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-rw-r--r--docs/articles/FOCUS_L.html38
-rw-r--r--docs/articles/web_only/compiled_models.html10
-rw-r--r--docs/reference/Extract.mmkin.html10
-rw-r--r--docs/reference/mccall81_245T.html12
-rw-r--r--docs/reference/mkinfit.html42
-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.html4
-rw-r--r--docs/reference/transform_odeparms.html24
10 files changed, 75 insertions, 75 deletions
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 37b4306f..e83664bc 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -110,15 +110,15 @@
<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 19:58:49 2018
-## Date of summary: Fri Nov 23 19:58:49 2018
+## Date of fit: Fri Nov 23 20:47:25 2018
+## Date of summary: Fri Nov 23 20:47:25 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.095 s
+## Fitted with method Port using 37 model solutions performed in 0.094 s
##
## Weighting: none
##
@@ -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 19:58:51 2018
-## Date of summary: Fri Nov 23 19:58:51 2018
+## Date of fit: Fri Nov 23 20:47:26 2018
+## Date of summary: Fri Nov 23 20:47:26 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 1.464 s
+## Fitted with method Port using 611 model solutions performed in 1.467 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 19:58:51 2018
-## Date of summary: Fri Nov 23 19:58:51 2018
+## Date of fit: Fri Nov 23 20:47:27 2018
+## Date of summary: Fri Nov 23 20:47:27 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 0.191 s
+## Fitted with method Port using 81 model solutions performed in 0.192 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 19:58:52 2018
-## Date of summary: Fri Nov 23 19:58:52 2018
+## Date of fit: Fri Nov 23 20:47:28 2018
+## Date of summary: Fri Nov 23 20:47:28 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 0.824 s
+## Fitted with method Port using 336 model solutions performed in 0.822 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 19:58:53 2018
-## Date of summary: Fri Nov 23 19:58:54 2018
+## Date of fit: Fri Nov 23 20:47:29 2018
+## Date of summary: Fri Nov 23 20:47:29 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 0.344 s
+## Fitted with method Port using 137 model solutions performed in 0.336 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 19:58:54 2018
-## Date of summary: Fri Nov 23 19:58:54 2018
+## Date of fit: Fri Nov 23 20:47:29 2018
+## Date of summary: Fri Nov 23 20:47:30 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 19:58:54 2018
-## Date of summary: Fri Nov 23 19:58:54 2018
+## Date of fit: Fri Nov 23 20:47:30 2018
+## Date of summary: Fri Nov 23 20:47:30 2018
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 85efff61..c47425fb 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 2.284 1.000 2.282 0
-## 1 deSolve, not compiled 3 17.732 7.764 17.724 0
-## 2 Eigenvalue based 3 2.812 1.231 2.809 0
+## 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
## 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 4.029 1.000 4.026 0
-## 1 deSolve, not compiled 3 37.760 9.372 37.744 0
+## 2 deSolve, compiled 3 4.038 1.000 4.035 0
+## 1 deSolve, not compiled 3 37.805 9.362 37.788 0
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index a74a3067..a595dd0d 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: 0x55555be47f20&gt;
-#&gt; &lt;environment: 0x55555bc31c70&gt;
+#&gt; &lt;bytecode: 0x55555be3c890&gt;
+#&gt; &lt;environment: 0x55555bc2f5a0&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -490,8 +490,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555cd8de90&gt;
-#&gt; &lt;environment: 0x55555bc31c70&gt;
+#&gt; &lt;bytecode: 0x55555cd74468&gt;
+#&gt; &lt;environment: 0x55555bc2f5a0&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 19:56:59 2018"
+#&gt; [1] "Fri Nov 23 20:45:37 2018"
#&gt;
#&gt; $version
#&gt; [1] "0.9.47.6"
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 9f937a12..90a538b6 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 19:57:18 2018
-#&gt; Date of summary: Fri Nov 23 19:57:18 2018
+#&gt; Date of fit: Fri Nov 23 20:45:55 2018
+#&gt; Date of summary: Fri Nov 23 20:45:55 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 3.661 s
+#&gt; Fitted with method Port using 574 model solutions performed in 3.63 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 19:57:19 2018
-#&gt; Date of summary: Fri Nov 23 19:57:19 2018
+#&gt; Date of fit: Fri Nov 23 20:45:57 2018
+#&gt; Date of summary: Fri Nov 23 20:45:57 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 1.549 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.547 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 9bbe3900..b2e7363d 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 19:57:22 2018
-#&gt; Date of summary: Fri Nov 23 19:57:22 2018
+#&gt; Date of fit: Fri Nov 23 20:46:00 2018
+#&gt; Date of summary: Fri Nov 23 20:46:00 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; 0.995 0.000 0.995 </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; 0.978 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; 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; 0.789 0.000 0.790 </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; 0.794 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; 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 19:57:34 2018
-#&gt; Date of summary: Fri Nov 23 19:57:34 2018
+#&gt; Date of fit: Fri Nov 23 20:46:12 2018
+#&gt; Date of summary: Fri Nov 23 20:46:12 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 0.825 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.816 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 19:57:36 2018
-#&gt; Date of summary: Fri Nov 23 19:57:36 2018
+#&gt; Date of fit: Fri Nov 23 20:46:14 2018
+#&gt; Date of summary: Fri Nov 23 20:46:14 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 2.528 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: Fri Nov 23 19:57:37 2018
-#&gt; Date of summary: Fri Nov 23 19:57:37 2018
+#&gt; Date of fit: Fri Nov 23 20:46:15 2018
+#&gt; Date of summary: Fri Nov 23 20:46:15 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -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 19:57:38 2018
-#&gt; Date of summary: Fri Nov 23 19:57:38 2018
+#&gt; Date of fit: Fri Nov 23 20:46:16 2018
+#&gt; Date of summary: Fri Nov 23 20:46:16 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 0.781 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.789 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 19:57:39 2018
-#&gt; Date of summary: Fri Nov 23 19:57:39 2018
+#&gt; Date of fit: Fri Nov 23 20:46:17 2018
+#&gt; Date of summary: Fri Nov 23 20:46:17 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 1.212 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 19:57:43 2018
-#&gt; Date of summary: Fri Nov 23 19:57:43 2018
+#&gt; Date of fit: Fri Nov 23 20:46:21 2018
+#&gt; Date of summary: Fri Nov 23 20:46:21 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 3.081 s
#&gt;
#&gt; Weighting: manual
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 3148efd8..e16a4147 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 file140043d42642.c 2&gt; file140043d42642.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file32ab4b1aa093.c 2&gt; file32ab4b1aa093.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 baa67000..9b8be306 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 0.004 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.004 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; 0.039 0.000 0.040 </div><div class='input'>
+#&gt; 0.047 0.000 0.047 </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 8bc7b18c..fda9ba60 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; 0.029 0.039 6.854 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 22.091 0.000 22.106 </div><div class='input'>
+#&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'>
<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 9428f187..a0ef5efe 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: Fri Nov 23 19:58:33 2018
-#&gt; Date of summary: Fri Nov 23 19:58:33 2018
+#&gt; Date of fit: Fri Nov 23 20:47:10 2018
+#&gt; Date of summary: Fri Nov 23 20:47:10 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 aa82269a..f98580cb 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 19:58:40 2018
-#&gt; Date of summary: Fri Nov 23 19:58:40 2018
+#&gt; Date of fit: Fri Nov 23 20:47:18 2018
+#&gt; Date of summary: Fri Nov 23 20:47:18 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 0.688 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.666 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 19:58:42 2018
-#&gt; Date of summary: Fri Nov 23 19:58:42 2018
+#&gt; Date of fit: Fri Nov 23 20:47:20 2018
+#&gt; Date of summary: Fri Nov 23 20:47:20 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 1.608 s
+#&gt; Fitted with method Port using 350 model solutions performed in 1.539 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 19:58:43 2018
-#&gt; Date of summary: Fri Nov 23 19:58:43 2018
+#&gt; Date of fit: Fri Nov 23 20:47:21 2018
+#&gt; Date of summary: Fri Nov 23 20:47:21 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 0.821 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.824 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 19:58:44 2018
-#&gt; Date of summary: Fri Nov 23 19:58:44 2018
+#&gt; Date of fit: Fri Nov 23 20:47:22 2018
+#&gt; Date of summary: Fri Nov 23 20:47:22 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 0.46 s
+#&gt; Fitted with method Port using 104 model solutions performed in 0.458 s
#&gt;
#&gt; Weighting: none
#&gt;

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