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-rw-r--r--docs/articles/FOCUS_L.html36
-rw-r--r--docs/articles/web_only/compiled_models.html12
-rw-r--r--docs/reference/Extract.mmkin.html12
-rw-r--r--docs/reference/logLik.mkinfit.html32
-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.html6
-rw-r--r--docs/reference/mmkin.html4
-rw-r--r--docs/reference/summary.mkinfit.html4
-rw-r--r--docs/reference/transform_odeparms.html24
-rw-r--r--man/logLik.mkinfit.Rd20
12 files changed, 127 insertions, 81 deletions
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index dc562002..02b3f60e 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -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: Mon Nov 26 09:07:07 2018
-## Date of summary: Mon Nov 26 09:07:07 2018
+## Date of fit: Mon Nov 26 09:29:29 2018
+## Date of summary: Mon Nov 26 09:29:29 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: Mon Nov 26 09:07:09 2018
-## Date of summary: Mon Nov 26 09:07:09 2018
+## Date of fit: Mon Nov 26 09:29:30 2018
+## Date of summary: Mon Nov 26 09:29:30 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 1.481 s
+## Fitted with method Port using 611 model solutions performed in 1.467 s
##
## Weighting: none
##
@@ -296,8 +296,8 @@
<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: Mon Nov 26 09:07:10 2018
-## Date of summary: Mon Nov 26 09:07:10 2018
+## Date of fit: Mon Nov 26 09:29:31 2018
+## Date of summary: Mon Nov 26 09:29:31 2018
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -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: Mon Nov 26 09:07:11 2018
-## Date of summary: Mon Nov 26 09:07:11 2018
+## Date of fit: Mon Nov 26 09:29:32 2018
+## Date of summary: Mon Nov 26 09:29:32 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 0.86 s
+## Fitted with method Port using 336 model solutions performed in 0.828 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: Mon Nov 26 09:07:12 2018
-## Date of summary: Mon Nov 26 09:07:12 2018
+## Date of fit: Mon Nov 26 09:29:33 2018
+## Date of summary: Mon Nov 26 09:29:33 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 0.339 s
+## Fitted with method Port using 137 model solutions performed in 0.334 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: Mon Nov 26 09:07:12 2018
-## Date of summary: Mon Nov 26 09:07:13 2018
+## Date of fit: Mon Nov 26 09:29:34 2018
+## Date of summary: Mon Nov 26 09:29:34 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
@@ -620,15 +620,15 @@
<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: Mon Nov 26 09:07:13 2018
-## Date of summary: Mon Nov 26 09:07:13 2018
+## Date of fit: Mon Nov 26 09:29:34 2018
+## Date of summary: Mon Nov 26 09:29:34 2018
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 66 model solutions performed in 0.159 s
+## Fitted with method Port using 66 model solutions performed in 0.158 s
##
## Weighting: none
##
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 25a3a62e..93c800bf 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -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 2.296 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
+## 3 deSolve, compiled 3 2.268 1.000 2.267 0
+## 1 deSolve, not compiled 3 18.698 8.244 18.690 0
+## 2 Eigenvalue based 3 2.812 1.240 2.811 0
## user.child sys.child
## 3 0 0
## 1 0 0
@@ -156,12 +156,12 @@
<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 4.020 1.000 4.017 0
-## 1 deSolve, not compiled 3 37.721 9.383 37.704 0
+## 2 deSolve, compiled 3 4.032 1.000 4.028 0
+## 1 deSolve, not compiled 3 39.759 9.861 39.741 0
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
-<p>Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!</p>
+<p>Here we get a performance benefit of a factor of 10 using the version of the differential equation model compiled from C code!</p>
<p>This vignette was built with mkin 0.9.47.6 on</p>
<pre><code>## R version 3.5.1 (2018-07-02)
## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index ec2c7eb7..33d90e5b 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -278,7 +278,7 @@
#&gt;
#&gt; $time
#&gt; User System verstrichen
-#&gt; 0.184 0.000 0.184
+#&gt; 0.182 0.000 0.183
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -467,8 +467,8 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555be327a0&gt;
-#&gt; &lt;environment: 0x55555bc27c20&gt;
+#&gt; &lt;bytecode: 0x55555be42410&gt;
+#&gt; &lt;environment: 0x55555bc697f8&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -490,8 +490,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555cd76230&gt;
-#&gt; &lt;environment: 0x55555bc27c20&gt;
+#&gt; &lt;bytecode: 0x55555cd2ca88&gt;
+#&gt; &lt;environment: 0x55555bc697f8&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -558,7 +558,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] "Mon Nov 26 09:05:19 2018"
+#&gt; [1] "Mon Nov 26 09:27:40 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 250bc1d8..5fd6c6d7 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -33,7 +33,21 @@
<meta property="og:title" content="Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit" />
<meta property="og:description" content="This function simply calculates the product of the likelihood densities
- calc" />
+ calculated using dnorm, i.e. assuming normal distribution.
+The total number of estimated parameters returned with the value
+ of the likelihood is calculated as the sum of fitted degradation
+ model parameters and the fitted error model parameters.
+For the case of unweighted least squares fitting, we calculate one
+ constant standard deviation from the residuals using sd
+ and add one to the number of fitted degradation model parameters.
+For the case of manual weighting, we use the weight given for each
+ observation as standard deviation in calculating its likelihood.
+In the case of iterative reweighting, the variances obtained by this
+ procedure are used in the likelihood calculations, and the number of
+ estimated parameters is obtained by the number of degradation model
+ parameters plus the number of variance model parameters, i.e. the number of
+ observed variables if the reweighting method is &quot;obs&quot;, and two if the
+ reweighting method is &quot;tc&quot;." />
<meta name="twitter:card" content="summary" />
@@ -125,7 +139,21 @@
<div class="ref-description">
<p>This function simply calculates the product of the likelihood densities
- calc</p>
+ calculated using <code>dnorm</code>, i.e. assuming normal distribution.</p>
+<p>The total number of estimated parameters returned with the value
+ of the likelihood is calculated as the sum of fitted degradation
+ model parameters and the fitted error model parameters.</p>
+<p>For the case of unweighted least squares fitting, we calculate one
+ constant standard deviation from the residuals using <code>sd</code>
+ and add one to the number of fitted degradation model parameters.</p>
+<p>For the case of manual weighting, we use the weight given for each
+ observation as standard deviation in calculating its likelihood.</p>
+<p>In the case of iterative reweighting, the variances obtained by this
+ procedure are used in the likelihood calculations, and the number of
+ estimated parameters is obtained by the number of degradation model
+ parameters plus the number of variance model parameters, i.e. the number of
+ observed variables if the reweighting method is "obs", and two if the
+ reweighting method is "tc".</p>
</div>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 505da201..2cd933e9 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: Mon Nov 26 09:05:38 2018
-#&gt; Date of summary: Mon Nov 26 09:05:38 2018
+#&gt; Date of fit: Mon Nov 26 09:27:59 2018
+#&gt; Date of summary: Mon Nov 26 09:27:59 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 3.64 s
+#&gt; Fitted with method Port using 574 model solutions performed in 3.635 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: Mon Nov 26 09:05:40 2018
-#&gt; Date of summary: Mon Nov 26 09:05:40 2018
+#&gt; Date of fit: Mon Nov 26 09:28:01 2018
+#&gt; Date of summary: Mon Nov 26 09:28:01 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 1.626 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.623 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 2017a35c..addd9c30 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: Mon Nov 26 09:05:43 2018
-#&gt; Date of summary: Mon Nov 26 09:05:43 2018
+#&gt; Date of fit: Mon Nov 26 09:28:04 2018
+#&gt; Date of summary: Mon Nov 26 09:28:04 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; 0.974 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; 1.009 0.000 1.009 </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; 0.796 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; 0.909 0.000 0.910 </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: Mon Nov 26 09:05:54 2018
-#&gt; Date of summary: Mon Nov 26 09:05:54 2018
+#&gt; Date of fit: Mon Nov 26 09:28:16 2018
+#&gt; Date of summary: Mon Nov 26 09:28:16 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 0.885 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.927 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: Mon Nov 26 09:05:57 2018
-#&gt; Date of summary: Mon Nov 26 09:05:57 2018
+#&gt; Date of fit: Mon Nov 26 09:28:18 2018
+#&gt; Date of summary: Mon Nov 26 09:28:18 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 2.451 s
+#&gt; Fitted with method Port using 551 model solutions performed in 2.509 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: Mon Nov 26 09:05:58 2018
-#&gt; Date of summary: Mon Nov 26 09:05:58 2018
+#&gt; Date of fit: Mon Nov 26 09:28:19 2018
+#&gt; Date of summary: Mon Nov 26 09:28:19 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 0.69 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.68 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: Mon Nov 26 09:05:59 2018
-#&gt; Date of summary: Mon Nov 26 09:05:59 2018
+#&gt; Date of fit: Mon Nov 26 09:28:20 2018
+#&gt; Date of summary: Mon Nov 26 09:28:20 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 0.772 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.775 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: Mon Nov 26 09:06:00 2018
-#&gt; Date of summary: Mon Nov 26 09:06:00 2018
+#&gt; Date of fit: Mon Nov 26 09:28:22 2018
+#&gt; Date of summary: Mon Nov 26 09:28:22 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 1.201 s
+#&gt; Fitted with method Port using 270 model solutions performed in 1.203 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: Mon Nov 26 09:06:03 2018
-#&gt; Date of summary: Mon Nov 26 09:06:03 2018
+#&gt; Date of fit: Mon Nov 26 09:28:25 2018
+#&gt; Date of summary: Mon Nov 26 09:28:25 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 3.087 s
+#&gt; Fitted with method Port using 692 model solutions performed in 3.078 s
#&gt;
#&gt; Weighting: manual
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index a7f26322..448c0e8e 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 file672328842b40.c 2&gt; file672328842b40.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file775a236112e7.c 2&gt; file775a236112e7.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 f26422a4..84e6591b 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -323,17 +323,17 @@
<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; 0.003 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.004 0.000 0.004 </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
#&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'>system.time</span>(
+#&gt; 0.001 0.000 0.002 </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='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; 0.041 0.000 0.040 </div><div class='input'>
+#&gt; 0.039 0.000 0.039 </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 eb2e5bcf..a27cf5db 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; 0.043 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'>
+#&gt; 0.038 0.036 6.851 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 21.780 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 9cb43d42..7f510c67 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -206,8 +206,8 @@
<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: Mon Nov 26 09:06:53 2018
-#&gt; Date of summary: Mon Nov 26 09:06:53 2018
+#&gt; Date of fit: Mon Nov 26 09:29:14 2018
+#&gt; Date of summary: Mon Nov 26 09:29:14 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 6178527b..24b50890 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: Mon Nov 26 09:07:01 2018
-#&gt; Date of summary: Mon Nov 26 09:07:01 2018
+#&gt; Date of fit: Mon Nov 26 09:29:22 2018
+#&gt; Date of summary: Mon Nov 26 09:29:22 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 0.687 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.683 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: Mon Nov 26 09:07:03 2018
-#&gt; Date of summary: Mon Nov 26 09:07:03 2018
+#&gt; Date of fit: Mon Nov 26 09:29:24 2018
+#&gt; Date of summary: Mon Nov 26 09:29:24 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 1.537 s
+#&gt; Fitted with method Port using 350 model solutions performed in 1.594 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: Mon Nov 26 09:07:04 2018
-#&gt; Date of summary: Mon Nov 26 09:07:04 2018
+#&gt; Date of fit: Mon Nov 26 09:29:25 2018
+#&gt; Date of summary: Mon Nov 26 09:29:25 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 0.827 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.819 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: Mon Nov 26 09:07:04 2018
-#&gt; Date of summary: Mon Nov 26 09:07:04 2018
+#&gt; Date of fit: Mon Nov 26 09:29:26 2018
+#&gt; Date of summary: Mon Nov 26 09:29:26 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 0.454 s
+#&gt; Fitted with method Port using 104 model solutions performed in 0.486 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/man/logLik.mkinfit.Rd b/man/logLik.mkinfit.Rd
index 2f911d5b..78c4e4c2 100644
--- a/man/logLik.mkinfit.Rd
+++ b/man/logLik.mkinfit.Rd
@@ -5,7 +5,25 @@
}
\description{
This function simply calculates the product of the likelihood densities
- calc
+ calculated using \code{\link{dnorm}}, i.e. assuming normal distribution.
+
+ The total number of estimated parameters returned with the value
+ of the likelihood is calculated as the sum of fitted degradation
+ model parameters and the fitted error model parameters.
+
+ For the case of unweighted least squares fitting, we calculate one
+ constant standard deviation from the residuals using \code{\link{sd}}
+ and add one to the number of fitted degradation model parameters.
+
+ For the case of manual weighting, we use the weight given for each
+ observation as standard deviation in calculating its likelihood.
+
+ In the case of iterative reweighting, the variances obtained by this
+ procedure are used in the likelihood calculations, and the number of
+ estimated parameters is obtained by the number of degradation model
+ parameters plus the number of variance model parameters, i.e. the number of
+ observed variables if the reweighting method is "obs", and two if the
+ reweighting method is "tc".
}
\usage{
\method{logLik}{mkinfit}(object, ...)

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