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authorJohannes Ranke <jranke@uni-bremen.de>2016-10-26 23:54:08 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-10-26 23:54:08 +0200
commit2409369d3a665f2b8e0b7333f4c2286a61614179 (patch)
tree218a40a7fb824e3d88e77007263e786a539d5ce6 /docs
parent8f38147e145c66ebd27f5d9fcc6f00172c25872f (diff)
Complete pkgdown conf, rerun with current master branch
Diffstat (limited to 'docs')
-rw-r--r--docs/index.html13
-rw-r--r--docs/reference/DFOP.solution.html14
-rw-r--r--docs/reference/Extract.mmkin.html38
-rw-r--r--docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html14
-rw-r--r--docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html14
-rw-r--r--docs/reference/FOCUS_2006_HS_ref_A_to_F.html14
-rw-r--r--docs/reference/FOCUS_2006_SFO_ref_A_to_F.html14
-rw-r--r--docs/reference/FOCUS_2006_datasets.html14
-rw-r--r--docs/reference/FOMC.solution.html14
-rw-r--r--docs/reference/HS.solution.html14
-rw-r--r--docs/reference/IORE.solution.html14
-rw-r--r--docs/reference/SFO.solution.html14
-rw-r--r--docs/reference/SFORB.solution.html14
-rw-r--r--docs/reference/add_err.html14
-rw-r--r--docs/reference/endpoints.html14
-rw-r--r--docs/reference/geometric_mean.html14
-rw-r--r--docs/reference/ilr.html14
-rw-r--r--docs/reference/index.html173
-rw-r--r--docs/reference/mccall81_245T.html20
-rw-r--r--docs/reference/mkin_long_to_wide.html14
-rw-r--r--docs/reference/mkin_wide_to_long.html14
-rw-r--r--docs/reference/mkinds.html14
-rw-r--r--docs/reference/mkinerrmin.html14
-rw-r--r--docs/reference/mkinfit.html22
-rw-r--r--docs/reference/mkinmod.html14
-rw-r--r--docs/reference/mkinparplot.html14
-rw-r--r--docs/reference/mkinplot.html14
-rw-r--r--docs/reference/mkinpredict.html20
-rw-r--r--docs/reference/mkinresplot.html14
-rw-r--r--docs/reference/mkinsub.html14
-rw-r--r--docs/reference/mmkin.html14
-rw-r--r--docs/reference/plot.mkinfit.html14
-rw-r--r--docs/reference/plot.mmkin.html14
-rw-r--r--docs/reference/print.mkinds.html14
-rw-r--r--docs/reference/print.mkinmod.html14
-rw-r--r--docs/reference/schaefer07_complex_case.html14
-rw-r--r--docs/reference/summary.mkinfit.html20
-rw-r--r--docs/reference/synthetic_data_for_UBA.html14
-rw-r--r--docs/reference/transform_odeparms.html20
39 files changed, 420 insertions, 340 deletions
diff --git a/docs/index.html b/docs/index.html
index 180fe5f9..04f10ed8 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -16,18 +16,15 @@
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
- <a href="index.html">Home</a>
+ <a href="reference/index.html">Reference</a>
</li>
<li>
- <a href="reference/index.html">Reference</a>
+ <a href="articles/index.html">Articles</a>
</li>
- </ul><ul class="nav navbar-nav navbar-right"><li>
- <a href="https://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
+<li>
+ <a href="news/index.html">News</a>
</li>
- </ul></div><!--/.nav-collapse -->
+ </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index 5c90809c..3b8e0e03 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index ee86854a..4ea16d10 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -49,20 +49,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -195,7 +193,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.268 0.000 0.264
+#&gt; 0.26 0.00 0.26
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -381,7 +379,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x49c37f0&gt;
+#&gt; &lt;environment: 0x5421f48&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -403,7 +401,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x49c37f0&gt;
+#&gt; &lt;environment: 0x5421f48&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 alpha beta
@@ -469,7 +467,7 @@
#&gt; 99.66619
#&gt;
#&gt; $date
-#&gt; [1] &quot;Wed Oct 26 23:16:41 2016&quot;
+#&gt; [1] &quot;Wed Oct 26 23:50:33 2016&quot;
#&gt;
#&gt; attr(,&quot;class&quot;)
#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot;
@@ -550,7 +548,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.072 0.004 0.074
+#&gt; 0.068 0.000 0.070
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -737,7 +735,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x4ae0880&gt;
+#&gt; &lt;environment: 0x2b30d68&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -759,7 +757,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x4ae0880&gt;
+#&gt; &lt;environment: 0x2b30d68&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -822,7 +820,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] &quot;Wed Oct 26 23:16:41 2016&quot;
+#&gt; [1] &quot;Wed Oct 26 23:50:32 2016&quot;
#&gt;
#&gt; attr(,&quot;class&quot;)
#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot;
@@ -899,7 +897,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.072 0.004 0.074
+#&gt; 0.068 0.000 0.070
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -1086,7 +1084,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x4ae0880&gt;
+#&gt; &lt;environment: 0x2b30d68&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -1108,7 +1106,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x4ae0880&gt;
+#&gt; &lt;environment: 0x2b30d68&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -1171,7 +1169,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] &quot;Wed Oct 26 23:16:41 2016&quot;
+#&gt; [1] &quot;Wed Oct 26 23:50:32 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 61871ba9..6f071674 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
index 4fdb5f45..d721b2d9 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
index d9e43f4a..11fcea7c 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
index 68475b64..17c34f0f 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 6221f53f..c5bdae8b 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/FOMC.solution.html b/docs/reference/FOMC.solution.html
index 99d95fcb..a2e84ce0 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -49,20 +49,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/HS.solution.html b/docs/reference/HS.solution.html
index 06c6e3c1..e41b7b6a 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -49,20 +49,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/IORE.solution.html b/docs/reference/IORE.solution.html
index 58546489..c39e7818 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -49,20 +49,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/SFO.solution.html b/docs/reference/SFO.solution.html
index b2d5526e..3ce813bf 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -49,20 +49,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/SFORB.solution.html b/docs/reference/SFORB.solution.html
index 135edb51..942fa576 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -49,20 +49,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/add_err.html b/docs/reference/add_err.html
index 9020a486..2500e092 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/endpoints.html b/docs/reference/endpoints.html
index 89e9cf52..73d7e746 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/geometric_mean.html b/docs/reference/geometric_mean.html
index 793d893c..62a9163f 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -49,20 +49,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/ilr.html b/docs/reference/ilr.html
index d249101d..82accca4 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/index.html b/docs/reference/index.html
index 60d11171..6fcf39c8 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -49,20 +49,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -98,8 +96,162 @@
<li><code><a href="mmkin.html">mmkin</a></code></li>
</ul>
<h2 id="section-show-results" class="hasAnchor"><a href="#section-show-results" class="anchor"></a>Show results</h2>
+ <p class="section-desc"><p>Functions working with mkinfit objects</p></p>
+
+ <p><a href="endpoints.html">
+</a></p>
+ <ul>
+ <li><code><a href="endpoints.html">endpoints</a></code></li>
+ </ul>
+ <p><a href="mkinerrmin.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkinerrmin.html">mkinerrmin</a></code></li>
+ </ul>
+ <p><a href="mkinparplot.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkinparplot.html">mkinparplot</a></code></li>
+ </ul>
+ <p><a href="mkinresplot.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkinresplot.html">mkinresplot</a></code></li>
+ </ul>
+ <p><a href="plot.mkinfit.html">
+</a></p>
+ <ul>
+ <li><code><a href="plot.mkinfit.html">plot.mkinfit</a></code></li><li><code><a href="plot.mkinfit.html">plot_sep</a></code></li>
+ </ul>
+ <p><a href="summary.mkinfit.html">
+</a></p>
+ <ul>
+ <li><code><a href="summary.mkinfit.html">summary.mkinfit</a></code></li><li><code><a href="summary.mkinfit.html">print.summary.mkinfit</a></code></li>
+ </ul>
+ <h2 id="section-work-with-mmkin-objects" class="hasAnchor"><a href="#section-work-with-mmkin-objects" class="anchor"></a>Work with mmkin objects</h2>
+ <p class="section-desc"><p>Functions working with aggregated results</p></p>
+
+ <p><a href="Extract.mmkin.html">Subsetting method for mmkin objects</a></p>
+ <ul>
+ <li><code><a href="Extract.mmkin.html">[.mmkin</a></code></li>
+ </ul>
+ <p><a href="plot.mmkin.html">
+</a></p>
+ <ul>
+ <li><code><a href="plot.mmkin.html">plot.mmkin</a></code></li>
+ </ul>
+ <h2 id="section-datasets-and-known-results" class="hasAnchor"><a href="#section-datasets-and-known-results" class="anchor"></a>Datasets and known results</h2>
<p class="section-desc"></p>
+ <p><a href="FOCUS_2006_DFOP_ref_A_to_B.html">
+</a></p>
+ <ul>
+ <li><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code></li>
+ </ul>
+ <p><a href="FOCUS_2006_FOMC_ref_A_to_F.html">
+</a></p>
+ <ul>
+ <li><code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code></li>
+ </ul>
+ <p><a href="FOCUS_2006_HS_ref_A_to_F.html">
+</a></p>
+ <ul>
+ <li><code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code></li>
+ </ul>
+ <p><a href="FOCUS_2006_SFO_ref_A_to_F.html">
+</a></p>
+ <ul>
+ <li><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code></li>
+ </ul>
+ <p><a href="mccall81_245T.html">
+</a></p>
+ <ul>
+ <li><code><a href="mccall81_245T.html">mccall81_245T</a></code></li>
+ </ul>
+ <p><a href="schaefer07_complex_case.html">
+</a></p>
+ <ul>
+ <li><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code></li><li><code><a href="schaefer07_complex_case.html">schaefer07_complex_results</a></code></li>
+ </ul>
+ <p><a href="synthetic_data_for_UBA.html">
+</a></p>
+ <ul>
+ <li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li>
+ </ul>
+ <h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2>
+ <p class="section-desc"></p>
+
+ <p><a href="geometric_mean.html"> Calculate the geometric mean </a></p>
+ <ul>
+ <li><code><a href="geometric_mean.html">geometric_mean</a></code></li>
+ </ul>
+ <p><a href="ilr.html">
+</a></p>
+ <ul>
+ <li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li>
+ </ul>
+ <p><a href="mkin_long_to_wide.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li>
+ </ul>
+ <p><a href="mkinpredict.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkinpredict.html">mkinpredict</a></code></li>
+ </ul>
+ <p><a href="mkinsub.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkinsub.html">mkinsub</a></code></li>
+ </ul>
+ <p><a href="mkin_wide_to_long.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li>
+ </ul>
+ <p><a href="print.mkinmod.html">
+</a></p>
+ <ul>
+ <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li>
+ </ul>
+ <p><a href="transform_odeparms.html">
+</a></p>
+ <ul>
+ <li><code><a href="transform_odeparms.html">transform_odeparms</a></code></li><li><code><a href="transform_odeparms.html">backtransform_odeparms</a></code></li>
+ </ul>
+ <h2 id="section-analytical-solutions" class="hasAnchor"><a href="#section-analytical-solutions" class="anchor"></a>Analytical solutions</h2>
+ <p class="section-desc"><p>Parent only model solutions</p></p>
+
+ <p><a href="DFOP.solution.html">
+</a></p>
+ <ul>
+ <li><code><a href="DFOP.solution.html">DFOP.solution</a></code></li>
+ </ul>
+ <p><a href="FOMC.solution.html"> First-Order Multi-Compartment kinetics </a></p>
+ <ul>
+ <li><code><a href="FOMC.solution.html">FOMC.solution</a></code></li>
+ </ul>
+ <p><a href="HS.solution.html"> Hockey-Stick kinetics </a></p>
+ <ul>
+ <li><code><a href="HS.solution.html">HS.solution</a></code></li>
+ </ul>
+ <p><a href="IORE.solution.html"> Indeterminate order rate equation kinetics </a></p>
+ <ul>
+ <li><code><a href="IORE.solution.html">IORE.solution</a></code></li>
+ </ul>
+ <p><a href="SFORB.solution.html"> Single First-Order Reversible Binding kinetics </a></p>
+ <ul>
+ <li><code><a href="SFORB.solution.html">SFORB.solution</a></code></li>
+ </ul>
+ <h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2>
+ <p class="section-desc"><p>Functions that have been superseeded</p></p>
+
+ <p><a href="mkinplot.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkinplot.html">mkinplot</a></code></li>
+ </ul>
</div>
</div>
@@ -109,6 +261,11 @@
<ul class="nav nav-pills nav-stacked">
<li><a href="#section-main-functions">Main functions</a></li>
<li><a href="#section-show-results">Show results</a></li>
+ <li><a href="#section-work-with-mmkin-objects">Work with mmkin objects</a></li>
+ <li><a href="#section-datasets-and-known-results">Datasets and known results</a></li>
+ <li><a href="#section-helper-functions">Helper functions</a></li>
+ <li><a href="#section-analytical-solutions">Analytical solutions</a></li>
+ <li><a href="#section-deprecated-functions">Deprecated functions</a></li>
</ul>
</div>
</div>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 7a96be3b..74b9c088 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -124,8 +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: 3.3.1
-#&gt; Date of fit: Wed Oct 26 23:16:47 2016
-#&gt; Date of summary: Wed Oct 26 23:16:47 2016
+#&gt; Date of fit: Wed Oct 26 23:50:40 2016
+#&gt; Date of summary: Wed Oct 26 23:50:40 2016
#&gt;
#&gt; Equations:
#&gt; d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -135,7 +133,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.487 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.43 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 d8b616c2..cc50bf7d 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index 31207861..bce6d6a4 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/mkinds.html b/docs/reference/mkinds.html
index 45cc315f..e5d99fd5 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -49,20 +49,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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 2e1833da..5b437b08 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/mkinfit.html b/docs/reference/mkinfit.html
index 3c9bd05c..6bfb9352 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -361,15 +359,15 @@
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.1
-#&gt; Date of fit: Wed Oct 26 23:16:49 2016
-#&gt; Date of summary: Wed Oct 26 23:16:49 2016
+#&gt; Date of fit: Wed Oct 26 23:50:42 2016
+#&gt; Date of summary: Wed Oct 26 23:50:42 2016
#&gt;
#&gt; Equations:
#&gt; d_parent = - (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 0.148 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.168 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -439,7 +437,7 @@
<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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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; 1.224 1.196 0.913
+#&gt; 1.272 1.204 0.943
#&gt; </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
#&gt; </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
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 53c87e92..40381656 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/mkinparplot.html b/docs/reference/mkinparplot.html
index 6d4f2cfd..dff30930 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/mkinplot.html b/docs/reference/mkinplot.html
index 925a6683..d3f0c1f6 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/mkinpredict.html b/docs/reference/mkinpredict.html
index cf04c6b6..31556527 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -288,21 +286,21 @@
<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
#&gt; </div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.008 0.024 0.004
+#&gt; 0.028 0.004 0.004
#&gt; </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227
#&gt; </div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.000 0.020 0.002
+#&gt; 0.016 0.004 0.002
#&gt; </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227
#&gt; </div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.036 0.000 0.035
+#&gt; 0.052 0.000 0.052
#&gt; </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index f16dee5d..d8c84191 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/mkinsub.html b/docs/reference/mkinsub.html
index 2432e981..89387468 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/mmkin.html b/docs/reference/mmkin.html
index 0ad3321c..a6e74b8a 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 631ea429..4eb7369a 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 44ae760f..e0a20f3d 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/print.mkinds.html b/docs/reference/print.mkinds.html
index c4bc08d5..a586a103 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/print.mkinmod.html b/docs/reference/print.mkinmod.html
index edc9cde7..73bfd60e 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 1cd71697..4714747a 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 1e1a0e2f..b88a5469 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -144,15 +142,15 @@
</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: 3.3.1
-#&gt; Date of fit: Wed Oct 26 23:16:57 2016
-#&gt; Date of summary: Wed Oct 26 23:16:57 2016
+#&gt; Date of fit: Wed Oct 26 23:50:50 2016
+#&gt; Date of summary: Wed Oct 26 23:50:50 2016
#&gt;
#&gt; Equations:
#&gt; d_parent = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 35 model solutions performed in 0.089 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.083 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index b45c07fc..45d5f53a 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://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/transform_odeparms.html b/docs/reference/transform_odeparms.html
index a07be0a0..ab5ce062 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -50,20 +50,18 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -151,8 +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: 3.3.1
-#&gt; Date of fit: Wed Oct 26 23:16:59 2016
-#&gt; Date of summary: Wed Oct 26 23:16:59 2016
+#&gt; Date of fit: Wed Oct 26 23:50:51 2016
+#&gt; Date of summary: Wed Oct 26 23:50:51 2016
#&gt;
#&gt; Equations:
#&gt; d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -160,7 +158,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.721 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.629 s
#&gt;
#&gt; Weighting: none
#&gt;

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