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-rw-r--r--docs/articles/FOCUS_L.html40
-rw-r--r--docs/articles/web_only/compiled_models.html10
-rw-r--r--docs/news/index.html10
-rw-r--r--docs/reference/Extract.mmkin.html12
-rw-r--r--docs/reference/mccall81_245T.html12
-rw-r--r--docs/reference/mkinfit.html46
-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.html6
-rw-r--r--docs/reference/transform_odeparms.html24
11 files changed, 82 insertions, 90 deletions
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index f1a91c04..2a99a609 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: 0.9.47.5
## R version used for fitting: 3.5.1
-## Date of fit: Fri Sep 14 18:22:23 2018
-## Date of summary: Fri Sep 14 18:22:23 2018
+## Date of fit: Fri Sep 14 21:00:22 2018
+## Date of summary: Fri Sep 14 21:00:22 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 0.092 s
+## Fitted with method Port using 37 model solutions performed in 0.087 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: 0.9.47.5
## R version used for fitting: 3.5.1
-## Date of fit: Fri Sep 14 18:22:25 2018
-## Date of summary: Fri Sep 14 18:22:25 2018
+## Date of fit: Fri Sep 14 21:00:23 2018
+## Date of summary: Fri Sep 14 21:00:23 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 1.355 s
+## Fitted with method Port using 611 model solutions performed in 1.352 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: 0.9.47.5
## R version used for fitting: 3.5.1
-## Date of fit: Fri Sep 14 18:22:25 2018
-## Date of summary: Fri Sep 14 18:22:25 2018
+## Date of fit: Fri Sep 14 21:00:24 2018
+## Date of summary: Fri Sep 14 21:00:24 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: 0.9.47.5
## R version used for fitting: 3.5.1
-## Date of fit: Fri Sep 14 18:22:26 2018
-## Date of summary: Fri Sep 14 18:22:26 2018
+## Date of fit: Fri Sep 14 21:00:25 2018
+## Date of summary: Fri Sep 14 21:00:25 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 0.756 s
+## Fitted with method Port using 336 model solutions performed in 0.758 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: 0.9.47.5
## R version used for fitting: 3.5.1
-## Date of fit: Fri Sep 14 18:22:27 2018
-## Date of summary: Fri Sep 14 18:22:28 2018
+## Date of fit: Fri Sep 14 21:00:26 2018
+## Date of summary: Fri Sep 14 21:00:26 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 0.322 s
+## Fitted with method Port using 137 model solutions performed in 0.31 s
##
## Weighting: none
##
@@ -560,15 +560,15 @@
<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: 0.9.47.5
## R version used for fitting: 3.5.1
-## Date of fit: Fri Sep 14 18:22:28 2018
-## Date of summary: Fri Sep 14 18:22:28 2018
+## Date of fit: Fri Sep 14 21:00:26 2018
+## Date of summary: Fri Sep 14 21:00:27 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.101 s
+## Fitted with method Port using 46 model solutions performed in 0.102 s
##
## Weighting: none
##
@@ -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: 0.9.47.5
## R version used for fitting: 3.5.1
-## Date of fit: Fri Sep 14 18:22:28 2018
-## Date of summary: Fri Sep 14 18:22:28 2018
+## Date of fit: Fri Sep 14 21:00:26 2018
+## Date of summary: Fri Sep 14 21:00:27 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 0.16 s
+## Fitted with method Port using 66 model solutions performed in 0.151 s
##
## Weighting: none
##
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 12c192f0..9aac1ab2 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 2.115 1.000 2.114 0
-## 1 deSolve, not compiled 3 16.235 7.676 16.228 0
-## 2 Eigenvalue based 3 2.589 1.224 2.587 0
+## 3 deSolve, compiled 3 2.134 1.000 2.132 0
+## 1 deSolve, not compiled 3 16.165 7.575 16.157 0
+## 2 Eigenvalue based 3 2.597 1.217 2.595 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 3.887 1.000 3.885 0
-## 1 deSolve, not compiled 3 35.492 9.131 35.474 0
+## 2 deSolve, compiled 3 3.717 1.000 3.715 0
+## 1 deSolve, not compiled 3 34.646 9.321 34.630 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 cbfcdde0..73eb7aa2 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -124,14 +124,7 @@
<ul>
<li><p>Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows</p></li>
<li><p>Move two vignettes to a location where they will not be built on CRAN (to avoid more NOTES from long execution times)</p></li>
-</ul>
-</div>
- <div id="mkin-0-9-47-4" class="section level1">
-<h1 class="page-header">
-<a href="#mkin-0-9-47-4" class="anchor"></a>mkin 0.9.47.4<small> Unreleased </small>
-</h1>
-<ul>
-<li>Exclude more example code from testing on CRAN to avoid NOTES from long execution times</li>
+<li><p>Exclude more example code from testing on CRAN to avoid NOTES from long execution times</p></li>
</ul>
</div>
<div id="mkin-0-9-47-3" class="section level1">
@@ -666,7 +659,6 @@
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#mkin-0-9-47-5-2018-09-14">0.9.47.5</a></li>
- <li><a href="#mkin-0-9-47-4">0.9.47.4</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>
<li><a href="#mkin-0-9-47-1-2018-02-06">0.9.47.1</a></li>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 91226e69..97562d44 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; 0.166 0.000 0.166
+#&gt; 0.177 0.000 0.176
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -467,8 +467,8 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555bd812a0&gt;
-#&gt; &lt;environment: 0x55555bc871e8&gt;
+#&gt; &lt;bytecode: 0x55555bd7f230&gt;
+#&gt; &lt;environment: 0x55555bc85178&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -490,8 +490,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555caa1d18&gt;
-#&gt; &lt;environment: 0x55555bc871e8&gt;
+#&gt; &lt;bytecode: 0x55555ca9fca8&gt;
+#&gt; &lt;environment: 0x55555bc85178&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -558,7 +558,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] "Fri Sep 14 18:20:46 2018"
+#&gt; [1] "Fri Sep 14 20:58:46 2018"
#&gt;
#&gt; $version
#&gt; [1] "0.9.47.5"
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index d91431f3..52c09969 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: 0.9.47.5
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 18:20:57 2018
-#&gt; Date of summary: Fri Sep 14 18:20:57 2018
+#&gt; Date of fit: Fri Sep 14 20:58:58 2018
+#&gt; Date of summary: Fri Sep 14 20:58:58 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 3.418 s
+#&gt; Fitted with method Port using 574 model solutions performed in 3.393 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: 0.9.47.5
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 18:20:59 2018
-#&gt; Date of summary: Fri Sep 14 18:20:59 2018
+#&gt; Date of fit: Fri Sep 14 20:58:59 2018
+#&gt; Date of summary: Fri Sep 14 20:59:00 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 1.458 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.451 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 261d48fb..f3c6d595 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -434,15 +434,15 @@
<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: 0.9.47.5
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 18:21:02 2018
-#&gt; Date of summary: Fri Sep 14 18:21:02 2018
+#&gt; Date of fit: Fri Sep 14 20:59:02 2018
+#&gt; Date of summary: Fri Sep 14 20:59:02 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 64 model solutions performed in 0.143 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.141 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -511,7 +511,7 @@
<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; 0.918 0.000 0.919 </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; 0.895 0.000 0.897 </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
@@ -586,7 +586,7 @@
#&gt; Model cost at call 146 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; User System verstrichen
-#&gt; 0.757 0.000 0.757 </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; 0.726 0.000 0.726 </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
@@ -624,8 +624,8 @@
<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: 0.9.47.5
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 18:21:13 2018
-#&gt; Date of summary: Fri Sep 14 18:21:13 2018
+#&gt; Date of fit: Fri Sep 14 20:59:13 2018
+#&gt; Date of summary: Fri Sep 14 20:59:13 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -633,7 +633,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 186 model solutions performed in 0.775 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.757 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -741,8 +741,8 @@
#&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: 0.9.47.5
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 18:21:15 2018
-#&gt; Date of summary: Fri Sep 14 18:21:15 2018
+#&gt; Date of fit: Fri Sep 14 20:59:15 2018
+#&gt; Date of summary: Fri Sep 14 20:59:16 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -750,7 +750,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 551 model solutions performed in 2.282 s
+#&gt; Fitted with method Port using 551 model solutions performed in 2.329 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -863,8 +863,8 @@
#&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: 0.9.47.5
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 18:21:16 2018
-#&gt; Date of summary: Fri Sep 14 18:21:16 2018
+#&gt; Date of fit: Fri Sep 14 20:59:16 2018
+#&gt; Date of summary: Fri Sep 14 20:59:16 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -872,7 +872,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.653 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.628 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -981,8 +981,8 @@
<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: 0.9.47.5
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 18:21:17 2018
-#&gt; Date of summary: Fri Sep 14 18:21:17 2018
+#&gt; Date of fit: Fri Sep 14 20:59:17 2018
+#&gt; Date of summary: Fri Sep 14 20:59:17 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -990,7 +990,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.721 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.713 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1101,8 +1101,8 @@
<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: 0.9.47.5
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 18:21:18 2018
-#&gt; Date of summary: Fri Sep 14 18:21:18 2018
+#&gt; Date of fit: Fri Sep 14 20:59:18 2018
+#&gt; Date of summary: Fri Sep 14 20:59:18 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1110,7 +1110,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 270 model solutions performed in 1.215 s
+#&gt; Fitted with method Port using 270 model solutions performed in 1.119 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1219,8 +1219,8 @@
<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: 0.9.47.5
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 18:21:22 2018
-#&gt; Date of summary: Fri Sep 14 18:21:22 2018
+#&gt; Date of fit: Fri Sep 14 20:59:21 2018
+#&gt; Date of summary: Fri Sep 14 20:59:21 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1228,7 +1228,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 692 model solutions performed in 3.114 s
+#&gt; Fitted with method Port using 692 model solutions performed in 2.955 s
#&gt;
#&gt; Weighting: manual
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 9048c1b1..464178bc 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 file49ec17c0788e.c 2&gt; file49ec17c0788e.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file7aee6cc2a6d.c 2&gt; file7aee6cc2a6d.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 6c30d7a8..dfcd08a8 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -321,17 +321,17 @@
<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 0.003 </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
#&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; 0.035 0.000 0.035 </div></pre>
+#&gt; 0.036 0.000 0.036 </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index d630ef3e..383e5928 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; 0.059 0.027 6.918 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 21.127 0.000 21.141 </div><div class='input'>
+#&gt; 0.056 0.024 6.712 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 20.446 0.000 20.459 </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 cb6beda2..317c7a87 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: 0.9.47.5
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 18:22:10 2018
-#&gt; Date of summary: Fri Sep 14 18:22:10 2018
+#&gt; Date of fit: Fri Sep 14 21:00:08 2018
+#&gt; Date of summary: Fri Sep 14 21:00:08 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 0.076 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.081 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index db92667c..6f7ec4a4 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: 0.9.47.5
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 18:22:17 2018
-#&gt; Date of summary: Fri Sep 14 18:22:17 2018
+#&gt; Date of fit: Fri Sep 14 21:00:16 2018
+#&gt; Date of summary: Fri Sep 14 21:00:16 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 0.701 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.71 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: 0.9.47.5
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 18:22:19 2018
-#&gt; Date of summary: Fri Sep 14 18:22:19 2018
+#&gt; Date of fit: Fri Sep 14 21:00:17 2018
+#&gt; Date of summary: Fri Sep 14 21:00:17 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 1.431 s
+#&gt; Fitted with method Port using 350 model solutions performed in 1.417 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: 0.9.47.5
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 18:22:20 2018
-#&gt; Date of summary: Fri Sep 14 18:22:20 2018
+#&gt; Date of fit: Fri Sep 14 21:00:18 2018
+#&gt; Date of summary: Fri Sep 14 21:00:18 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 0.778 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.755 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: 0.9.47.5
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 18:22:20 2018
-#&gt; Date of summary: Fri Sep 14 18:22:20 2018
+#&gt; Date of fit: Fri Sep 14 21:00:19 2018
+#&gt; Date of summary: Fri Sep 14 21:00:19 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 0.417 s
+#&gt; Fitted with method Port using 104 model solutions performed in 0.416 s
#&gt;
#&gt; Weighting: none
#&gt;

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