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authorJohannes Ranke <jranke@uni-bremen.de>2019-09-18 13:23:23 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2019-09-18 13:23:23 +0200
commita401a9225d212ed4dc64e96765f04aaaf17cc8c1 (patch)
tree998d055acecd0e8e1aaf66e441ccdfb205084795 /docs
parente05656d57668688b971c28e32b4cfd4d3eac4662 (diff)
Further corrections of the twa vignette
Static documentation rebuilt by pkgdown
Diffstat (limited to 'docs')
-rw-r--r--docs/articles/FOCUS_D.html6
-rw-r--r--docs/articles/FOCUS_L.html42
-rw-r--r--docs/articles/twa.html2
-rw-r--r--docs/articles/web_only/benchmarks.html22
-rw-r--r--docs/articles/web_only/compiled_models.html10
-rw-r--r--docs/reference/mkinfit.html28
-rw-r--r--docs/reference/mkinmod.html2
-rw-r--r--docs/reference/mkinpredict.html4
-rw-r--r--docs/reference/mmkin.html4
-rw-r--r--docs/reference/summary.mkinfit.html6
10 files changed, 63 insertions, 63 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 70739ae6..b62afbf8 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -170,8 +170,8 @@
<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://rdrr.io/r/base/summary.html">summary</a></span>(fit)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 12:57:33 2019
-## Date of summary: Wed Sep 18 12:57:33 2019
+## Date of fit: Wed Sep 18 13:17:00 2019
+## Date of summary: Wed Sep 18 13:17:00 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -179,7 +179,7 @@
##
## Model predictions using solution type deSolve
##
-## Fitted using 389 model solutions performed in 1.01 s
+## Fitted using 389 model solutions performed in 1.115 s
##
## Error model: Constant variance
##
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 81659030..0d5667f5 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -116,15 +116,15 @@
<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.L1.SFO)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 12:57:35 2019
-## Date of summary: Wed Sep 18 12:57:35 2019
+## Date of fit: Wed Sep 18 13:17:02 2019
+## Date of summary: Wed Sep 18 13:17:02 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 133 model solutions performed in 0.287 s
+## Fitted using 133 model solutions performed in 0.297 s
##
## Error model: Constant variance
##
@@ -218,8 +218,8 @@
## finite result is doubtful</code></pre>
<pre><code>## mkin version used for fitting: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 12:57:37 2019
-## Date of summary: Wed Sep 18 12:57:37 2019
+## Date of fit: Wed Sep 18 13:17:05 2019
+## Date of summary: Wed Sep 18 13:17:05 2019
##
##
## Warning: Optimisation did not converge:
@@ -231,7 +231,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 899 model solutions performed in 1.921 s
+## Fitted using 899 model solutions performed in 2.099 s
##
## Error model: Constant variance
##
@@ -323,15 +323,15 @@
<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://rdrr.io/r/base/summary.html">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: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 12:57:38 2019
-## Date of summary: Wed Sep 18 12:57:38 2019
+## Date of fit: Wed Sep 18 13:17:06 2019
+## Date of summary: Wed Sep 18 13:17:06 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 0.49 s
+## Fitted using 239 model solutions performed in 0.554 s
##
## Error model: Constant variance
##
@@ -399,8 +399,8 @@
<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://rdrr.io/r/base/summary.html">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: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 12:57:40 2019
-## Date of summary: Wed Sep 18 12:57:40 2019
+## Date of fit: Wed Sep 18 13:17:07 2019
+## Date of summary: Wed Sep 18 13:17:07 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -409,7 +409,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 572 model solutions performed in 1.209 s
+## Fitted using 572 model solutions performed in 1.273 s
##
## Error model: Constant variance
##
@@ -499,8 +499,8 @@
<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://rdrr.io/r/base/summary.html">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: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 12:57:42 2019
-## Date of summary: Wed Sep 18 12:57:42 2019
+## Date of fit: Wed Sep 18 13:17:09 2019
+## Date of summary: Wed Sep 18 13:17:09 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -509,7 +509,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 373 model solutions performed in 0.783 s
+## Fitted using 373 model solutions performed in 0.792 s
##
## Error model: Constant variance
##
@@ -605,15 +605,15 @@
<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://rdrr.io/r/base/summary.html">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: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 12:57:42 2019
-## Date of summary: Wed Sep 18 12:57:43 2019
+## Date of fit: Wed Sep 18 13:17:10 2019
+## Date of summary: Wed Sep 18 13:17:11 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 142 model solutions performed in 0.288 s
+## Fitted using 142 model solutions performed in 0.299 s
##
## Error model: Constant variance
##
@@ -670,15 +670,15 @@
<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://rdrr.io/r/base/summary.html">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: 0.9.49.6
## R version used for fitting: 3.6.1
-## Date of fit: Wed Sep 18 12:57:43 2019
-## Date of summary: Wed Sep 18 12:57:43 2019
+## Date of fit: Wed Sep 18 13:17:10 2019
+## Date of summary: Wed Sep 18 13:17:11 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 0.463 s
+## Fitted using 224 model solutions performed in 0.488 s
##
## Error model: Constant variance
##
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index b15f1522..799349d9 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -130,7 +130,7 @@
<p><span class="math display">\[f_\textrm{twa} = \frac{1}{t} \left(
\frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) +
\frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right) \right) \]</span></p>
-<p>Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ is include in the ‘mkin’ package (<a href="https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html">‘max_twa_parent’</a>. If the same is needed for metabolites, the function <a href="https://pkgdown.jrwb.de/pfm/reference/max_twa.html">‘max_twa’</a> can be used.</p>
+<p>Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the <a href="https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html">‘max_twa_parent’</a> function. If the same is needed for metabolites, the function <a href="https://pkgdown.jrwb.de/pfm/reference/max_twa.html">‘max_twa’</a> from the ‘pfm’ package can be used.</p>
<div id="refs" class="references">
<div id="ref-FOCUSkinetics2014">
<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="uri">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p>
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index f1ed1f96..0c78d346 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -204,77 +204,77 @@
## 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 0.9.49.6 5.920
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 6.106
## 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 0.9.49.6 36.932
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 37.249
## 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 0.9.49.6 4.519
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.739
## 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 0.9.49.6 31.518
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 31.761
## 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 0.9.49.6 10.619
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.794
## 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 0.9.49.6 2.61
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.702
## 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 0.9.49.6 4.312
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.351
## 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 0.9.49.6 8.07
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.303
## 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 0.9.49.6 16.102
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.339
## 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 0.9.49.6 8.013
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.12
## t11
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 5.636
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.574
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.365
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.626
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.805</code></pre>
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 11.22</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://rdrr.io/r/base/save.html">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 89977591..99b05623 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -165,9 +165,9 @@
## 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 3.124 1.000 3.122 0
-## 1 deSolve, not compiled 3 28.822 9.226 28.807 0
-## 2 Eigenvalue based 3 4.416 1.414 4.413 0
+## 3 deSolve, compiled 3 3.153 1.000 3.152 0
+## 1 deSolve, not compiled 3 28.771 9.125 28.756 0
+## 2 Eigenvalue based 3 4.444 1.409 4.443 0
## user.child sys.child
## 3 0 0
## 1 0 0
@@ -216,8 +216,8 @@
## 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 4.878 1.000 4.875 0
-## 1 deSolve, not compiled 3 53.602 10.989 53.568 0
+## 2 deSolve, compiled 3 4.978 1.000 4.975 0.000
+## 1 deSolve, not compiled 3 54.194 10.887 54.160 0.004
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index b620f364..c1cfc228 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -408,15 +408,15 @@ 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://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
#&gt; R version used for fitting: 3.6.1
-#&gt; Date of fit: Wed Sep 18 12:55:32 2019
-#&gt; Date of summary: Wed Sep 18 12:55:32 2019
+#&gt; Date of fit: Wed Sep 18 13:14:54 2019
+#&gt; Date of summary: Wed Sep 18 13:14:54 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 0.459 s
+#&gt; Fitted using 222 model solutions performed in 0.475 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -490,7 +490,7 @@ 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://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>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; 1.480 0.000 1.482 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>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; 1.561 0.000 1.568 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>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;
@@ -563,7 +563,7 @@ 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; 1.045 0.000 1.046 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>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; 1.06 0.00 1.06 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>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;
@@ -599,8 +599,8 @@ 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://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
#&gt; R version used for fitting: 3.6.1
-#&gt; Date of fit: Wed Sep 18 12:55:47 2019
-#&gt; Date of summary: Wed Sep 18 12:55:47 2019
+#&gt; Date of fit: Wed Sep 18 13:15:10 2019
+#&gt; Date of summary: Wed Sep 18 13:15:10 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -608,7 +608,7 @@ 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 1.077 s
+#&gt; Fitted using 421 model solutions performed in 1.095 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -718,8 +718,8 @@ 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://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
#&gt; R version used for fitting: 3.6.1
-#&gt; Date of fit: Wed Sep 18 12:55:50 2019
-#&gt; Date of summary: Wed Sep 18 12:55:50 2019
+#&gt; Date of fit: Wed Sep 18 13:15:12 2019
+#&gt; Date of summary: Wed Sep 18 13:15:12 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -727,7 +727,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 979 model solutions performed in 2.624 s
+#&gt; Fitted using 979 model solutions performed in 2.639 s
#&gt;
#&gt; Error model: Variance unique to each observed variable
#&gt;
@@ -850,8 +850,8 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; 120 m1 25.15 28.80429 -3.654e+00
#&gt; 120 m1 33.31 28.80429 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://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
#&gt; R version used for fitting: 3.6.1
-#&gt; Date of fit: Wed Sep 18 12:55:59 2019
-#&gt; Date of summary: Wed Sep 18 12:55:59 2019
+#&gt; Date of fit: Wed Sep 18 13:15:22 2019
+#&gt; Date of summary: Wed Sep 18 13:15:22 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -859,7 +859,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 2289 model solutions performed in 9.376 s
+#&gt; Fitted using 2289 model solutions performed in 9.723 s
#&gt;
#&gt; Error model: Two-component variance function
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 81fed454..ca243e3c 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -239,7 +239,7 @@ 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 file419a1fa6c394.c 2&gt; file419a1fa6c394.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file4e7a49f4ff50.c 2&gt; file4e7a49f4ff50.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 d162135a..f5401c1d 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -332,12 +332,12 @@
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>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://rdrr.io/r/base/seq.html'>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; 0.004 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(
+#&gt; 0.004 0.000 0.004 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>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://rdrr.io/r/base/c.html'>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://rdrr.io/r/base/seq.html'>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://rdrr.io/r/base/system.time.html'>system.time</a></span>(
+#&gt; 0.002 0.000 0.002 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>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://rdrr.io/r/base/c.html'>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://rdrr.io/r/base/seq.html'>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 9bb7926b..ea695d9a 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -199,8 +199,8 @@
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>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; 0.012 0.024 5.064 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 19.094 0.000 19.104 </div><div class='input'>
+#&gt; 0.007 0.031 4.920 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 19.290 0.000 19.301 </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/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index fafca9ce..a10859fc 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -215,15 +215,15 @@
<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://rdrr.io/r/base/summary.html'>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: 0.9.49.6
#&gt; R version used for fitting: 3.6.1
-#&gt; Date of fit: Wed Sep 18 12:57:18 2019
-#&gt; Date of summary: Wed Sep 18 12:57:18 2019
+#&gt; Date of fit: Wed Sep 18 13:16:44 2019
+#&gt; Date of summary: Wed Sep 18 13:16:44 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 0.267 s
+#&gt; Fitted using 131 model solutions performed in 0.273 s
#&gt;
#&gt; Error model: Constant variance
#&gt;

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