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-rw-r--r--docs/articles/FOCUS_D.html6
-rw-r--r--docs/articles/FOCUS_L.html38
-rw-r--r--docs/articles/web_only/compiled_models.html10
-rw-r--r--docs/index.html1
-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.html2
-rw-r--r--docs/reference/mmkin.html4
-rw-r--r--docs/reference/summary.mkinfit.html6
-rw-r--r--docs/reference/transform_odeparms.html24
12 files changed, 82 insertions, 81 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 4dd23fd2..33424756 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -163,8 +163,8 @@
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Thu Feb 21 15:13:35 2019
-## Date of summary: Thu Feb 21 15:13:35 2019
+## Date of fit: Thu Feb 21 16:13:41 2019
+## Date of summary: Thu Feb 21 16:13:41 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -172,7 +172,7 @@
##
## Model predictions using solution type deSolve
##
-## Fitted with method Port using 153 model solutions performed in 0.683 s
+## Fitted with method Port using 153 model solutions performed in 0.697 s
##
## Weighting: none
##
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 0820b21a..b422b315 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -111,15 +111,15 @@
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Thu Feb 21 15:13:37 2019
-## Date of summary: Thu Feb 21 15:13:37 2019
+## Date of fit: Thu Feb 21 16:13:43 2019
+## Date of summary: Thu Feb 21 16:13:43 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.101 s
+## Fitted with method Port using 37 model solutions performed in 0.095 s
##
## Weighting: none
##
@@ -202,15 +202,15 @@
<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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Thu Feb 21 15:13:39 2019
-## Date of summary: Thu Feb 21 15:13:39 2019
+## Date of fit: Thu Feb 21 16:13:45 2019
+## Date of summary: Thu Feb 21 16:13:45 2019
##
## 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 1.545 s
+## Fitted with method Port using 611 model solutions performed in 1.509 s
##
## Weighting: none
##
@@ -297,8 +297,8 @@
<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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Thu Feb 21 15:13:39 2019
-## Date of summary: Thu Feb 21 15:13:39 2019
+## Date of fit: Thu Feb 21 16:13:45 2019
+## Date of summary: Thu Feb 21 16:13:45 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -368,8 +368,8 @@
<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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Thu Feb 21 15:13:40 2019
-## Date of summary: Thu Feb 21 15:13:40 2019
+## Date of fit: Thu Feb 21 16:13:46 2019
+## Date of summary: Thu Feb 21 16:13:46 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -378,7 +378,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.852 s
+## Fitted with method Port using 336 model solutions performed in 0.842 s
##
## Weighting: none
##
@@ -460,8 +460,8 @@
<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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Thu Feb 21 15:13:41 2019
-## Date of summary: Thu Feb 21 15:13:41 2019
+## Date of fit: Thu Feb 21 16:13:47 2019
+## Date of summary: Thu Feb 21 16:13:48 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -561,15 +561,15 @@
<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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Thu Feb 21 15:13:42 2019
-## Date of summary: Thu Feb 21 15:13:42 2019
+## Date of fit: Thu Feb 21 16:13:48 2019
+## Date of summary: Thu Feb 21 16:13:48 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.112 s
+## Fitted with method Port using 46 model solutions performed in 0.11 s
##
## Weighting: none
##
@@ -621,15 +621,15 @@
<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"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Thu Feb 21 15:13:42 2019
-## Date of summary: Thu Feb 21 15:13:42 2019
+## Date of fit: Thu Feb 21 16:13:48 2019
+## Date of summary: Thu Feb 21 16:13:48 2019
##
## 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 0.169 s
+## Fitted with method Port using 66 model solutions performed in 0.163 s
##
## Weighting: none
##
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index b00fda46..8f13b969 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -126,9 +126,9 @@
<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 2.340 1.000 2.338 0
-## 1 deSolve, not compiled 3 17.729 7.576 17.720 0
-## 2 Eigenvalue based 3 2.889 1.235 2.888 0
+## 3 deSolve, compiled 3 2.347 1.000 2.346 0
+## 1 deSolve, not compiled 3 17.693 7.539 17.684 0
+## 2 Eigenvalue based 3 2.907 1.239 2.905 0
## user.child sys.child
## 3 0 0
## 1 0 0
@@ -157,8 +157,8 @@
<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 4.122 1.00 4.120 0
-## 1 deSolve, not compiled 3 37.471 9.09 37.452 0
+## 2 deSolve, compiled 3 4.278 1.000 4.276 0
+## 1 deSolve, not compiled 3 37.855 8.849 37.833 0
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
diff --git a/docs/index.html b/docs/index.html
index d7908ca2..1fe49776 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -191,6 +191,7 @@
<ul class="list-unstyled">
<li><a href="https://cran.r-project.org/package=mkin"><img src="https://www.r-pkg.org/badges/version/mkin"></a></li>
<li><a href="https://travis-ci.com/jranke/mkin"><img src="https://travis-ci.com/jranke/mkin.svg?branch=master" alt="Build Status"></a></li>
+<li><a href="https://codecov.io/github/jranke/mkin"><img src="https://codecov.io/github/jranke/mkin/branch/master/graphs/badge.svg" alt="codecov"></a></li>
</ul>
</div>
</div>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 39228ba7..8e018e96 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -280,7 +280,7 @@
#&gt;
#&gt; $time
#&gt; User System verstrichen
-#&gt; 0.197 0.000 0.197
+#&gt; 0.198 0.000 0.198
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -469,8 +469,8 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555920c328&gt;
-#&gt; &lt;environment: 0x555555b0eb48&gt;
+#&gt; &lt;bytecode: 0x55555920cdf0&gt;
+#&gt; &lt;environment: 0x5555562c5500&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -492,8 +492,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555a39faa0&gt;
-#&gt; &lt;environment: 0x555555b0eb48&gt;
+#&gt; &lt;bytecode: 0x55555a399838&gt;
+#&gt; &lt;environment: 0x5555562c5500&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -560,7 +560,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] "Thu Feb 21 15:11:41 2019"
+#&gt; [1] "Thu Feb 21 16:11:47 2019"
#&gt;
#&gt; $version
#&gt; [1] "0.9.48.1"
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index ce1c88e9..7d865dcf 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -160,8 +160,8 @@
<span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Feb 21 15:12:02 2019
-#&gt; Date of summary: Thu Feb 21 15:12:02 2019
+#&gt; Date of fit: Thu Feb 21 16:12:08 2019
+#&gt; Date of summary: Thu Feb 21 16:12:08 2019
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -171,7 +171,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 574 model solutions performed in 3.856 s
+#&gt; Fitted with method Port using 574 model solutions performed in 3.846 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -249,8 +249,8 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Feb 21 15:12:04 2019
-#&gt; Date of summary: Thu Feb 21 15:12:04 2019
+#&gt; Date of fit: Thu Feb 21 16:12:10 2019
+#&gt; Date of summary: Thu Feb 21 16:12:10 2019
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -260,7 +260,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.607 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.602 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 369d7bbe..5f57189c 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -438,15 +438,15 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Feb 21 15:12:07 2019
-#&gt; Date of summary: Thu Feb 21 15:12:07 2019
+#&gt; Date of fit: Thu Feb 21 16:12:13 2019
+#&gt; Date of summary: Thu Feb 21 16:12:13 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 64 model solutions performed in 0.164 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.16 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -515,7 +515,7 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.045 0.000 1.046 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 1.035 0.004 1.040 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; 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
@@ -590,7 +590,7 @@
#&gt; Model cost at call 146 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; User System verstrichen
-#&gt; 0.835 0.000 0.835 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.819 0.000 0.819 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; 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
@@ -628,8 +628,8 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Feb 21 15:12:19 2019
-#&gt; Date of summary: Thu Feb 21 15:12:19 2019
+#&gt; Date of fit: Thu Feb 21 16:12:25 2019
+#&gt; Date of summary: Thu Feb 21 16:12:25 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -637,7 +637,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 186 model solutions performed in 0.853 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.877 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -745,8 +745,8 @@
#&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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Feb 21 15:12:22 2019
-#&gt; Date of summary: Thu Feb 21 15:12:22 2019
+#&gt; Date of fit: Thu Feb 21 16:12:28 2019
+#&gt; Date of summary: Thu Feb 21 16:12:28 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -754,7 +754,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 551 model solutions performed in 2.573 s
+#&gt; Fitted with method Port using 551 model solutions performed in 2.574 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -867,8 +867,8 @@
#&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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Feb 21 15:12:22 2019
-#&gt; Date of summary: Thu Feb 21 15:12:22 2019
+#&gt; Date of fit: Thu Feb 21 16:12:29 2019
+#&gt; Date of summary: Thu Feb 21 16:12:29 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -876,7 +876,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.718 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.756 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -985,8 +985,8 @@
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Feb 21 15:12:23 2019
-#&gt; Date of summary: Thu Feb 21 15:12:23 2019
+#&gt; Date of fit: Thu Feb 21 16:12:30 2019
+#&gt; Date of summary: Thu Feb 21 16:12:30 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -994,7 +994,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.802 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.864 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1105,8 +1105,8 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Feb 21 15:12:25 2019
-#&gt; Date of summary: Thu Feb 21 15:12:25 2019
+#&gt; Date of fit: Thu Feb 21 16:12:31 2019
+#&gt; Date of summary: Thu Feb 21 16:12:31 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1114,7 +1114,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 270 model solutions performed in 1.251 s
+#&gt; Fitted with method Port using 270 model solutions performed in 1.306 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1223,8 +1223,8 @@
<span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Feb 21 15:12:28 2019
-#&gt; Date of summary: Thu Feb 21 15:12:28 2019
+#&gt; Date of fit: Thu Feb 21 16:12:35 2019
+#&gt; Date of summary: Thu Feb 21 16:12:35 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1232,7 +1232,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 692 model solutions performed in 3.31 s
+#&gt; Fitted with method Port using 692 model solutions performed in 3.309 s
#&gt;
#&gt; Weighting: manual
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index e4509e8a..79eb89d3 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -231,7 +231,7 @@ 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 file6490632228a0.c 2&gt; file6490632228a0.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file23f474fcf31d.c 2&gt; file23f474fcf31d.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 deb1335a..02b809a0 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -325,7 +325,7 @@
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.004 0.000 0.004 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
+#&gt; 0.004 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index af52e38a..71c347fd 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -191,8 +191,8 @@
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
<span class='no'>time_default</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.036 0.050 7.160 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 22.888 0.000 22.902 </div><div class='input'>
+#&gt; 0.051 0.032 7.366 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 23.290 0.000 23.305 </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 80298bb4..3b55635c 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -208,15 +208,15 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Feb 21 15:13:20 2019
-#&gt; Date of summary: Thu Feb 21 15:13:20 2019
+#&gt; Date of fit: Thu Feb 21 16:13:27 2019
+#&gt; Date of summary: Thu Feb 21 16:13:27 2019
#&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 0.087 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.086 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 088ea9d0..d15b0213 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -202,8 +202,8 @@ 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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Feb 21 15:13:29 2019
-#&gt; Date of summary: Thu Feb 21 15:13:29 2019
+#&gt; Date of fit: Thu Feb 21 16:13:35 2019
+#&gt; Date of summary: Thu Feb 21 16:13:35 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -211,7 +211,7 @@ 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 0.84 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.782 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -278,8 +278,8 @@ 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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Feb 21 15:13:30 2019
-#&gt; Date of summary: Thu Feb 21 15:13:30 2019
+#&gt; Date of fit: Thu Feb 21 16:13:37 2019
+#&gt; Date of summary: Thu Feb 21 16:13:37 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -287,7 +287,7 @@ 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 1.631 s
+#&gt; Fitted with method Port using 350 model solutions performed in 1.579 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -366,8 +366,8 @@ 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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Feb 21 15:13:32 2019
-#&gt; Date of summary: Thu Feb 21 15:13:32 2019
+#&gt; Date of fit: Thu Feb 21 16:13:38 2019
+#&gt; Date of summary: Thu Feb 21 16:13:38 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -375,7 +375,7 @@ 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 0.852 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.859 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -450,8 +450,8 @@ 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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Feb 21 15:13:32 2019
-#&gt; Date of summary: Thu Feb 21 15:13:32 2019
+#&gt; Date of fit: Thu Feb 21 16:13:39 2019
+#&gt; Date of summary: Thu Feb 21 16:13:39 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -459,7 +459,7 @@ 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 0.473 s
+#&gt; Fitted with method Port using 104 model solutions performed in 0.47 s
#&gt;
#&gt; Weighting: none
#&gt;

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