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-rw-r--r--docs/reference/DFOP.solution.html7
-rw-r--r--docs/reference/Extract.mmkin.html31
-rw-r--r--docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html7
-rw-r--r--docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html7
-rw-r--r--docs/reference/FOCUS_2006_HS_ref_A_to_F.html7
-rw-r--r--docs/reference/FOCUS_2006_SFO_ref_A_to_F.html7
-rw-r--r--docs/reference/FOCUS_2006_datasets.html7
-rw-r--r--docs/reference/FOMC.solution.html7
-rw-r--r--docs/reference/HS.solution.html7
-rw-r--r--docs/reference/IORE.solution.html7
-rw-r--r--docs/reference/SFO.solution.html7
-rw-r--r--docs/reference/SFORB.solution.html7
-rw-r--r--docs/reference/add_err.html7
-rw-r--r--docs/reference/endpoints.html9
-rw-r--r--docs/reference/geometric_mean.html7
-rw-r--r--docs/reference/ilr.html7
-rw-r--r--docs/reference/index.html34
-rw-r--r--docs/reference/mccall81_245T.html13
-rw-r--r--docs/reference/mkin_long_to_wide.html7
-rw-r--r--docs/reference/mkin_wide_to_long.html7
-rw-r--r--docs/reference/mkinds.html7
-rw-r--r--docs/reference/mkinerrmin.html9
-rw-r--r--docs/reference/mkinfit.html21
-rw-r--r--docs/reference/mkinmod.html7
-rw-r--r--docs/reference/mkinparplot.html7
-rw-r--r--docs/reference/mkinplot.html11
-rw-r--r--docs/reference/mkinpredict.html13
-rw-r--r--docs/reference/mkinresplot.html9
-rw-r--r--docs/reference/mkinsub.html7
-rw-r--r--docs/reference/mmkin.html7
-rw-r--r--docs/reference/plot.mkinfit.html7
-rw-r--r--docs/reference/plot.mmkin.html9
-rw-r--r--docs/reference/print.mkinds.html7
-rw-r--r--docs/reference/print.mkinmod.html7
-rw-r--r--docs/reference/schaefer07_complex_case.html7
-rw-r--r--docs/reference/summary.mkinfit.html13
-rw-r--r--docs/reference/synthetic_data_for_UBA.html7
-rw-r--r--docs/reference/transform_odeparms.html19
38 files changed, 104 insertions, 269 deletions
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index e05cdc29..7d036804 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -61,12 +61,7 @@
</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/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index fe39ce6e..cfe6329b 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -60,12 +60,7 @@
</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 -->
@@ -193,7 +188,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.256 0.000 0.256
+#&gt; 0.316 0.000 0.317
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -379,7 +374,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x5b47f50&gt;
+#&gt; &lt;environment: 0x5d4a3b0&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -401,7 +396,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x5b47f50&gt;
+#&gt; &lt;environment: 0x5d4a3b0&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 alpha beta
@@ -467,7 +462,7 @@
#&gt; 99.66619
#&gt;
#&gt; $date
-#&gt; [1] &quot;Thu Nov 3 17:46:18 2016&quot;
+#&gt; [1] &quot;Fri Nov 4 15:36:31 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
@@ -546,7 +541,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.068 0.000 0.070
+#&gt; 0.076 0.000 0.077
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -733,7 +728,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x46881c0&gt;
+#&gt; &lt;environment: 0x5d98970&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -755,7 +750,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x46881c0&gt;
+#&gt; &lt;environment: 0x5d98970&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -818,7 +813,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] &quot;Thu Nov 3 17:46:18 2016&quot;
+#&gt; [1] &quot;Fri Nov 4 15:36:30 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]]
@@ -894,7 +889,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.068 0.000 0.070
+#&gt; 0.076 0.000 0.077
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -1081,7 +1076,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x46881c0&gt;
+#&gt; &lt;environment: 0x5d98970&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -1103,7 +1098,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x46881c0&gt;
+#&gt; &lt;environment: 0x5d98970&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -1166,7 +1161,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] &quot;Thu Nov 3 17:46:18 2016&quot;
+#&gt; [1] &quot;Fri Nov 4 15:36:30 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 9f098ff3..97af2f9c 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -61,12 +61,7 @@
</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/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
index e45463ba..1487e2c9 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -61,12 +61,7 @@
</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/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
index 247c3e00..4571c175 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -61,12 +61,7 @@
</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/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
index 006a3876..7003fa0e 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -61,12 +61,7 @@
</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/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index c2501a7f..83edd323 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -61,12 +61,7 @@
</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/FOMC.solution.html b/docs/reference/FOMC.solution.html
index 1fbf7741..83bca886 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -60,12 +60,7 @@
</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/HS.solution.html b/docs/reference/HS.solution.html
index 2cecda28..13db29aa 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -60,12 +60,7 @@
</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/IORE.solution.html b/docs/reference/IORE.solution.html
index 68b7be44..56c2b48e 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -60,12 +60,7 @@
</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/SFO.solution.html b/docs/reference/SFO.solution.html
index 51c35eee..8ff5b5ba 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -60,12 +60,7 @@
</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/SFORB.solution.html b/docs/reference/SFORB.solution.html
index 2f7dcb5d..43b6028a 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -60,12 +60,7 @@
</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/add_err.html b/docs/reference/add_err.html
index 82a0b039..8e491bc9 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -61,12 +61,7 @@
</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/endpoints.html b/docs/reference/endpoints.html
index 6ff7ac36..a3716060 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -61,12 +61,7 @@
</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 -->
@@ -101,7 +96,7 @@ with the advantage that the SFORB model can also be used for metabolites.</p>
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
- <p>The function is used internally by <code>summary.mkinfit</code>.</p>
+ <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index a4b661e2..633e0865 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -60,12 +60,7 @@
</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/ilr.html b/docs/reference/ilr.html
index d2551059..955b5c58 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -61,12 +61,7 @@
</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/index.html b/docs/reference/index.html
index 23eb608b..b7d59a21 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -60,12 +60,7 @@
</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 -->
@@ -115,7 +110,7 @@
</ul>
<p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using
- mkinfit</a></p>
+ list(list(&quot;mkinfit&quot;))</a></p>
<ul>
<li><code><a href="mkinparplot.html">mkinparplot</a></code></li>
</ul>
@@ -124,6 +119,16 @@
<ul>
<li><code><a href="mkinresplot.html">mkinresplot</a></code></li>
</ul>
+
+ <p><a href="plot.mkinfit.html">Plot the observed data and the fitted model of an mkinfit object</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">Summary method for class &quot;mkinfit&quot;</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>
@@ -176,6 +181,11 @@
<li><code><a href="print.mkinds.html">print.mkinds</a></code></li>
</ul>
+ <p><a href="schaefer07_complex_case.html">Metabolism data set used for checking the software quality of KinGUI</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">Synthetic datasets for one parent compound with two metabolites</a></p>
<ul>
<li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li>
@@ -189,6 +199,11 @@
<li><code><a href="geometric_mean.html">geometric_mean</a></code></li>
</ul>
+ <p><a href="ilr.html">Function to perform isometric log-ratio transformation</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">Convert a dataframe from long to wide format</a></p>
<ul>
<li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li>
@@ -213,6 +228,11 @@
<ul>
<li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li>
</ul>
+
+ <p><a href="transform_odeparms.html">Functions to transform and backtransform kinetic parameters for fitting</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>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 8309a23e..d32acb5b 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -61,12 +61,7 @@
</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 -->
@@ -124,8 +119,8 @@
<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: Thu Nov 3 17:46:24 2016
-#&gt; Date of summary: Thu Nov 3 17:46:24 2016
+#&gt; Date of fit: Fri Nov 4 15:36:38 2016
+#&gt; Date of summary: Fri Nov 4 15:36:38 2016
#&gt;
#&gt; Equations:
#&gt; d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -135,7 +130,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.662 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.886 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 0385ccbb..21a8a8f8 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -61,12 +61,7 @@
</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/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index 965262ce..fe6e47e4 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -61,12 +61,7 @@
</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/mkinds.html b/docs/reference/mkinds.html
index 522aab33..f5dd4c88 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -60,12 +60,7 @@
</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 4e1be39c..8d420165 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -61,12 +61,7 @@
</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 -->
@@ -110,7 +105,7 @@ as defined in the FOCUS kinetics report from 2006.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>This function is used internally by <code>summary.mkinfit</code>.</p>
+ <p>This function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 867fb9ff..b298d90a 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -61,12 +61,7 @@
</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 -->
@@ -256,7 +251,7 @@
to do transformations. If TRUE, the g parameter of the DFOP and HS
models are also transformed, as they can also be seen as compositional
data. The transformation used for these transformations is the
- <code>ilr</code> transformation.
+ <code><a href='ilr.html'>ilr</a></code> transformation.
</dd>
<dt>plot</dt>
<dd>
@@ -332,11 +327,11 @@
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A list with &quot;mkinfit&quot; and &quot;modFit&quot; in the class attribute.
- A summary can be obtained by <code>summary.mkinfit</code>.</p>
+ A summary can be obtained by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
- <p>Plotting methods <code>plot.mkinfit</code> and
+ <p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and
<code><a href='mkinparplot.html'>mkinparplot</a></code>.</p>
<p>Fitting of several models to several datasets in a single call to
<code><a href='mmkin.html'>mmkin</a></code>.</p>
@@ -361,15 +356,15 @@
<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: 3.3.2
-#&gt; Date of fit: Thu Nov 3 17:46:27 2016
-#&gt; Date of summary: Thu Nov 3 17:46:27 2016
+#&gt; Date of fit: Fri Nov 4 15:36:41 2016
+#&gt; Date of summary: Fri Nov 4 15:36:41 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 0.147 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.156 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -438,7 +433,7 @@
<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; 1.204 1.244 0.932 </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; 1.244 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; 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 bdfd0e09..7dba1b6d 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -61,12 +61,7 @@
</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/mkinparplot.html b/docs/reference/mkinparplot.html
index f8151c16..923abc6d 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -61,12 +61,7 @@
</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/mkinplot.html b/docs/reference/mkinplot.html
index 9ed92dd0..5fe94a8a 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -61,12 +61,7 @@
</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 -->
@@ -83,7 +78,7 @@
</div>
- <p>Deprecated function. It now only calls the plot method <code>plot.mkinfit</code>.</p>
+ <p>Deprecated function. It now only calls the plot method <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p>
<pre><span class='fu'>mkinplot</span>(<span class='no'>fit</span>, <span class='no'>...</span>)</pre>
@@ -96,7 +91,7 @@
</dd>
<dt>&amp;#8230;</dt>
<dd>
- further arguments passed to <code>plot.mkinfit</code>.
+ further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.
</dd>
</dl>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 57bb747c..f7eb950a 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -61,12 +61,7 @@
</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 -->
@@ -277,17 +272,17 @@
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.004 0.024 0.004 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.008 0.024 0.005 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.004 0.016 0.003 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.000 0.020 0.003 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='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 0.033 </div></pre>
+#&gt; 0.036 0.000 0.037 </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 53c4f62f..a0dcd06d 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -61,12 +61,7 @@
</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 -->
@@ -85,7 +80,7 @@
<p>This function plots the residuals for the specified subset of the
observed variables from an mkinfit object. A combined plot of the fitted
- model and the residuals can be obtained using <code>plot.mkinfit</code>
+ model and the residuals can be obtained using <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>
using the argument <code>show_residuals = TRUE</code>.</p>
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 86374e4b..8424eaab 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -61,12 +61,7 @@
</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/mmkin.html b/docs/reference/mmkin.html
index 21461986..5613a720 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -61,12 +61,7 @@
</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/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 61a597e7..e7158180 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -61,12 +61,7 @@
</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/plot.mmkin.html b/docs/reference/plot.mmkin.html
index b107ca70..ef5c04b7 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -61,12 +61,7 @@
</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 -->
@@ -124,7 +119,7 @@
</dd>
<dt>&amp;#8230;</dt>
<dd>
- Further arguments passed to <code>plot.mkinfit</code> and <code><a href='mkinresplot.html'>mkinresplot</a></code>.
+ Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinresplot.html'>mkinresplot</a></code>.
</dd>
</dl>
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index 9bd088b1..c578f4ee 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -61,12 +61,7 @@
</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/print.mkinmod.html b/docs/reference/print.mkinmod.html
index 11b96036..3f653971 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -61,12 +61,7 @@
</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/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 526dde10..c63ba490 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -61,12 +61,7 @@
</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/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 46d078bf..241964a7 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -61,12 +61,7 @@
</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 -->
@@ -144,15 +139,15 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>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: Thu Nov 3 17:46:35 2016
-#&gt; Date of summary: Thu Nov 3 17:46:35 2016
+#&gt; Date of fit: Fri Nov 4 15:36:49 2016
+#&gt; Date of summary: Fri Nov 4 15:36:49 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 0.08 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.086 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index a46a5781..333b3dbf 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -61,12 +61,7 @@
</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/transform_odeparms.html b/docs/reference/transform_odeparms.html
index ccd56ca4..5ee1e9cc 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -61,12 +61,7 @@
</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 -->
@@ -88,7 +83,7 @@
constants and other paramters that can only take on positive values, a
simple log transformation is used. For compositional parameters, such as
the formations fractions that should always sum up to 1 and can not be
- negative, the <code>ilr</code> transformation is used.</p>
+ negative, the <code><a href='ilr.html'>ilr</a></code> transformation is used.</p>
<p>The transformation of sets of formation fractions is fragile, as it supposes
the same ordering of the components in forward and backward transformation.
@@ -114,7 +109,7 @@
<dd>
The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the names of
the model variables that are needed for grouping the formation fractions
- before <code>ilr</code> transformation, the parameter names and
+ before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter names and
the information if the pathway to sink is included in the model.
</dd>
<dt>transform_rates</dt>
@@ -133,7 +128,7 @@
assumption of normal distribution of the estimator. The default (TRUE) is
to do transformations. The g parameter of the DFOP and HS models are also
transformed, as they can also be seen as compositional data. The
- transformation used for these transformations is the <code>ilr</code>
+ transformation used for these transformations is the <code><a href='ilr.html'>ilr</a></code>
transformation.
</dd>
</dl>
@@ -151,8 +146,8 @@
<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: Thu Nov 3 17:46:36 2016
-#&gt; Date of summary: Thu Nov 3 17:46:36 2016
+#&gt; Date of fit: Fri Nov 4 15:36:50 2016
+#&gt; Date of summary: Fri Nov 4 15:36:50 2016
#&gt;
#&gt; Equations:
#&gt; d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -160,7 +155,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.657 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.663 s
#&gt;
#&gt; Weighting: none
#&gt;

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