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-rw-r--r--docs/articles/FOCUS_D.html8
-rw-r--r--docs/articles/FOCUS_L.html44
-rw-r--r--docs/articles/mkin.html2
-rw-r--r--docs/articles/twa.html2
-rw-r--r--docs/articles/web_only/FOCUS_Z.html2
-rw-r--r--docs/articles/web_only/NAFTA_examples.html2
-rw-r--r--docs/articles/web_only/benchmarks.html24
-rw-r--r--docs/articles/web_only/compiled_models.html12
-rw-r--r--docs/news/index.html7
-rw-r--r--docs/reference/mkinerrplot-1.pngbin0 -> 35936 bytes
-rw-r--r--docs/reference/mkinerrplot.html250
-rw-r--r--docs/reference/mkinfit.html28
-rw-r--r--docs/reference/mkinmod.html2
-rw-r--r--docs/reference/mkinpredict.html6
-rw-r--r--docs/reference/mmkin.html4
-rw-r--r--docs/reference/plot.mkinfit-1.pngbin45182 -> 45207 bytes
-rw-r--r--docs/reference/plot.mkinfit-2.pngbin52916 -> 52884 bytes
-rw-r--r--docs/reference/plot.mkinfit-3.pngbin43718 -> 51737 bytes
-rw-r--r--docs/reference/plot.mkinfit-4.pngbin59800 -> 43712 bytes
-rw-r--r--docs/reference/plot.mkinfit-5.pngbin0 -> 59934 bytes
-rw-r--r--docs/reference/plot.mkinfit-6.pngbin0 -> 65811 bytes
-rw-r--r--docs/reference/plot.mkinfit.html29
-rw-r--r--docs/reference/plot.mmkin-2.pngbin34829 -> 34725 bytes
-rw-r--r--docs/reference/plot.mmkin-4.pngbin0 -> 37126 bytes
-rw-r--r--docs/reference/plot.mmkin.html19
-rw-r--r--docs/reference/summary.mkinfit.html6
26 files changed, 360 insertions, 87 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 644a35b5..ba694065 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -88,7 +88,7 @@
<h1>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-05-07</h4>
+ <h4 class="date">2019-05-08</h4>
<div class="hidden name"><code>FOCUS_D.Rmd</code></div>
@@ -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: Tue May 7 08:37:46 2019
-## Date of summary: Tue May 7 08:37:46 2019
+## Date of fit: Wed May 8 20:52:27 2019
+## Date of summary: Wed May 8 20:52:27 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 389 model solutions performed in 1.018 s
+## Fitted using 389 model solutions performed in 0.998 s
##
## Error model:
## Constant variance
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 2cffb323..6771bf63 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -88,7 +88,7 @@
<h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-05-07</h4>
+ <h4 class="date">2019-05-08</h4>
<div class="hidden name"><code>FOCUS_L.Rmd</code></div>
@@ -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: Tue May 7 08:37:48 2019
-## Date of summary: Tue May 7 08:37:48 2019
+## Date of fit: Wed May 8 20:52:29 2019
+## Date of summary: Wed May 8 20:52:29 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 133 model solutions performed in 0.284 s
+## Fitted using 133 model solutions performed in 0.276 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: Tue May 7 08:37:50 2019
-## Date of summary: Tue May 7 08:37:50 2019
+## Date of fit: Wed May 8 20:52:31 2019
+## Date of summary: Wed May 8 20:52:31 2019
##
##
## Warning: Optimisation did not converge:
@@ -228,7 +228,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 899 model solutions performed in 1.913 s
+## Fitted using 899 model solutions performed in 1.868 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: Tue May 7 08:37:51 2019
-## Date of summary: Tue May 7 08:37:51 2019
+## Date of fit: Wed May 8 20:52:32 2019
+## Date of summary: Wed May 8 20:52:32 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 239 model solutions performed in 0.494 s
+## Fitted using 239 model solutions performed in 0.483 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: Tue May 7 08:37:53 2019
-## Date of summary: Tue May 7 08:37:53 2019
+## Date of fit: Wed May 8 20:52:33 2019
+## Date of summary: Wed May 8 20:52:33 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 572 model solutions performed in 1.244 s
+## Fitted using 572 model solutions performed in 1.185 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: Tue May 7 08:37:55 2019
-## Date of summary: Tue May 7 08:37:55 2019
+## Date of fit: Wed May 8 20:52:35 2019
+## Date of summary: Wed May 8 20:52:35 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 373 model solutions performed in 0.791 s
+## Fitted using 373 model solutions performed in 0.768 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: Tue May 7 08:37:56 2019
-## Date of summary: Tue May 7 08:37:56 2019
+## Date of fit: Wed May 8 20:52:36 2019
+## Date of summary: Wed May 8 20:52:37 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 142 model solutions performed in 0.29 s
+## Fitted using 142 model solutions performed in 0.289 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: Tue May 7 08:37:56 2019
-## Date of summary: Tue May 7 08:37:56 2019
+## Date of fit: Wed May 8 20:52:36 2019
+## Date of summary: Wed May 8 20:52:37 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 0.453 s
+## Fitted using 224 model solutions performed in 0.45 s
##
## Error model:
## Constant variance
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 271da77e..c274696c 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -88,7 +88,7 @@
<h1>Introduction to mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-05-07</h4>
+ <h4 class="date">2019-05-08</h4>
<div class="hidden name"><code>mkin.Rmd</code></div>
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 9f08036a..9f660fab 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -88,7 +88,7 @@
<h1>Calculation of time weighted average concentrations with mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-05-07</h4>
+ <h4 class="date">2019-05-08</h4>
<div class="hidden name"><code>twa.Rmd</code></div>
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 3cda0261..9184fad5 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -88,7 +88,7 @@
<h1>Example evaluation of FOCUS dataset Z</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-05-07</h4>
+ <h4 class="date">2019-05-08</h4>
<div class="hidden name"><code>FOCUS_Z.Rmd</code></div>
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index 237b506e..4d9e9b2d 100644
--- a/docs/articles/web_only/NAFTA_examples.html
+++ b/docs/articles/web_only/NAFTA_examples.html
@@ -88,7 +88,7 @@
<h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-05-07</h4>
+ <h4 class="date">2019-05-08</h4>
<div class="hidden name"><code>NAFTA_examples.Rmd</code></div>
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index a250f005..a53f1927 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -88,7 +88,7 @@
<h1>Benchmark timings for mkin on various systems</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-05-07</h4>
+ <h4 class="date">2019-05-08</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@@ -198,67 +198,67 @@
## 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 5.982
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.792
## 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 17.777
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 17.398
## 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 4.545
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.427
## 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 16.684
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 16.104
## 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 7.868
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.527
## 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 2.66
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.541
## 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 4.496
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.308
## 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 4.919
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.775
## 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 11.683
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 11.116
## 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 5.344
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.063
## 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 7.752</code></pre>
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.784</code></pre>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" 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 54d3148f..f296c8a4 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -88,7 +88,7 @@
<h1>Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-05-07</h4>
+ <h4 class="date">2019-05-08</h4>
<div class="hidden name"><code>compiled_models.Rmd</code></div>
@@ -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 3.067 1.000 3.065 0
-## 1 deSolve, not compiled 3 28.135 9.173 28.122 0
-## 2 Eigenvalue based 3 4.306 1.404 4.303 0
+## 3 deSolve, compiled 3 3.131 1.000 3.129 0
+## 1 deSolve, not compiled 3 28.306 9.041 28.290 0
+## 2 Eigenvalue based 3 4.361 1.393 4.358 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 4.827 1.000 4.825 0
-## 1 deSolve, not compiled 3 52.646 10.907 52.622 0
+## 2 deSolve, compiled 3 5.023 1.000 5.021 0
+## 1 deSolve, not compiled 3 53.267 10.605 53.235 0
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
diff --git a/docs/news/index.html b/docs/news/index.html
index d165b6f9..11414ed3 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -122,13 +122,14 @@
</div>
- <div id="mkin-0-9-49-4-2019-05-07" class="section level1">
+ <div id="mkin-0-9-49-4-2019-05-08" class="section level1">
<h1 class="page-header">
-<a href="#mkin-0-9-49-4-2019-05-07" class="anchor"></a>mkin 0.9.49.4 (2019-05-07)<small> Unreleased </small>
+<a href="#mkin-0-9-49-4-2019-05-08" class="anchor"></a>mkin 0.9.49.4 (2019-05-08)<small> Unreleased </small>
</h1>
<ul>
<li><p>Direct minimization of the negative log-likelihood for non-constant error models (two-component and variance by variable). In the case the error model is constant variance, least squares is used as this is more stable</p></li>
<li><p>The argument ‘reweight.method’ to mkinfit and mmkin is now obsolete, use ‘error_model’ instead</p></li>
+<li><p>New function ‘mkinerrplot’. This function is also used for residual plots in ‘plot.mmkin’ if the argument ‘resplot = “errmod”’ is given, and in ‘plot.mkinfit’ if ‘show_errplot’ is set to TRUE.</p></li>
<li><p>Remove dependency on FME, only use nlminb for optimisation</p></li>
<li><p>Use the numDeriv package to calculate hessians</p></li>
<li><p>Add a benchmark vignette to document the impact on performance. For very simple fits, the new code is a bit slower, presumably because of the time it takes to calculate the hessian matrices with and without parameter transformation</p></li>
@@ -695,7 +696,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
- <li><a href="#mkin-0-9-49-4-2019-05-07">0.9.49.4</a></li>
+ <li><a href="#mkin-0-9-49-4-2019-05-08">0.9.49.4</a></li>
<li><a href="#mkin-0-9-48-1-2019-03-04">0.9.48.1</a></li>
<li><a href="#mkin-0-9-47-5-2018-09-14">0.9.47.5</a></li>
<li><a href="#mkin-0-9-47-3">0.9.47.3</a></li>
diff --git a/docs/reference/mkinerrplot-1.png b/docs/reference/mkinerrplot-1.png
new file mode 100644
index 00000000..9c663646
--- /dev/null
+++ b/docs/reference/mkinerrplot-1.png
Binary files differ
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+++ b/docs/reference/mkinerrplot.html
@@ -0,0 +1,250 @@
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+<meta property="og:description" content="This function plots the squared residuals for the specified subset of the
+ observed variables from an mkinfit object. In addition, one or more
+ dashed line(s) show the fitted error model.
+ A combined plot of the fitted model and this error model plot can be
+ obtained with plot.mkinfit
+ using the argument show_errplot = TRUE." />
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+ <h1>Function to plot squared residuals and the error model for an mkin object</h1>
+
+ <div class="hidden name"><code>mkinerrplot.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+
+ <p>This function plots the squared residuals for the specified subset of the
+ observed variables from an mkinfit object. In addition, one or more
+ dashed line(s) show the fitted error model.
+ A combined plot of the fitted model and this error model plot can be
+ obtained with <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>
+ using the argument <code>show_errplot = TRUE</code>.</p>
+
+ </div>
+
+ <pre class="usage"><span class='fu'>mkinerrplot</span>(<span class='no'>object</span>,
+ <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>),
+ <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1.1</span> * <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Extremes'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>predicted</span>)),
+ <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Predicted"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Squared residual"</span>,
+ <span class='kw'>maxy</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span><span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>,
+ <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>object</th>
+ <td><p>A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object.</p></td>
+ </tr>
+ <tr>
+ <th>obs_vars</th>
+ <td><p>A character vector of names of the observed variables for which residuals
+ should be plotted. Defaults to all observed variables in the model</p></td>
+ </tr>
+ <tr>
+ <th>xlim</th>
+ <td><p>plot range in x direction.</p></td>
+ </tr>
+ <tr>
+ <th>xlab</th>
+ <td><p>Label for the x axis.</p></td>
+ </tr>
+ <tr>
+ <th>ylab</th>
+ <td><p>Label for the y axis.</p></td>
+ </tr>
+ <tr>
+ <th>maxy</th>
+ <td><p>Maximum value of the residuals. This is used for the scaling of
+ the y axis and defaults to "auto".</p></td>
+ </tr>
+ <tr>
+ <th>legend</th>
+ <td><p>Should a legend be plotted?</p></td>
+ </tr>
+ <tr>
+ <th>lpos</th>
+ <td><p>Where should the legend be placed? Default is "topright". Will be passed on to
+ <code><a href='https://www.rdocumentation.org/packages/graphics/topics/legend'>legend</a></code>.</p></td>
+ </tr>
+ <tr>
+ <th>col_obs</th>
+ <td><p>Colors for the observed variables.</p></td>
+ </tr>
+ <tr>
+ <th>pch_obs</th>
+ <td><p>Symbols to be used for the observed variables.</p></td>
+ </tr>
+ <tr>
+ <th>&#8230;</th>
+ <td><p>further arguments passed to <code><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p>
+
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted lines of the
+ mkinfit object.</p></div>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>model</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>))</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'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</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'>mkinerrplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinerrplot-1.png' alt='' width='700' height='433' /></div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#see-also">See also</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+ <p>Johannes Ranke</p>
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+</div>
+ </footer>
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+
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+
+ </body>
+</html>
+
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 09329a86..bfca44fc 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -362,15 +362,15 @@ 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: Tue May 7 08:36:16 2019
-#&gt; Date of summary: Tue May 7 08:36:16 2019
+#&gt; Date of fit: Wed May 8 20:50:50 2019
+#&gt; Date of summary: Wed May 8 20:50:50 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted using 222 model solutions performed in 0.89 s
+#&gt; Fitted using 222 model solutions performed in 0.456 s
#&gt;
#&gt; Error model:
#&gt; Constant variance
@@ -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; 2.251 0.000 2.253 </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; 1.488 0.000 1.488 </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;
@@ -515,7 +515,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; Sum of squared residuals at call 126: 371.2134
#&gt; Sum of squared residuals at call 135: 371.2134
#&gt; Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.151 0.000 1.152 </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; 1.086 0.000 1.087 </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;
@@ -547,8 +547,8 @@ 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: Tue May 7 08:36:33 2019
-#&gt; Date of summary: Tue May 7 08:36:33 2019
+#&gt; Date of fit: Wed May 8 20:51:06 2019
+#&gt; Date of summary: Wed May 8 20:51:06 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -556,7 +556,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 421 model solutions performed in 1.1 s
+#&gt; Fitted using 421 model solutions performed in 1.082 s
#&gt;
#&gt; Error model:
#&gt; Constant variance
@@ -665,8 +665,8 @@ 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: Tue May 7 08:36:35 2019
-#&gt; Date of summary: Tue May 7 08:36:35 2019
+#&gt; Date of fit: Wed May 8 20:51:08 2019
+#&gt; Date of summary: Wed May 8 20:51:08 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -674,7 +674,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 758 model solutions performed in 1.991 s
+#&gt; Fitted using 758 model solutions performed in 1.971 s
#&gt;
#&gt; Error model:
#&gt; Variance unique to each observed variable
@@ -795,8 +795,8 @@ 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: Tue May 7 08:36:39 2019
-#&gt; Date of summary: Tue May 7 08:36:39 2019
+#&gt; Date of fit: Wed May 8 20:51:11 2019
+#&gt; Date of summary: Wed May 8 20:51:11 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -804,7 +804,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 821 model solutions performed in 3.304 s
+#&gt; Fitted using 821 model solutions performed in 3.29 s
#&gt;
#&gt; Error model:
#&gt; Two-component variance function
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index d0b2a0eb..51be5465 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 fileb5a1e31297a.c 2&gt; fileb5a1e31297a.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file4bbd307f8763.c 2&gt; file4bbd307f8763.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 522cbbfe..8e2e307b 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -328,17 +328,17 @@
<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'>"eigen"</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; 0.003 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
+#&gt; 0.003 0.000 0.004 </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='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; 0.001 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>(
+#&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>(
<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
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.021 0.000 0.022 </div><div class='input'>
+#&gt; 0.021 0.000 0.021 </div><div class='input'>
</div><div class='input'> <span class='co'># Predict from a fitted model</span>
<span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#&gt; <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#&gt; Sum of squared residuals at call 1: 552.5739
#&gt; Sum of squared residuals at call 3: 552.5739
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index d0cd748c..3e297eb3 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; 0.047 0.033 5.463 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 19.909 0.004 19.967 </div><div class='input'>
+#&gt; 0.048 0.024 5.085 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 19.074 0.004 19.089 </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 0.7505684 0.2494316
diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png
index e7b3bac7..f70e9e31 100644
--- a/docs/reference/plot.mkinfit-1.png
+++ b/docs/reference/plot.mkinfit-1.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png
index 15bdba55..6facce0f 100644
--- a/docs/reference/plot.mkinfit-2.png
+++ b/docs/reference/plot.mkinfit-2.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png
index 52de09bd..b53b3134 100644
--- a/docs/reference/plot.mkinfit-3.png
+++ b/docs/reference/plot.mkinfit-3.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png
index a832ede2..70a936ee 100644
--- a/docs/reference/plot.mkinfit-4.png
+++ b/docs/reference/plot.mkinfit-4.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png
new file mode 100644
index 00000000..2e208996
--- /dev/null
+++ b/docs/reference/plot.mkinfit-5.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png
new file mode 100644
index 00000000..1da876b4
--- /dev/null
+++ b/docs/reference/plot.mkinfit-6.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 525200ff..7bfc17f6 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -36,7 +36,7 @@
from a previous successful call to mkinfit and plots
the observed data together with the solution of the fitted model.
If the current plot device is a tikz device,
- then latex is being used for the formatting of the chi2 error level,
+ then latex is being used for the formatting of the chi2 error level,
if show_errmin = TRUE." />
<meta name="twitter:card" content="summary" />
@@ -137,7 +137,7 @@ If the current plot device is a tikz device,
from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots
the observed data together with the solution of the fitted model.</p>
<p>If the current plot device is a <code><a href='https://www.rdocumentation.org/packages/tikzDevice/topics/tikz'>tikz</a></code> device,
- then latex is being used for the formatting of the chi2 error level,
+ then latex is being used for the formatting of the chi2 error level,
if <code>show_errmin = TRUE</code>.</p>
</div>
@@ -151,7 +151,9 @@ plot(x, fit = x,
col_obs = 1:length(obs_vars), pch_obs = col_obs,
lty_obs = rep(1, length(obs_vars)),
add = FALSE, legend = !add,
- show_residuals = FALSE, maxabs = "auto",
+ show_residuals = FALSE,
+ show_errplot = FALSE,
+ maxabs = "auto",
sep_obs = FALSE, rel.height.middle = 0.9,
lpos = "topright", inset = c(0.05, 0.05),
show_errmin = FALSE, errmin_digits = 3, &#8230;)
@@ -213,11 +215,18 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, &#8230
<tr>
<th>show_residuals</th>
<td><p>Should residuals be shown? If only one plot of the fits is shown, the
- residual plot is in the lower third of the plot? Otherwise, i.e. if
+ residual plot is in the lower third of the plot. Otherwise, i.e. if
"sep_obs" is given, the residual plots will be located to the right of
the plots of the fitted curves.</p></td>
</tr>
<tr>
+ <th>show_errplot</th>
+ <td><p>Should squared residuals and the error model be shown? If only one plot of
+ the fits is shown, this plot is in the lower third of the plot.
+ Otherwise, i.e. if "sep_obs" is given, the residual plots will be located
+ to the right of the plots of the fitted curves.</p></td>
+ </tr>
+ <tr>
<th>maxabs</th>
<td><p>Maximum absolute value of the residuals. This is used for the scaling of
the y axis and defaults to "auto".</p></td>
@@ -263,14 +272,18 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, &#8230
<pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order, path from</span>
<span class='co'># parent to sink included</span>
<span class='no'>SFO_SFO</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'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</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'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</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'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</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/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'>
+ <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'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</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'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># Show the observed variables separately</span>
-<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># Show the observed variables separately, with residuals</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>),
- <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'>
+ <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-5.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># The same can be obtained with less typing, using the convenience function plot_sep</span>
-<span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div></pre>
+<span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))
+
+<span class='co'># Show the observed variables separately, with the error model</span>
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>),
+ <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-6.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/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png
index 555cb7d6..25ed01cc 100644
--- a/docs/reference/plot.mmkin-2.png
+++ b/docs/reference/plot.mmkin-2.png
Binary files differ
diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png
new file mode 100644
index 00000000..b03dffb2
--- /dev/null
+++ b/docs/reference/plot.mmkin-4.png
Binary files differ
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index b3f2de66..3037ca24 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -141,8 +141,9 @@ If the current plot device is a tikz device,
</div>
<pre class="usage"><span class='co'># S3 method for mmkin</span>
-<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>errmin_var</span> <span class='kw'>=</span> <span class='st'>"All data"</span>, <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>,
- <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, <span class='no'>...</span>)</pre>
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>,
+ <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"time"</span>, <span class='st'>"errmod"</span>), <span class='kw'>errmin_var</span> <span class='kw'>=</span> <span class='st'>"All data"</span>, <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>,
+ <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -160,6 +161,12 @@ If the current plot device is a tikz device,
<td><p>An index for the fits for which legends should be shown.</p></td>
</tr>
<tr>
+ <th>resplot</th>
+ <td><p>Should the residuals plotted against time, using <code><a href='mkinresplot.html'>mkinresplot</a></code>,
+ or as squared residuals against predicted values, with the error model,
+ using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td>
+ </tr>
+ <tr>
<th>errmin_var</th>
<td><p>The variable for which the FOCUS chi2 error value should be shown.</p></td>
</tr>
@@ -187,15 +194,17 @@ If the current plot device is a tikz device,
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='co'># Only use one core not to offend CRAN checks</span>
+ <pre class="examples"><div class='input'> </div><div class='input'> <span class='co'># Only use one core not to offend CRAN checks</span>
<span class='no'>fits</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/c'>c</a></span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>),
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='co'># named list for titles</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='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='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='img'><img src='plot.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><div class='img'><img src='plot.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span>
<span class='co'># height should be smaller than the plot width (this is not possible for the html pages</span>
<span class='co'># generated by pkgdown, as far as I know).</span>
- <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span>]) <span class='co'># same as plot(fits[1, 2])</span></div><div class='img'><img src='plot.mmkin-3.png' alt='' width='700' height='433' /></div></pre>
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span>]) <span class='co'># same as plot(fits[1, 2])</span></div><div class='img'><img src='plot.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
+ <span class='co'># Show the error models</span>
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ], <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='st'>"errmod"</span>)</div><div class='img'><img src='plot.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 9c4a21a9..b3151da1 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -211,15 +211,15 @@
<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: Tue May 7 08:37:31 2019
-#&gt; Date of summary: Tue May 7 08:37:31 2019
+#&gt; Date of fit: Wed May 8 20:52:12 2019
+#&gt; Date of summary: Wed May 8 20:52:12 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted using 131 model solutions performed in 0.277 s
+#&gt; Fitted using 131 model solutions performed in 0.266 s
#&gt;
#&gt; Error model:
#&gt; Constant variance

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