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authorJohannes Ranke <jranke@uni-bremen.de>2018-11-26 09:09:43 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2018-11-26 09:12:41 +0100
commit3621588c04cbaa393ba62c97137f6aec746d114f (patch)
treeb70b6a84fa28c8e71463f661b969f575e90220e8
parent82bf34f1b0db8d202abf8cd4f5b6ce8b8aecfc1a (diff)
Support logLik and AIC for manual weights
Static documentation rebuilt by pkgdown
-rw-r--r--DESCRIPTION2
-rw-r--r--NEWS.md4
-rw-r--r--R/logLik.mkinfit.R13
-rw-r--r--docs/articles/FOCUS_D.html2
-rw-r--r--docs/articles/FOCUS_L.html38
-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/compiled_models.html12
-rw-r--r--docs/news/index.html7
-rw-r--r--docs/reference/Extract.mmkin.html10
-rw-r--r--docs/reference/logLik.mkinfit.html9
-rw-r--r--docs/reference/mccall81_245T.html12
-rw-r--r--docs/reference/mkinfit.html44
-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
-rw-r--r--docs/reference/transform_odeparms.html24
-rw-r--r--man/logLik.mkinfit.Rd6
20 files changed, 111 insertions, 94 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 4b5fd905..f2f1d6ea 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: mkin
Type: Package
Title: Kinetic Evaluation of Chemical Degradation Data
Version: 0.9.47.6
-Date: 2018-11-23
+Date: 2018-11-26
Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
email = "jranke@uni-bremen.de",
comment = c(ORCID = "0000-0003-4371-6538")),
diff --git a/NEWS.md b/NEWS.md
index cce1bea6..10211f96 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,6 @@
-# mkin 0.9.47.6 (2018-09-21)
+# mkin 0.9.47.6 (2018-11-26)
+
+- Add the function 'logLik.mkinfit.R' which makes it possible to calculate an AIC for mkinfit objects
- 'add_err': Respect the argument giving the number of replicates in the synthetic dataset
diff --git a/R/logLik.mkinfit.R b/R/logLik.mkinfit.R
index c30cc099..d3f4232d 100644
--- a/R/logLik.mkinfit.R
+++ b/R/logLik.mkinfit.R
@@ -19,12 +19,21 @@ logLik.mkinfit <- function(object, ...) {
y_ij <- object$data$observed
yhat_ij <- object$data$predicted
if (is.null(object$data$err)) {
+ # For unweighted fits we estimate a single value for sigma from the residuals
err <- sd(object$data$residual)
n_var_comp <- 1 # Number of variance components estimated
} else {
err <- object$data$err
- if (object$reweight.method == "obs") n_var_comp <- length(object$var_ms_unweighted)
- else n_var_comp <- 2
+ # For weighted fits we check for variance models used in IRLS
+ # If the variance values (err) were given and were not
+ # reweighted, the number of variance components estimated is zero
+ if (is.null(object$reweight.method)) {
+ n_var_comp <- 0
+ } else {
+ n_var_comp <- switch(object$reweight.method,
+ obs = length(object$var_ms_unweighted),
+ tc = 2)
+ }
}
prob_dens <- dnorm(y_ij, yhat_ij, err)
val <- log(prod(prob_dens))
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index b03e7612..0d463f63 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -84,7 +84,7 @@
<h1>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-11-23</h4>
+ <h4 class="date">2018-11-26</h4>
<div class="hidden name"><code>FOCUS_D.Rmd</code></div>
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index e83664bc..dc562002 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -84,7 +84,7 @@
<h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-11-23</h4>
+ <h4 class="date">2018-11-26</h4>
<div class="hidden name"><code>FOCUS_L.Rmd</code></div>
@@ -110,8 +110,8 @@
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw">summary</span>(m.L1.SFO)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.6
## R version used for fitting: 3.5.1
-## Date of fit: Fri Nov 23 20:47:25 2018
-## Date of summary: Fri Nov 23 20:47:25 2018
+## Date of fit: Mon Nov 26 09:07:07 2018
+## Date of summary: Mon Nov 26 09:07:07 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
@@ -201,15 +201,15 @@
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.6
## R version used for fitting: 3.5.1
-## Date of fit: Fri Nov 23 20:47:26 2018
-## Date of summary: Fri Nov 23 20:47:26 2018
+## Date of fit: Mon Nov 26 09:07:09 2018
+## Date of summary: Mon Nov 26 09:07:09 2018
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 611 model solutions performed in 1.467 s
+## Fitted with method Port using 611 model solutions performed in 1.481 s
##
## Weighting: none
##
@@ -296,15 +296,15 @@
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw">summary</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: 0.9.47.6
## R version used for fitting: 3.5.1
-## Date of fit: Fri Nov 23 20:47:27 2018
-## Date of summary: Fri Nov 23 20:47:27 2018
+## Date of fit: Mon Nov 26 09:07:10 2018
+## Date of summary: Mon Nov 26 09:07:10 2018
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 81 model solutions performed in 0.192 s
+## Fitted with method Port using 81 model solutions performed in 0.191 s
##
## Weighting: none
##
@@ -367,8 +367,8 @@
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw">summary</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: 0.9.47.6
## R version used for fitting: 3.5.1
-## Date of fit: Fri Nov 23 20:47:28 2018
-## Date of summary: Fri Nov 23 20:47:28 2018
+## Date of fit: Mon Nov 26 09:07:11 2018
+## Date of summary: Mon Nov 26 09:07:11 2018
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -377,7 +377,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.822 s
+## Fitted with method Port using 336 model solutions performed in 0.86 s
##
## Weighting: none
##
@@ -459,8 +459,8 @@
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.6
## R version used for fitting: 3.5.1
-## Date of fit: Fri Nov 23 20:47:29 2018
-## Date of summary: Fri Nov 23 20:47:29 2018
+## Date of fit: Mon Nov 26 09:07:12 2018
+## Date of summary: Mon Nov 26 09:07:12 2018
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -469,7 +469,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.336 s
+## Fitted with method Port using 137 model solutions performed in 0.339 s
##
## Weighting: none
##
@@ -560,8 +560,8 @@
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><span class="kw">summary</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: 0.9.47.6
## R version used for fitting: 3.5.1
-## Date of fit: Fri Nov 23 20:47:29 2018
-## Date of summary: Fri Nov 23 20:47:30 2018
+## Date of fit: Mon Nov 26 09:07:12 2018
+## Date of summary: Mon Nov 26 09:07:13 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
@@ -620,8 +620,8 @@
<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><span class="kw">summary</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: 0.9.47.6
## R version used for fitting: 3.5.1
-## Date of fit: Fri Nov 23 20:47:30 2018
-## Date of summary: Fri Nov 23 20:47:30 2018
+## Date of fit: Mon Nov 26 09:07:13 2018
+## Date of summary: Mon Nov 26 09:07:13 2018
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 4ead1062..e73b989a 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -84,7 +84,7 @@
<h1>Introduction to mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-11-23</h4>
+ <h4 class="date">2018-11-26</h4>
<div class="hidden name"><code>mkin.Rmd</code></div>
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 8c053c10..6ba7e1a7 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -84,7 +84,7 @@
<h1>Calculation of time weighted average concentrations with mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-11-23</h4>
+ <h4 class="date">2018-11-26</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 5215e039..6ebe3c73 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -84,7 +84,7 @@
<h1>Example evaluation of FOCUS dataset Z</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-11-23</h4>
+ <h4 class="date">2018-11-26</h4>
<div class="hidden name"><code>FOCUS_Z.Rmd</code></div>
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index c47425fb..25a3a62e 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -84,7 +84,7 @@
<h1>Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-11-23</h4>
+ <h4 class="date">2018-11-26</h4>
<div class="hidden name"><code>compiled_models.Rmd</code></div>
@@ -125,9 +125,9 @@
<a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div>
<pre><code>## Lade nötiges Paket: rbenchmark</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 3 deSolve, compiled 3 2.274 1.000 2.273 0
-## 1 deSolve, not compiled 3 17.686 7.777 17.676 0
-## 2 Eigenvalue based 3 2.800 1.231 2.799 0
+## 3 deSolve, compiled 3 2.296 1.000 2.295 0
+## 1 deSolve, not compiled 3 17.937 7.812 17.928 0
+## 2 Eigenvalue based 3 2.861 1.246 2.859 0
## user.child sys.child
## 3 0 0
## 1 0 0
@@ -156,8 +156,8 @@
<a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 2 deSolve, compiled 3 4.038 1.000 4.035 0
-## 1 deSolve, not compiled 3 37.805 9.362 37.788 0
+## 2 deSolve, compiled 3 4.020 1.000 4.017 0
+## 1 deSolve, not compiled 3 37.721 9.383 37.704 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 f3e57dd0..9f658dad 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -117,11 +117,12 @@
</div>
- <div id="mkin-0-9-47-6-2018-09-21" class="section level1">
+ <div id="mkin-0-9-47-6-2018-11-26" class="section level1">
<h1 class="page-header">
-<a href="#mkin-0-9-47-6-2018-09-21" class="anchor"></a>mkin 0.9.47.6 (2018-09-21)<small> Unreleased </small>
+<a href="#mkin-0-9-47-6-2018-11-26" class="anchor"></a>mkin 0.9.47.6 (2018-11-26)<small> Unreleased </small>
</h1>
<ul>
+<li><p>Add the function ‘logLik.mkinfit.R’ which makes it possible to calculate an AIC for mkinfit objects</p></li>
<li><p>‘add_err’: Respect the argument giving the number of replicates in the synthetic dataset</p></li>
<li><p>‘max_twa_parent’: Support maximum time weighted average concentration calculations for the hockey stick (HS) model</p></li>
<li><p>‘mkinpredict’: Make the function generic and create a method for mkinfit objects</p></li>
@@ -670,7 +671,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
- <li><a href="#mkin-0-9-47-6-2018-09-21">0.9.47.6</a></li>
+ <li><a href="#mkin-0-9-47-6-2018-11-26">0.9.47.6</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>
<li><a href="#mkin-0-9-47-2-2018-07-19">0.9.47.2</a></li>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index a595dd0d..ec2c7eb7 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -467,8 +467,8 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555be3c890&gt;
-#&gt; &lt;environment: 0x55555bc2f5a0&gt;
+#&gt; &lt;bytecode: 0x55555be327a0&gt;
+#&gt; &lt;environment: 0x55555bc27c20&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -490,8 +490,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555cd74468&gt;
-#&gt; &lt;environment: 0x55555bc2f5a0&gt;
+#&gt; &lt;bytecode: 0x55555cd76230&gt;
+#&gt; &lt;environment: 0x55555bc27c20&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -558,7 +558,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] "Fri Nov 23 20:45:37 2018"
+#&gt; [1] "Mon Nov 26 09:05:19 2018"
#&gt;
#&gt; $version
#&gt; [1] "0.9.47.6"
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index 1dda313f..250bc1d8 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -158,13 +158,16 @@
<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'>d_t</span> <span class='kw'>&lt;-</span> <span class='no'>FOCUS_2006_D</span>
<span class='no'>d_t</span>[<span class='fl'>23</span>:<span class='fl'>24</span>, <span class='st'>"value"</span>] <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='fl'>NA</span>) <span class='co'># can't cope with zero values at the moment</span>
- <span class='no'>f_nw</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'>d_t</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='no'>f_nw</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'>d_t</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># no weighting (weights are unity)</span>
<span class='no'>f_obs</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'>d_t</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>f_tc</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'>d_t</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'>AIC</span>(<span class='no'>f_nw</span>, <span class='no'>f_obs</span>, <span class='no'>f_tc</span>)</div><div class='output co'>#&gt; df AIC
+ <span class='no'>d_t</span>$<span class='no'>err</span> <span class='kw'>&lt;-</span> <span class='no'>d_t</span>$<span class='no'>value</span> <span class='co'># Manual weighting assuming sigma ~ y</span>
+ <span class='no'>f_man</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'>d_t</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='fu'>AIC</span>(<span class='no'>f_nw</span>, <span class='no'>f_obs</span>, <span class='no'>f_tc</span>, <span class='no'>f_man</span>)</div><div class='output co'>#&gt; df AIC
#&gt; f_nw 5 204.4619
#&gt; f_obs 6 205.8727
-#&gt; f_tc 6 143.8773</div></pre>
+#&gt; f_tc 6 143.8773
+#&gt; f_man 4 291.8000</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 90a538b6..505da201 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -158,8 +158,8 @@
<span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Nov 23 20:45:55 2018
-#&gt; Date of summary: Fri Nov 23 20:45:55 2018
+#&gt; Date of fit: Mon Nov 26 09:05:38 2018
+#&gt; Date of summary: Mon Nov 26 09:05:38 2018
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -169,7 +169,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 574 model solutions performed in 3.63 s
+#&gt; Fitted with method Port using 574 model solutions performed in 3.64 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -247,8 +247,8 @@
<span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Nov 23 20:45:57 2018
-#&gt; Date of summary: Fri Nov 23 20:45:57 2018
+#&gt; Date of fit: Mon Nov 26 09:05:40 2018
+#&gt; Date of summary: Mon Nov 26 09:05:40 2018
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -258,7 +258,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.547 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.626 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index b2e7363d..2017a35c 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -436,8 +436,8 @@
<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'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Nov 23 20:46:00 2018
-#&gt; Date of summary: Fri Nov 23 20:46:00 2018
+#&gt; Date of fit: Mon Nov 26 09:05:43 2018
+#&gt; Date of summary: Mon Nov 26 09:05:43 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -513,7 +513,7 @@
<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'>print</span>(<span class='fu'>system.time</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; User System verstrichen
-#&gt; 0.978 0.000 0.978 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.974 0.000 0.975 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </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
@@ -588,7 +588,7 @@
#&gt; Model cost at call 146 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; User System verstrichen
-#&gt; 0.794 0.000 0.795 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.796 0.000 0.796 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </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
@@ -626,8 +626,8 @@
<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>)
<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Nov 23 20:46:12 2018
-#&gt; Date of summary: Fri Nov 23 20:46:12 2018
+#&gt; Date of fit: Mon Nov 26 09:05:54 2018
+#&gt; Date of summary: Mon Nov 26 09:05:54 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -635,7 +635,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 186 model solutions performed in 0.816 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.885 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -743,8 +743,8 @@
#&gt; 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.irls</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'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Nov 23 20:46:14 2018
-#&gt; Date of summary: Fri Nov 23 20:46:14 2018
+#&gt; Date of fit: Mon Nov 26 09:05:57 2018
+#&gt; Date of summary: Mon Nov 26 09:05:57 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -752,7 +752,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 551 model solutions performed in 2.509 s
+#&gt; Fitted with method Port using 551 model solutions performed in 2.451 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -865,8 +865,8 @@
#&gt; 120 m1 33.31 28.80898 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</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'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Nov 23 20:46:15 2018
-#&gt; Date of summary: Fri Nov 23 20:46:15 2018
+#&gt; Date of fit: Mon Nov 26 09:05:58 2018
+#&gt; Date of summary: Mon Nov 26 09:05:58 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -874,7 +874,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.687 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.69 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -983,8 +983,8 @@
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Nov 23 20:46:16 2018
-#&gt; Date of summary: Fri Nov 23 20:46:16 2018
+#&gt; Date of fit: Mon Nov 26 09:05:59 2018
+#&gt; Date of summary: Mon Nov 26 09:05:59 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -992,7 +992,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.789 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.772 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1103,8 +1103,8 @@
<span class='no'>f.w.man</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Nov 23 20:46:17 2018
-#&gt; Date of summary: Fri Nov 23 20:46:17 2018
+#&gt; Date of fit: Mon Nov 26 09:06:00 2018
+#&gt; Date of summary: Mon Nov 26 09:06:00 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1112,7 +1112,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 270 model solutions performed in 1.212 s
+#&gt; Fitted with method Port using 270 model solutions performed in 1.201 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1221,8 +1221,8 @@
<span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)
<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Nov 23 20:46:21 2018
-#&gt; Date of summary: Fri Nov 23 20:46:21 2018
+#&gt; Date of fit: Mon Nov 26 09:06:03 2018
+#&gt; Date of summary: Mon Nov 26 09:06:03 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1230,7 +1230,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 692 model solutions performed in 3.081 s
+#&gt; Fitted with method Port using 692 model solutions performed in 3.087 s
#&gt;
#&gt; Weighting: manual
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index e16a4147..a7f26322 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -229,7 +229,7 @@ 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 file32ab4b1aa093.c 2&gt; file32ab4b1aa093.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file672328842b40.c 2&gt; file672328842b40.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 9b8be306..f26422a4 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -323,7 +323,7 @@
<span class='fu'>c</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'>seq</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'>system.time</span>(
+#&gt; 0.003 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</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'>c</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'>seq</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
@@ -333,7 +333,7 @@
<span class='fu'>c</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'>seq</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; 0.047 0.000 0.047 </div><div class='input'>
+#&gt; 0.041 0.000 0.040 </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; Model cost at call 1 : 552.5739
#&gt; Model cost at call 3 : 552.5739
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index fda9ba60..eb2e5bcf 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -189,8 +189,8 @@
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</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; 0.033 0.040 6.952 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 21.739 0.000 21.752 </div><div class='input'>
+#&gt; 0.043 0.032 6.850 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 21.779 0.000 21.791 </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; 0.7340480 0.2659520 0.7505686 0.2494314
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index a0ef5efe..9cb43d42 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -206,15 +206,15 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='fu'>summary</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: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Nov 23 20:47:10 2018
-#&gt; Date of summary: Fri Nov 23 20:47:10 2018
+#&gt; Date of fit: Mon Nov 26 09:06:53 2018
+#&gt; Date of summary: Mon Nov 26 09:06:53 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 35 model solutions performed in 0.081 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.083 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index f98580cb..6178527b 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -200,8 +200,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
<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='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Nov 23 20:47:18 2018
-#&gt; Date of summary: Fri Nov 23 20:47:18 2018
+#&gt; Date of fit: Mon Nov 26 09:07:01 2018
+#&gt; Date of summary: Mon Nov 26 09:07:01 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -209,7 +209,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.666 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.687 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -276,8 +276,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
</div><div class='input'><span class='no'>fit.2</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'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Nov 23 20:47:20 2018
-#&gt; Date of summary: Fri Nov 23 20:47:20 2018
+#&gt; Date of fit: Mon Nov 26 09:07:03 2018
+#&gt; Date of summary: Mon Nov 26 09:07:03 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -285,7 +285,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 350 model solutions performed in 1.539 s
+#&gt; Fitted with method Port using 350 model solutions performed in 1.537 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -364,8 +364,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='no'>fit.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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>)
<span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Nov 23 20:47:21 2018
-#&gt; Date of summary: Fri Nov 23 20:47:21 2018
+#&gt; Date of fit: Mon Nov 26 09:07:04 2018
+#&gt; Date of summary: Mon Nov 26 09:07:04 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -373,7 +373,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 186 model solutions performed in 0.824 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.827 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -448,8 +448,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='no'>fit.ff.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Nov 23 20:47:22 2018
-#&gt; Date of summary: Fri Nov 23 20:47:22 2018
+#&gt; Date of fit: Mon Nov 26 09:07:04 2018
+#&gt; Date of summary: Mon Nov 26 09:07:04 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -457,7 +457,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 104 model solutions performed in 0.458 s
+#&gt; Fitted with method Port using 104 model solutions performed in 0.454 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/man/logLik.mkinfit.Rd b/man/logLik.mkinfit.Rd
index 2f3e58a1..2f911d5b 100644
--- a/man/logLik.mkinfit.Rd
+++ b/man/logLik.mkinfit.Rd
@@ -30,10 +30,12 @@
)
d_t <- FOCUS_2006_D
d_t[23:24, "value"] <- c(NA, NA) # can't cope with zero values at the moment
- f_nw <- mkinfit(sfo_sfo, d_t, quiet = TRUE)
+ f_nw <- mkinfit(sfo_sfo, d_t, quiet = TRUE) # no weighting (weights are unity)
f_obs <- mkinfit(sfo_sfo, d_t, reweight.method = "obs", quiet = TRUE)
f_tc <- mkinfit(sfo_sfo, d_t, reweight.method = "tc", quiet = TRUE)
- AIC(f_nw, f_obs, f_tc)
+ d_t$err <- d_t$value # Manual weighting assuming sigma ~ y
+ f_man <- mkinfit(sfo_sfo, d_t, err = "err", quiet = TRUE)
+ AIC(f_nw, f_obs, f_tc, f_man)
}
\author{
Johannes Ranke

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