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authorJohannes Ranke <jranke@uni-bremen.de>2019-06-05 15:16:59 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2019-06-05 15:16:59 +0200
commitb6027bbd157734e1c7f8c3ba6373451f5c85fc38 (patch)
tree62462fd7768d48ab772dbb68833bd4f2ebd4303f /docs/reference
parent307a317666b8a1cdfe2293371ad8671403680a36 (diff)
Add error model algorithm to output
Diffstat (limited to 'docs/reference')
-rw-r--r--docs/reference/Extract.mmkin.html8
-rw-r--r--docs/reference/experimental_data_for_UBA.html66
-rw-r--r--docs/reference/mkinfit.html50
-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/summary.mkinfit.html11
7 files changed, 108 insertions, 39 deletions
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 1d1da50e..37c0b361 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -172,16 +172,16 @@
<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'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#&gt; dataset
#&gt; model B C
-#&gt; FOMC List,36 List,36
+#&gt; FOMC List,37 List,37
#&gt; attr(,"class")
#&gt; [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#&gt; dataset
#&gt; model B
-#&gt; SFO List,36
-#&gt; FOMC List,36
+#&gt; SFO List,37
+#&gt; FOMC List,37
#&gt; attr(,"class")
#&gt; [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#&gt; dataset
#&gt; model B
-#&gt; SFO List,36
+#&gt; SFO List,37
#&gt; attr(,"class")
#&gt; [1] "mmkin"</div><div class='input'>
<span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>(
diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html
index 3e8d20ef..bb94fd11 100644
--- a/docs/reference/experimental_data_for_UBA.html
+++ b/docs/reference/experimental_data_for_UBA.html
@@ -37,7 +37,30 @@
and advance error model specifications. The fact that these data and some
results are shown here do not imply a license to use them in the context of
pesticide registrations, as the use of the data may be constrained by
- data protection regulations." />
+ data protection regulations.
+Preprocessing of data was performed based on the recommendations of the FOCUS
+ kinetics workgroup (FOCUS, 2014) as described below.
+Datasets 1 and 2 are from the Renewal Assessment Report (RAR) for imazamox
+ (France, 2015, p. 15). For setting values reported as zero, an LOQ of 0.1
+ was assumed. Metabolite residues reported for day zero were added to the
+ parent compound residues.
+Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid
+ (Belgium, 2014, p. 8) and show the data for two different radiolabels. For
+ dataset 4, the value given for the metabolite in the day zero sampling
+ in replicate B was added to the parent compound, following the respective
+ FOCUS recommendation.
+Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate
+ (Austria, 2015, p. 16).
+Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate
+ (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling,
+ the residues given for the metabolite were added to the parent
+ value, following the recommendation of the FOCUS kinetics workgroup.
+Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D
+ (Germany, 2013b, p. 644). Values reported as zero were set to NA, with
+ the exception of the day three sampling of metabolite A2, which was set
+ to one half of the LOD reported to be 1% AR.
+Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
+ (United Kingdom, 2014, p. 81)." />
<meta name="twitter:card" content="summary" />
@@ -139,6 +162,29 @@
results are shown here do not imply a license to use them in the context of
pesticide registrations, as the use of the data may be constrained by
data protection regulations.</p>
+<p>Preprocessing of data was performed based on the recommendations of the FOCUS
+ kinetics workgroup (FOCUS, 2014) as described below.</p>
+<p>Datasets 1 and 2 are from the Renewal Assessment Report (RAR) for imazamox
+ (France, 2015, p. 15). For setting values reported as zero, an LOQ of 0.1
+ was assumed. Metabolite residues reported for day zero were added to the
+ parent compound residues.</p>
+<p>Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid
+ (Belgium, 2014, p. 8) and show the data for two different radiolabels. For
+ dataset 4, the value given for the metabolite in the day zero sampling
+ in replicate B was added to the parent compound, following the respective
+ FOCUS recommendation.</p>
+<p>Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate
+ (Austria, 2015, p. 16).</p>
+<p>Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate
+ (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling,
+ the residues given for the metabolite were added to the parent
+ value, following the recommendation of the FOCUS kinetics workgroup.</p>
+<p>Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D
+ (Germany, 2013b, p. 644). Values reported as zero were set to NA, with
+ the exception of the day three sampling of metabolite A2, which was set
+ to one half of the LOD reported to be 1% AR.</p>
+<p>Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
+ (United Kingdom, 2014, p. 81).</p>
</div>
@@ -154,8 +200,24 @@
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
- <p>Ranke (2019) Documentation of results obtained for the error model expertise
+
+ <p>Austria (2015). Ethofumesate Renewal Assessment Report Volume 3 Annex B.8 (AS)</p>
+<p>Belgium (2014). Isofetamid (IKF-5411) Draft Assessment Report Volume 3 Annex B.8 (AS)</p>
+<p>France (2015). Imazamox Draft Renewal Assessment Report Volume 3 Annex B.8 (AS)</p>
+<p>FOCUS (2014) &#8220;Generic guidance for Estimating Persistence and
+ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+ Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ Version 1.1, 18 December 2014
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+<p>Germany (2013a). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate
+ and Behaviour</p>
+<p>Germany (2013b). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate and behaviour in the
+ environment</p>
+<p>Ranke (2019) Documentation of results obtained for the error model expertise
written for the German Umweltbundesamt.</p>
+<p>United Kingdom (2014). Thifensulfuron-methyl - Annex B.8 (Volume 3) to the Report and Proposed
+ Decision of the United Kingdom made to the European Commission under Regulation (EC) No.
+ 1141/2010 for renewal of an active substance</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 8cabcb21..700b6805 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -399,18 +399,19 @@ 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: 0.9.49.5
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Tue Jun 4 15:01:15 2019
-#&gt; Date of summary: Tue Jun 4 15:01:15 2019
+#&gt; Date of fit: Wed Jun 5 15:08:20 2019
+#&gt; Date of summary: Wed Jun 5 15:08:20 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 0.461 s
+#&gt; Fitted using 222 model solutions performed in 0.469 s
#&gt;
-#&gt; Error model:
-#&gt; Constant variance
+#&gt; Error model: Constant variance
+#&gt;
+#&gt; Error model algorithm: d_3
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
@@ -480,7 +481,7 @@ Per default, parameters in the kinetic models are internally transformed in
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.521 0.000 1.526 </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; 1.579 0.000 1.581 </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;
@@ -552,7 +553,7 @@ 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; 1.093 0.000 1.093 </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; 1.159 0.000 1.160 </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;
@@ -584,8 +585,8 @@ 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: 0.9.49.5
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Tue Jun 4 15:01:31 2019
-#&gt; Date of summary: Tue Jun 4 15:01:31 2019
+#&gt; Date of fit: Wed Jun 5 15:08:36 2019
+#&gt; Date of summary: Wed Jun 5 15:08:36 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -593,10 +594,11 @@ 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 1.096 s
+#&gt; Fitted using 421 model solutions performed in 1.181 s
+#&gt;
+#&gt; Error model: Constant variance
#&gt;
-#&gt; Error model:
-#&gt; Constant variance
+#&gt; Error model algorithm: d_3
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
@@ -702,8 +704,8 @@ 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: 0.9.49.5
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Tue Jun 4 15:01:34 2019
-#&gt; Date of summary: Tue Jun 4 15:01:34 2019
+#&gt; Date of fit: Wed Jun 5 15:08:39 2019
+#&gt; Date of summary: Wed Jun 5 15:08:39 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -711,10 +713,12 @@ 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 2.603 s
+#&gt; Fitted using 979 model solutions performed in 2.672 s
#&gt;
-#&gt; Error model:
-#&gt; Variance unique to each observed variable
+#&gt; Error model: Variance unique to each observed variable
+#&gt;
+#&gt; Error model algorithm: d_3
+#&gt; Direct fitting and three-step fitting yield approximately the same likelihood
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
@@ -832,8 +836,8 @@ 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://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: 0.9.49.5
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Tue Jun 4 15:01:43 2019
-#&gt; Date of summary: Tue Jun 4 15:01:43 2019
+#&gt; Date of fit: Wed Jun 5 15:08:50 2019
+#&gt; Date of summary: Wed Jun 5 15:08:50 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -841,10 +845,12 @@ 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 9.499 s
+#&gt; Fitted using 2289 model solutions performed in 10.959 s
+#&gt;
+#&gt; Error model: Two-component variance function
#&gt;
-#&gt; Error model:
-#&gt; Two-component variance function
+#&gt; Error model algorithm: d_3
+#&gt; Direct fitting and three-step fitting yield approximately the same likelihood
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 2c5f056e..ddab656c 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 filebbe6b539c4f.c 2&gt; filebbe6b539c4f.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file50a55c3108b2.c 2&gt; file50a55c3108b2.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 f339b26a..7e71ec27 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; 0.004 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; 0.002 0.000 0.002 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
+#&gt; 0.003 0.000 0.002 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&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; 0.022 0.000 0.022 </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 a830646f..61a029fc 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; 0.046 0.032 5.094 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 19.798 0.004 19.814 </div><div class='input'>
+#&gt; 0.038 0.050 6.779 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 27.209 0.004 27.278 </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 ffe1edb1..68b36542 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -211,18 +211,19 @@
<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: 0.9.49.5
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Tue Jun 4 15:03:02 2019
-#&gt; Date of summary: Tue Jun 4 15:03:02 2019
+#&gt; Date of fit: Wed Jun 5 15:10:34 2019
+#&gt; Date of summary: Wed Jun 5 15:10:34 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 0.266 s
+#&gt; Fitted using 131 model solutions performed in 0.268 s
#&gt;
-#&gt; Error model:
-#&gt; Constant variance
+#&gt; Error model: Constant variance
+#&gt;
+#&gt; Error model algorithm: d_3
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type

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