</a>
-<a class="sourceLine" id="cb1-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/load">load</a></span>(<span class="st">"~/git/mkin/inst/benchmark_data/mkin_benchmarks.rda"</span>)</a>
+<a class="sourceLine" id="cb1-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/load">load</a></span>(<span class="st">"~/git/mkin/vignettes/web_only/mkin_benchmarks.rda"</span>)</a>
<a class="sourceLine" id="cb1-6" title="6">mkin_benchmarks[system_string, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"CPU"</span>, <span class="st">"OS"</span>, <span class="st">"mkin"</span>)] &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(cpu_model, operating_system, mkin_version)</a>
<a class="sourceLine" id="cb1-7" title="7"></a>
<a class="sourceLine" id="cb1-8" title="8"><span class="cf">if</span> (mkin_version <span class="op">&gt;</span><span class="st"> "0.9.48.1"</span>) {</a>
@@ -198,68 +198,68 @@
## 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 0.9.49.4 5.853
## 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 0.9.49.4 19.968
## 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 0.9.49.4 4.320
## 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 0.9.49.4 14.542
## 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 6.002
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.786
## 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 2.635
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.524
## 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 4.259
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.224
## 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 4.737
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.696
## 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 0.9.49.4 7.776
## 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 0.9.49.4 3.432
## 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</code></pre>
-<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/save">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/inst/benchmark_data/mkin_benchmarks.rda"</span>)</a></code></pre></div>
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.599</code></pre>
+<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/save">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</a></code></pre></div>
</div>
</div>
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index ee279f51..3174a067 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -163,9 +163,9 @@
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
## = TRUE): Observations with value of zero were removed from the data</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 3 deSolve, compiled 3 3.178 1.000 3.176 0
-## 1 deSolve, not compiled 3 28.700 9.031 28.685 0
-## 2 Eigenvalue based 3 4.401 1.385 4.398 0
+## 3 deSolve, compiled 3 3.199 1.000 3.198 0
+## 1 deSolve, not compiled 3 28.591 8.937 28.578 0
+## 2 Eigenvalue based 3 4.405 1.377 4.403 0
## user.child sys.child
## 3 0 0
## 1 0 0
@@ -214,8 +214,8 @@
## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
## value of zero were removed from the data</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 2 deSolve, compiled 3 4.549 1.000 4.547 0
-## 1 deSolve, not compiled 3 49.752 10.937 49.729 0
+## 2 deSolve, compiled 3 4.553 1.000 4.551 0
+## 1 deSolve, not compiled 3 49.844 10.948 49.822 0
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index 2eee6131..63aa358c 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -217,8 +217,7 @@
<span class='co'># Name the model in the list of models (with only one member in this case) for</span>
<span class='co'># nicer plotting later on. Be quiet and use only one core not to offend CRAN</span>
-<span class='co'># checks</span>
-<span class='no'>f_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>m_SFO_SFO</span>),
+<span class='co'># checks</span></div><div class='input'><span class='no'>f_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>m_SFO_SFO</span>),
<span class='no'>d_SFO_SFO_err</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>,
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
@@ -229,8 +228,7 @@
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_SFO_SFO</span><span class='kw'>[[</span><span class='fl'>3</span>]], <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='add_err-2.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># If we use single brackets, we should give two indices (model and dataset),</span>
<span class='co'># and plot.mmkin is used</span>
-<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><div class='img'><img src='add_err-3.png' alt='' width='700' height='433' /></div><div class='input'>
-</div></pre>
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><div class='img'><img src='add_err-3.png' alt='' width='700' height='433' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 7693287e..cd4f91e5 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -362,8 +362,8 @@ Per default, parameters in the kinetic models are internally transformed in
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Thu May 2 12:38:56 2019
-#&gt; Date of summary: Thu May 2 12:38:56 2019
+#&gt; Date of fit: Thu May 2 17:41:11 2019
+#&gt; Date of summary: Thu May 2 17:41:11 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -443,7 +443,7 @@ Per default, parameters in the kinetic models are internally transformed in
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.551 0.000 1.552 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
+#&gt; 1.54 0.00 1.54 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
#&gt;
@@ -520,7 +520,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; Negative log-likelihood at call 152: 97.22429
#&gt; Optimisation successfully terminated.
#&gt; User System verstrichen
-#&gt; 1.152 0.000 1.153 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
+#&gt; 1.1 0.0 1.1 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
#&gt;
@@ -552,8 +552,8 @@ Per default, parameters in the kinetic models are internally transformed in
<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Thu May 2 12:39:13 2019
-#&gt; Date of summary: Thu May 2 12:39:13 2019
+#&gt; Date of fit: Thu May 2 17:41:27 2019
+#&gt; Date of summary: Thu May 2 17:41:27 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -561,7 +561,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 404 model solutions performed in 1.178 s
+#&gt; Fitted using 404 model solutions performed in 1.067 s
#&gt;
#&gt; Error model:
#&gt; Constant variance
@@ -670,8 +670,8 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; 120 m1 25.15 28.78984 -3.640e+00
#&gt; 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Thu May 2 12:39:14 2019
-#&gt; Date of summary: Thu May 2 12:39:14 2019
+#&gt; Date of fit: Thu May 2 17:41:28 2019
+#&gt; Date of summary: Thu May 2 17:41:28 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -679,7 +679,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 558 model solutions performed in 1.518 s
+#&gt; Fitted using 558 model solutions performed in 1.447 s
#&gt;
#&gt; Error model:
#&gt; Variance unique to each observed variable
@@ -800,8 +800,8 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; 120 m1 25.15 28.80430 -3.654e+00
#&gt; 120 m1 33.31 28.80430 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Thu May 2 12:39:18 2019
-#&gt; Date of summary: Thu May 2 12:39:18 2019
+#&gt; Date of fit: Thu May 2 17:41:32 2019
+#&gt; Date of summary: Thu May 2 17:41:32 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -809,7 +809,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 844 model solutions performed in 3.501 s
+#&gt; Fitted using 844 model solutions performed in 3.407 s
#&gt;
#&gt; Error model:
#&gt; Two-component variance function
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index b545dad1..0b96c6cb 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -234,7 +234,7 @@ For the definition of model types and their parameters, the equations given
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; Compilation argument:
-#&gt; /usr/lib/R/bin/R CMD SHLIB file35fe67db2b2a.c 2&gt; file35fe67db2b2a.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file7e6c2d3bf9bc.c 2&gt; file7e6c2d3bf9bc.c.err.txt
#&gt; Program source:
#&gt; 1: #include &lt;R.h&gt;
#&gt; 2:
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 4b75603f..e3e17e78 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -333,7 +333,7 @@
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.002 0.000 0.001 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
+#&gt; 0.002 0.000 0.002 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index a16cb6d7..d61c0565 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -194,8 +194,8 @@
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
<span class='no'>time_default</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.040 0.035 7.515 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 21.597 0.000 21.609 </div><div class='input'>
+#&gt; 0.044 0.026 7.470 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 21.144 0.004 21.161 </div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
#&gt; 0.7340481 0.2659519 0.7505683 0.2494317
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 1a08132f..7e767ab3 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -211,8 +211,8 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Thu May 2 12:40:14 2019
-#&gt; Date of summary: Thu May 2 12:40:14 2019
+#&gt; Date of fit: Thu May 2 17:42:27 2019
+#&gt; Date of summary: Thu May 2 17:42:27 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
diff --git a/man/add_err.Rd b/man/add_err.Rd
index 506c6fdc..00b50878 100644
--- a/man/add_err.Rd
+++ b/man/add_err.Rd
@@ -81,6 +81,7 @@ names(d_SFO_SFO_err) <- paste("Dataset", 1:3)
# Name the model in the list of models (with only one member in this case) for
# nicer plotting later on. Be quiet and use only one core not to offend CRAN
# checks
+\dontrun{
f_SFO_SFO <- mmkin(list("SFO-SFO" = m_SFO_SFO),
d_SFO_SFO_err, cores = 1,
quiet = TRUE)
@@ -95,6 +96,6 @@ plot(f_SFO_SFO[[3]], show_residuals = TRUE)
# If we use single brackets, we should give two indices (model and dataset),
# and plot.mmkin is used
plot(f_SFO_SFO[1, 3])
-
+}
}
\keyword{ manip }
diff --git a/tests/testthat/test_error_models.R b/tests/testthat/test_error_models.R
index 1ec48605..d7a5cea8 100644
--- a/tests/testthat/test_error_models.R
+++ b/tests/testthat/test_error_models.R
@@ -159,6 +159,7 @@ test_that("Reweighting method 'tc' produces reasonable variance estimates", {
# Doing more takes a lot of computing power
skip_on_travis()
+ skip_on_cran()
f_met_2_15_tc_e4 <- mmkin(list(m_synth_DFOP_lin), d_met_2_15, quiet = TRUE,
error_model = "tc", cores = n_cores)
diff --git a/vignettes/mkin_benchmarks.rda b/vignettes/mkin_benchmarks.rda
new file mode 100644
index 00000000..cb16a6d3
--- /dev/null
+++ b/vignettes/mkin_benchmarks.rda
Binary files differ
diff --git a/vignettes/web_only/benchmarks.Rmd b/vignettes/web_only/benchmarks.Rmd
index 83381717..4849635f 100644
--- a/vignettes/web_only/benchmarks.Rmd
+++ b/vignettes/web_only/benchmarks.Rmd
@@ -29,7 +29,7 @@ cpu_model <- benchmarkme::get_cpu()$model_name
operating_system <- Sys.info()[["sysname"]]
mkin_version <- as.character(packageVersion("mkin"))
system_string <- paste0(operating_system, ", ", cpu_model, ", mkin version ", mkin_version)
-load("~/git/mkin/inst/benchmark_data/mkin_benchmarks.rda")
+load("~/git/mkin/vignettes/web_only/mkin_benchmarks.rda")
mkin_benchmarks[system_string, c("CPU", "OS", "mkin")] <- c(cpu_model, operating_system, mkin_version)
if (mkin_version > "0.9.48.1") {
@@ -86,5 +86,5 @@ mkin_benchmarks[system_string, paste0("t", 1:11)] <- c(t1, t2, t3, t4, t5, t6, t
mkin_benchmarks
-save(mkin_benchmarks, file = "~/git/mkin/inst/benchmark_data/mkin_benchmarks.rda")
+save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")
```
diff --git a/vignettes/web_only/benchmarks.html b/vignettes/web_only/benchmarks.html
index b35a9695..054b4afc 100644
--- a/vignettes/web_only/benchmarks.html
+++ b/vignettes/web_only/benchmarks.html
@@ -11,7 +11,7 @@
<meta name="author" content="Johannes Ranke" />
-<meta name="date" content="2019-04-09" />
+<meta name="date" content="2019-05-02" />
<title>Benchmark timings for mkin on various systems</title>
@@ -1280,7 +1280,7 @@ window.initializeCodeFolding = function(show) {
var currentIndex = 1;
// select all R code blocks
- var rCodeBlocks = $('pre.r, pre.python, pre.bash, pre.sql, pre.cpp, pre.stan');
+ var rCodeBlocks = $('pre.r, pre.python, pre.bash, pre.sql, pre.cpp, pre.stan, pre.julia');
rCodeBlocks.each(function() {
// create a collapsable div to wrap the code in
@@ -1387,9 +1387,7 @@ h6 {
</style>
-</head>
-<body>
<style type="text/css">
.main-container {
@@ -1421,8 +1419,6 @@ summary {
-<div class="container-fluid main-container">
-
<!-- tabsets -->
<style type="text/css">
@@ -1588,6 +1584,16 @@ div.tocify {
</style>
+
+
+</head>
+
+<body>
+
+
+<div class="container-fluid main-container">
+
+
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="col-xs-12 col-sm-4 col-md-3">
@@ -1613,8 +1619,8 @@ div.tocify {
<h1 class="title toc-ignore">Benchmark timings for mkin on various systems</h1>
-<h4 class="author"><em>Johannes Ranke</em></h4>
-<h4 class="date"><em>2019-04-09</em></h4>
+<h4 class="author">Johannes Ranke</h4>
+<h4 class="date">2019-05-02</h4>
</div>
@@ -1626,7 +1632,7 @@ div.tocify {
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/inst/benchmark_data/mkin_benchmarks.rda&quot;)
+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)
if (mkin_version &gt; &quot;0.9.48.1&quot;) {
@@ -1636,9 +1642,10 @@ if (mkin_version &gt; &quot;0.9.48.1&quot;) {
}</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;]]
-
-# One metabolite
+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><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
+## false convergence (8)</code></pre>
+<pre class="r"><code># One metabolite
SFO_SFO &lt;- mkinmod(
parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;),
m1 = mkinsub(&quot;SFO&quot;))</code></pre>
@@ -1653,9 +1660,8 @@ SFO_SFO &lt;- mkinmod(
<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
-
-## 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]], ...):
@@ -1719,68 +1725,68 @@ mkin_benchmarks</code></pre>
## 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 6.712
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.023
## 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 23.082
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.409
## 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 3.595
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.283
## 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 11.975
+## 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 4.881
+## 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 1.981
+## 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 3.32
+## 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 3.309
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.557
## 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 6.075
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.739
## 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 2.518
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.413
## 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 4.289</code></pre>
-<pre class="r"><code>save(mkin_benchmarks, file = &quot;~/git/mkin/inst/benchmark_data/mkin_benchmarks.rda&quot;)</code></pre>
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.588</code></pre>
+<pre class="r"><code>save(mkin_benchmarks, file = &quot;~/git/mkin/vignettes/mkin_benchmarks.rda&quot;)</code></pre>
</div>
diff --git a/inst/benchmark_data/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda
index 388a7886..388a7886 100644
--- a/inst/benchmark_data/mkin_benchmarks.rda
+++ b/vignettes/web_only/mkin_benchmarks.rda
Binary files differ

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