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132 files changed, 405 insertions, 250 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index f32d7f82..1c4edbd0 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -24,7 +24,13 @@
<li>
<a href="../news/index.html">News</a>
</li>
- </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
+ </ul><ul class="nav navbar-nav navbar-right"><li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul></div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -110,8 +116,8 @@
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Wed Nov 2 16:25:22 2016
-## Date of summary: Wed Nov 2 16:25:22 2016
+## Date of fit: Fri Nov 4 16:56:20 2016
+## Date of summary: Fri Nov 4 16:56:20 2016
##
## Equations:
## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -119,7 +125,7 @@
##
## Model predictions using solution type deSolve
##
-## Fitted with method Port using 153 model solutions performed in 0.665 s
+## Fitted with method Port using 153 model solutions performed in 0.661 s
##
## Weighting: none
##
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diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 6a9c6ba5..2244a359 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -24,7 +24,13 @@
<li>
<a href="../news/index.html">News</a>
</li>
- </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
+ </ul><ul class="nav navbar-nav navbar-right"><li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul></div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -57,15 +63,15 @@ FOCUS_2006_L1_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<span class="kw">summary</span>(m.L1.SFO)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 4 15:38:03 2016
-## Date of summary: Fri Nov 4 15:38:03 2016
+## Date of fit: Fri Nov 4 16:56:21 2016
+## Date of summary: Fri Nov 4 16:56:21 2016
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.089 s
+## Fitted with method Port using 37 model solutions performed in 0.087 s
##
## Weighting: none
##
@@ -150,8 +156,8 @@ FOCUS_2006_L1_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 4 15:38:04 2016
-## Date of summary: Fri Nov 4 15:38:04 2016
+## Date of fit: Fri Nov 4 16:56:21 2016
+## Date of summary: Fri Nov 4 16:56:21 2016
##
##
## Warning: Optimisation by method Port did not converge.
@@ -163,7 +169,7 @@ FOCUS_2006_L1_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 188 model solutions performed in 0.446 s
+## Fitted with method Port using 188 model solutions performed in 0.46 s
##
## Weighting: none
##
@@ -247,15 +253,15 @@ FOCUS_2006_L2_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 4 15:38:05 2016
-## Date of summary: Fri Nov 4 15:38:05 2016
+## Date of fit: Fri Nov 4 16:56:22 2016
+## Date of summary: Fri Nov 4 16:56:22 2016
##
## Equations:
## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 81 model solutions performed in 0.19 s
+## Fitted with method Port using 81 model solutions performed in 0.199 s
##
## Weighting: none
##
@@ -317,8 +323,8 @@ FOCUS_2006_L2_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 4 15:38:06 2016
-## Date of summary: Fri Nov 4 15:38:06 2016
+## Date of fit: Fri Nov 4 16:56:23 2016
+## Date of summary: Fri Nov 4 16:56:23 2016
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -327,7 +333,7 @@ FOCUS_2006_L2_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.815 s
+## Fitted with method Port using 336 model solutions performed in 0.81 s
##
## Weighting: none
##
@@ -406,8 +412,8 @@ mm.L3 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 4 15:38:07 2016
-## Date of summary: Fri Nov 4 15:38:07 2016
+## Date of fit: Fri Nov 4 16:56:24 2016
+## Date of summary: Fri Nov 4 16:56:25 2016
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -416,7 +422,7 @@ mm.L3 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.339 s
+## Fitted with method Port using 137 model solutions performed in 0.335 s
##
## Weighting: none
##
@@ -506,15 +512,15 @@ mm.L4 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><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>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 4 15:38:07 2016
-## Date of summary: Fri Nov 4 15:38:08 2016
+## Date of fit: Fri Nov 4 16:56:25 2016
+## Date of summary: Fri Nov 4 16:56:25 2016
##
## Equations:
## d_parent = - 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 0.109 s
##
## Weighting: none
##
@@ -566,15 +572,15 @@ mm.L4 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><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>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 4 15:38:08 2016
-## Date of summary: Fri Nov 4 15:38:08 2016
+## Date of fit: Fri Nov 4 16:56:25 2016
+## Date of summary: Fri Nov 4 16:56:25 2016
##
## Equations:
## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 66 model solutions performed in 0.148 s
+## Fitted with method Port using 66 model solutions performed in 0.16 s
##
## Weighting: none
##
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+++ /dev/null
@@ -1,8 +0,0 @@
-base
-minpack.lm
-rootSolve
-inline
-mkin
-knitr
-microbenchmark
-ggplot2
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index 09039f62..e1572b17 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -24,7 +24,13 @@
<li>
<a href="../news/index.html">News</a>
</li>
- </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
+ </ul><ul class="nav navbar-nav navbar-right"><li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul></div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -72,21 +78,21 @@ mb<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw">micr
<span class="kw">print</span>(mb<span class="fl">.1</span>)</code></pre></div>
<pre><code>## Unit: milliseconds
## expr min lq mean median uq
-## deSolve, not compiled 6581.1731 6598.7831 6630.0395 6616.3931 6654.4726
-## Eigenvalue based 880.1617 890.3517 911.2758 900.5416 926.8328
-## deSolve, compiled 739.4343 749.6078 753.6543 759.7813 760.7643
+## deSolve, not compiled 6326.4518 6378.7429 6476.2219 6431.0341 6551.1069
+## Eigenvalue based 925.7797 935.9924 939.8725 946.2051 946.9189
+## deSolve, compiled 740.2821 750.0017 767.8440 759.7212 781.6249
## max neval cld
-## 6692.5522 3 c
-## 953.1240 3 b
-## 761.7474 3 a</code></pre>
+## 6671.1797 3 b
+## 947.6327 3 a
+## 803.5287 3 a</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.1</span>)</code></pre></div>
<p><img src="compiled_models_files/figure-html/benchmark_SFO_SFO-1.png" width="672"></p>
-<p>We see that using the compiled model is by a factor of 8.7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p>
+<p>We see that using the compiled model is by a factor of 8.5 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rownames</span>(smb<span class="fl">.1</span>) &lt;-<span class="st"> </span>smb<span class="fl">.1</span>$expr
smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="fl">.1</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div>
<pre><code>## median
-## deSolve, not compiled 8.708286
-## Eigenvalue based 1.185264
+## deSolve, not compiled 8.464993
+## Eigenvalue based 1.245464
## deSolve, compiled 1.000000</code></pre>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -108,18 +114,18 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="
<span class="kw">print</span>(mb<span class="fl">.2</span>)</code></pre></div>
<pre><code>## Unit: seconds
## expr min lq mean median uq
-## deSolve, not compiled 13.756286 13.813205 13.874083 13.870125 13.932982
-## deSolve, compiled 1.323196 1.372916 1.391915 1.422635 1.426274
+## deSolve, not compiled 13.619556 13.761382 13.825679 13.903207 13.928741
+## deSolve, compiled 1.316871 1.322577 1.358847 1.328283 1.379834
## max neval cld
-## 13.995838 3 b
-## 1.429913 3 a</code></pre>
+## 13.954275 3 b
+## 1.431386 3 a</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span>[<span class="st">"median"</span>]/smb<span class="fl">.2</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div>
<pre><code>## median
## 1 NA
## 2 NA</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.2</span>)</code></pre></div>
<p><img src="compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png" width="672"></p>
-<p>Here we get a performance benefit of a factor of 9.7 using the version of the differential equation model compiled from C code!</p>
+<p>Here we get a performance benefit of a factor of 10.5 using the version of the differential equation model compiled from C code!</p>
<p>This vignette was built with mkin 0.9.44.9000 on</p>
<pre><code>## R version 3.3.2 (2016-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
index 51846e6c..57730131 100644
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index f6e4cb08..50adff32 100644
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index 9f7cdd74..cd6a7bea 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -60,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 5f6ae46c..8a24352c 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -24,7 +24,13 @@
<li>
<a href="../news/index.html">News</a>
</li>
- </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
+ </ul><ul class="nav navbar-nav navbar-right"><li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul></div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages
index 03ece635..c8b1e877 100644
--- a/docs/articles/mkin_cache/html/__packages
+++ b/docs/articles/mkin_cache/html/__packages
@@ -1,13 +1,8 @@
base
-datasets
-utils
-grDevices
-graphics
-stats
knitr
minpack.lm
rootSolve
-methods
inline
-parallel
mkin
+microbenchmark
+ggplot2
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diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx
deleted file mode 100644
index 8983f69e..00000000
--- a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx
+++ /dev/null
Binary files differ
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.RData
index 8fd3567d..e52d9b7b 100644
--- a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.RData
+++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.RData
Binary files differ
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdb
index 7f4d6c92..ff7ed49e 100644
--- a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdb
+++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdb
Binary files differ
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdx
index 7f5f16b7..7ec72c33 100644
--- a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdx
+++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdx
Binary files differ
diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
index 2e7e2244..d34e3805 100644
--- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
+++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
Binary files differ
diff --git a/docs/news/index.html b/docs/news/index.html
index 7c9b63f7..dc316b7a 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -60,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index 7d036804..c0690f41 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — DFOP.solution • mkin</title>
+<title>Double First-Order in Parallel kinetics — DFOP.solution • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Double First-Order in Parallel kinetics</h1>
</div>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index cfe6329b..ad4614fb 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -60,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -188,7 +193,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.316 0.000 0.317
+#&gt; 0.264 0.000 0.262
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -374,7 +379,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x5d4a3b0&gt;
+#&gt; &lt;environment: 0x50d32d0&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -396,7 +401,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x5d4a3b0&gt;
+#&gt; &lt;environment: 0x50d32d0&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 alpha beta
@@ -462,7 +467,7 @@
#&gt; 99.66619
#&gt;
#&gt; $date
-#&gt; [1] &quot;Fri Nov 4 15:36:31 2016&quot;
+#&gt; [1] &quot;Fri Nov 4 17:08:52 2016&quot;
#&gt;
#&gt; attr(,&quot;class&quot;)
#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot; </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#&gt; dataset
@@ -541,7 +546,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.076 0.000 0.077
+#&gt; 0.068 0.000 0.067
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -728,7 +733,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x5d98970&gt;
+#&gt; &lt;environment: 0x4f17408&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -750,7 +755,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x5d98970&gt;
+#&gt; &lt;environment: 0x4f17408&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -813,7 +818,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] &quot;Fri Nov 4 15:36:30 2016&quot;
+#&gt; [1] &quot;Fri Nov 4 17:08:51 2016&quot;
#&gt;
#&gt; attr(,&quot;class&quot;)
#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot; </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#&gt; [[1]]
@@ -889,7 +894,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.076 0.000 0.077
+#&gt; 0.068 0.000 0.067
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -1076,7 +1081,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x5d98970&gt;
+#&gt; &lt;environment: 0x4f17408&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -1098,7 +1103,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x5d98970&gt;
+#&gt; &lt;environment: 0x4f17408&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -1161,7 +1166,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] &quot;Fri Nov 4 15:36:30 2016&quot;
+#&gt; [1] &quot;Fri Nov 4 17:08:51 2016&quot;
#&gt;
#&gt; attr(,&quot;class&quot;)
#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot;
diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
index 97af2f9c..13dfa186 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — FOCUS_2006_DFOP_ref_A_to_B • mkin</title>
+<title>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</h1>
</div>
diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
index 1487e2c9..5b36ac74 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — FOCUS_2006_FOMC_ref_A_to_F • mkin</title>
+<title>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</h1>
</div>
diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
index 4571c175..446ce4d7 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — FOCUS_2006_HS_ref_A_to_F • mkin</title>
+<title>Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Results of fitting the HS model to Datasets A to F of FOCUS (2006)</h1>
</div>
diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
index 7003fa0e..db462f10 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — FOCUS_2006_SFO_ref_A_to_F • mkin</title>
+<title>Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</h1>
</div>
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 83edd323..ffc7558e 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — FOCUS_2006_datasets • mkin</title>
+<title>Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Datasets A to F from the FOCUS Kinetics report from 2006</h1>
</div>
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index 83bca886..fdbf0d1f 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title> First-Order Multi-Compartment kinetics — FOMC.solution • mkin</title>
+<title>First-Order Multi-Compartment kinetics — FOMC.solution • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -60,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -72,7 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1> First-Order Multi-Compartment kinetics </h1>
+ <h1>First-Order Multi-Compartment kinetics</h1>
</div>
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 13db29aa..fbe0b590 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title> Hockey-Stick kinetics — HS.solution • mkin</title>
+<title>Hockey-Stick kinetics — HS.solution • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -60,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -72,7 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1> Hockey-Stick kinetics </h1>
+ <h1>Hockey-Stick kinetics</h1>
</div>
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index 56c2b48e..553c38b0 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title> Indeterminate order rate equation kinetics — IORE.solution • mkin</title>
+<title>Indeterminate order rate equation kinetics — IORE.solution • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -60,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -72,7 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1> Indeterminate order rate equation kinetics </h1>
+ <h1>Indeterminate order rate equation kinetics</h1>
</div>
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index 8ff5b5ba..2ead8f24 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title> Single First-Order kinetics — SFO.solution • mkin</title>
+<title>Single First-Order kinetics — SFO.solution • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -60,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -72,7 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1> Single First-Order kinetics </h1>
+ <h1>Single First-Order kinetics</h1>
</div>
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index 43b6028a..be425d83 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title> Single First-Order Reversible Binding kinetics — SFORB.solution • mkin</title>
+<title>Single First-Order Reversible Binding kinetics — SFORB.solution • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -60,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -72,7 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1> Single First-Order Reversible Binding kinetics </h1>
+ <h1>Single First-Order Reversible Binding kinetics</h1>
</div>
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index 8e491bc9..0a126c5c 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — add_err • mkin</title>
+<title>Add normally distributed errors to simulated kinetic degradation data — add_err • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Add normally distributed errors to simulated kinetic degradation data</h1>
</div>
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index a3716060..44a8f4c4 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — endpoints • mkin</title>
+<title>Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</h1>
</div>
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index 633e0865..97352ff8 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title> Calculate the geometric mean — geometric_mean • mkin</title>
+<title>Calculate the geometric mean — geometric_mean • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -60,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -72,7 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1> Calculate the geometric mean </h1>
+ <h1>Calculate the geometric mean</h1>
</div>
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 955b5c58..95fed72e 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — ilr • mkin</title>
+<title>Function to perform isometric log-ratio transformation — ilr • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Function to perform isometric log-ratio transformation</h1>
</div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index b7d59a21..32455baa 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -60,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index d32acb5b..6eb4741b 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — mccall81_245T • mkin</title>
+<title>Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</h1>
</div>
@@ -119,8 +122,8 @@
<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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 4 15:36:38 2016
-#&gt; Date of summary: Fri Nov 4 15:36:38 2016
+#&gt; Date of fit: Fri Nov 4 17:08:59 2016
+#&gt; Date of summary: Fri Nov 4 17:08:59 2016
#&gt;
#&gt; Equations:
#&gt; d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -130,7 +133,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.886 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.497 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index 21a8a8f8..fa131a6d 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — mkin_long_to_wide • mkin</title>
+<title>Convert a dataframe from long to wide format — mkin_long_to_wide • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Convert a dataframe from long to wide format</h1>
</div>
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index fe6e47e4..077c0b7d 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — mkin_wide_to_long • mkin</title>
+<title>Convert a dataframe with observations over time into long format — mkin_wide_to_long • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Convert a dataframe with observations over time into long format</h1>
</div>
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index f5dd4c88..522aab33 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -60,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index 8d420165..d212e3b2 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — mkinerrmin • mkin</title>
+<title>Calculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Calculate the minimum error to assume in order to pass the variance test</h1>
</div>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index b298d90a..93185eff 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — mkinfit • mkin</title>
+<title>Fit a kinetic model to data with one or more state variables — mkinfit • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Fit a kinetic model to data with one or more state variables</h1>
</div>
@@ -356,8 +359,8 @@
<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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 4 15:36:41 2016
-#&gt; Date of summary: Fri Nov 4 15:36:41 2016
+#&gt; Date of fit: Fri Nov 4 17:09:01 2016
+#&gt; Date of summary: Fri Nov 4 17:09:01 2016
#&gt;
#&gt; Equations:
#&gt; d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -433,7 +436,7 @@
<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 elapsed
-#&gt; 1.244 1.208 0.933 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 1.256 1.216 0.946 </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
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 7dba1b6d..f328c34a 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — mkinmod • mkin</title>
+<title>Function to set up a kinetic model with one or more state variables — mkinmod • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Function to set up a kinetic model with one or more state variables</h1>
</div>
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 923abc6d..764f1ab4 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -6,8 +6,8 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — mkinparplot • mkin</title>
+<title>Function to plot the confidence intervals obtained using
+ list(list("mkinfit")) — mkinparplot • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +61,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +78,8 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Function to plot the confidence intervals obtained using
+ list(list("mkinfit"))</h1>
</div>
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 5fe94a8a..921affdc 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — mkinplot • mkin</title>
+<title>Plot the observed data and the fitted model of an mkinfit object — mkinplot • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Plot the observed data and the fitted model of an mkinfit object</h1>
</div>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index f7eb950a..9f00dab7 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — mkinpredict • mkin</title>
+<title>Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Produce predictions from a kinetic model using specific parameters</h1>
</div>
@@ -272,7 +275,7 @@
<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 elapsed
-#&gt; 0.008 0.024 0.005 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.004 0.028 0.004 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
@@ -282,7 +285,7 @@
<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 elapsed
-#&gt; 0.036 0.000 0.037 </div></pre>
+#&gt; 0.052 0.000 0.052 </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index a0dcd06d..ae9131ac 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — mkinresplot • mkin</title>
+<title>Function to plot residuals stored in an mkin object — mkinresplot • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Function to plot residuals stored in an mkin object</h1>
</div>
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 8424eaab..8bb2ce1c 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — mkinsub • mkin</title>
+<title>Function to set up a kinetic submodel for one state variable — mkinsub • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Function to set up a kinetic submodel for one state variable</h1>
</div>
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 5613a720..a21a980b 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — mmkin • mkin</title>
+<title>Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Fit one or more kinetic models with one or more state variables to one or more datasets</h1>
</div>
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index e7158180..52db9bc6 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — plot.mkinfit • mkin</title>
+<title>Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Plot the observed data and the fitted model of an mkinfit object</h1>
</div>
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index ef5c04b7..eac31273 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — plot.mmkin • mkin</title>
+<title>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</h1>
</div>
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index c578f4ee..9057114d 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — print.mkinds • mkin</title>
+<title>Print mkinds objects — print.mkinds • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Print mkinds objects</h1>
</div>
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index 3f653971..2034ea10 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — print.mkinmod • mkin</title>
+<title>Print mkinmod objects — print.mkinmod • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Print mkinmod objects</h1>
</div>
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index c63ba490..e2f845d9 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — schaefer07_complex_case • mkin</title>
+<title>Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Metabolism data set used for checking the software quality of KinGUI</h1>
</div>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 241964a7..f67bc1d1 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — summary.mkinfit • mkin</title>
+<title>Summary method for class "mkinfit" — summary.mkinfit • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Summary method for class "mkinfit"</h1>
</div>
@@ -139,8 +142,8 @@
<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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 4 15:36:49 2016
-#&gt; Date of summary: Fri Nov 4 15:36:49 2016
+#&gt; Date of fit: Fri Nov 4 17:09:10 2016
+#&gt; Date of summary: Fri Nov 4 17:09:10 2016
#&gt;
#&gt; Equations:
#&gt; d_parent = - k_parent_sink * parent
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 333b3dbf..c6f29582 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — synthetic_data_for_UBA_2014 • mkin</title>
+<title>Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Synthetic datasets for one parent compound with two metabolites</h1>
</div>
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 5ee1e9cc..60208ff4 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>
- — transform_odeparms • mkin</title>
+<title>Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -61,7 +60,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -73,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>
-</h1>
+ <h1>Functions to transform and backtransform kinetic parameters for fitting</h1>
</div>
@@ -146,8 +149,8 @@
<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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 4 15:36:50 2016
-#&gt; Date of summary: Fri Nov 4 15:36:50 2016
+#&gt; Date of fit: Fri Nov 4 17:09:11 2016
+#&gt; Date of summary: Fri Nov 4 17:09:11 2016
#&gt;
#&gt; Equations:
#&gt; d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -155,7 +158,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.663 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.638 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/unknown-10.png b/docs/reference/unknown-10.png
deleted file mode 100644
index 09bb687c..00000000
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+++ /dev/null
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deleted file mode 100644
index f23ed172..00000000
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+++ /dev/null
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deleted file mode 100644
index e4ab674a..00000000
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+++ /dev/null
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