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-rw-r--r--docs/reference/DFOP.solution.html2
-rw-r--r--docs/reference/Extract.mmkin.html16
-rw-r--r--docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html2
-rw-r--r--docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html2
-rw-r--r--docs/reference/FOCUS_2006_HS_ref_A_to_F.html2
-rw-r--r--docs/reference/FOCUS_2006_SFO_ref_A_to_F.html2
-rw-r--r--docs/reference/FOCUS_2006_datasets.html2
-rw-r--r--docs/reference/FOMC.solution.html2
-rw-r--r--docs/reference/HS.solution.html2
-rw-r--r--docs/reference/IORE.solution.html2
-rw-r--r--docs/reference/SFO.solution.html2
-rw-r--r--docs/reference/SFORB.solution.html2
-rw-r--r--docs/reference/add_err.html2
-rw-r--r--docs/reference/endpoints.html2
-rw-r--r--docs/reference/geometric_mean.html2
-rw-r--r--docs/reference/ilr.html2
-rw-r--r--docs/reference/index.html2
-rw-r--r--docs/reference/max_twa_parent.html2
-rw-r--r--docs/reference/mccall81_245T.html10
-rw-r--r--docs/reference/mkin_long_to_wide.html2
-rw-r--r--docs/reference/mkin_wide_to_long.html2
-rw-r--r--docs/reference/mkinds.html2
-rw-r--r--docs/reference/mkinerrmin.html2
-rw-r--r--docs/reference/mkinfit.html17
-rw-r--r--docs/reference/mkinmod.html2
-rw-r--r--docs/reference/mkinparplot.html2
-rw-r--r--docs/reference/mkinplot.html2
-rw-r--r--docs/reference/mkinpredict.html8
-rw-r--r--docs/reference/mkinresplot.html2
-rw-r--r--docs/reference/mkinsub.html2
-rw-r--r--docs/reference/mmkin.html2
-rw-r--r--docs/reference/plot.mkinfit.html2
-rw-r--r--docs/reference/plot.mmkin.html2
-rw-r--r--docs/reference/print.mkinds.html2
-rw-r--r--docs/reference/print.mkinmod.html2
-rw-r--r--docs/reference/schaefer07_complex_case.html2
-rw-r--r--docs/reference/sigma_twocomp.html2
-rw-r--r--docs/reference/summary.mkinfit.html10
-rw-r--r--docs/reference/synthetic_data_for_UBA.html2
-rw-r--r--docs/reference/test_data_from_UBA_2014.html2
-rw-r--r--docs/reference/transform_odeparms.html10
41 files changed, 71 insertions, 70 deletions
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index c1177306..22709123 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 8771b53b..94c4d336 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
@@ -278,7 +278,7 @@
#&gt;
#&gt; $time
#&gt; User System verstrichen
-#&gt; 0.171 0.001 0.171
+#&gt; 0.165 0.000 0.165
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -467,8 +467,8 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555bd7f970&gt;
-#&gt; &lt;environment: 0x55555bc8fca8&gt;
+#&gt; &lt;bytecode: 0x55555bd36378&gt;
+#&gt; &lt;environment: 0x55555bd42bc8&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -490,8 +490,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555ca84338&gt;
-#&gt; &lt;environment: 0x55555bc8fca8&gt;
+#&gt; &lt;bytecode: 0x55555c995188&gt;
+#&gt; &lt;environment: 0x55555bd42bc8&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -558,10 +558,10 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] "Thu Sep 6 13:35:24 2018"
+#&gt; [1] "Fri Sep 14 06:38:57 2018"
#&gt;
#&gt; $version
-#&gt; [1] "0.9.47.2"
+#&gt; [1] "0.9.47.3"
#&gt;
#&gt; $Rversion
#&gt; [1] "3.5.1"
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 6888c0ba..2b6886ff 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -65,7 +65,7 @@ in this fit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</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 624f3908..73b2450b 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -65,7 +65,7 @@ in this fit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</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 c089e5e7..e5621863 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -65,7 +65,7 @@ in this fit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</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 e6846a38..872d68a9 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -65,7 +65,7 @@ in this fit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 42ff6926..232be6f3 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index 9f7db6c1..c4f3158d 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -65,7 +65,7 @@ The form given here differs slightly from the original reference by Gustafson
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 87ee2d20..8f1ff8de 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index 18c8a751..ae09fcf7 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index ac26f950..f4e8eb42 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index bb782104..e568bd5a 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -65,7 +65,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index 9d71c18c..99871884 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -63,7 +63,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index 46cb10e1..e39d1c15 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -64,7 +64,7 @@ with the advantage that the SFORB model can also be used for metabolites." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index 091e65ea..a5c63aeb 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 34edfc08..ec49468a 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index d9705ce3..af7642e6 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -58,7 +58,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index 447d9fda..8d31b0d2 100644
--- a/docs/reference/max_twa_parent.html
+++ b/docs/reference/max_twa_parent.html
@@ -65,7 +65,7 @@ guidance." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 9894f8eb..cea92155 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -63,7 +63,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
@@ -164,10 +164,10 @@
<span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
<span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
<span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.2
+ <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.3
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Thu Sep 6 13:35:34 2018
-#&gt; Date of summary: Thu Sep 6 13:35:34 2018
+#&gt; Date of fit: Fri Sep 14 06:39:07 2018
+#&gt; Date of summary: Fri Sep 14 06:39:07 2018
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -177,7 +177,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.549 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.423 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 2bf67d39..8d53bc1b 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -63,7 +63,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index 3e0f10f7..e7342cee 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index 3f4a84ec..16086f3e 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index 44fc1e51..c8fd8272 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -62,7 +62,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index f9c6c117..b1c42168 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
@@ -161,7 +161,7 @@
<span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>plot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>weight</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"none"</span>, <span class='st'>"std"</span>, <span class='st'>"mean"</span>, <span class='st'>"tc"</span>),
+ <span class='kw'>weight</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"none"</span>, <span class='st'>"manual"</span>, <span class='st'>"std"</span>, <span class='st'>"mean"</span>, <span class='st'>"tc"</span>),
<span class='kw'>tc</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>sigma_low</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>rsd_high</span> <span class='kw'>=</span> <span class='fl'>0.07</span>),
<span class='kw'>scaleVar</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>,
@@ -326,7 +326,8 @@
<th>weight</th>
<td><p>only if <code>err</code>=<code>NULL</code>: how to weight the residuals, one of "none",
"std", "mean", see details of <code>modCost</code>, or "tc" for the
- two component error model.</p></td>
+ two component error model. The option "manual" is available for
+ the case that <code>err</code>!=<code>NULL</code>, but it is not necessary to specify it.</p></td>
</tr>
<tr>
<th>tc</th>
@@ -431,17 +432,17 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.2
+<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.3
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Thu Sep 6 13:35:36 2018
-#&gt; Date of summary: Thu Sep 6 13:35:36 2018
+#&gt; Date of fit: Fri Sep 14 06:39:09 2018
+#&gt; Date of summary: Fri Sep 14 06:39:09 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 64 model solutions performed in 0.144 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.157 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -510,7 +511,7 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.919 0.000 0.920 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.892 0.000 0.892 </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 a9c6bb26..a0eade3b 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -66,7 +66,7 @@ For the definition of model types and their parameters, the equations given
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 33eeefbd..75d22288 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 71437181..6aa67e5b 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 59b67a5d..6c2ba992 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -63,7 +63,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
@@ -321,17 +321,17 @@
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.003 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.004 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.002 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.001 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.037 0.000 0.038 </div></pre>
+#&gt; 0.035 0.000 0.036 </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index e73b4905..4ba540b2 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -64,7 +64,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 85345135..65de0664 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 2a060628..557da0d7 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 07fc4854..765f1628 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -66,7 +66,7 @@ If the current plot device is a tikz device,
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 829105bd..0599907d 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -65,7 +65,7 @@ If the current plot device is a tikz device,
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index 70c4f768..86bb58e5 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index 141dd1c9..bc4c644a 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 18f3b78f..b212aa53 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -63,7 +63,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html
index 8bf1d5f6..c8000ae5 100644
--- a/docs/reference/sigma_twocomp.html
+++ b/docs/reference/sigma_twocomp.html
@@ -66,7 +66,7 @@ This is the error model used for example by Werner et al. (1978). The model
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 7b7b0a31..28447e64 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -64,7 +64,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
@@ -204,17 +204,17 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.2
+ <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.3
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Thu Sep 6 13:35:46 2018
-#&gt; Date of summary: Thu Sep 6 13:35:46 2018
+#&gt; Date of fit: Fri Sep 14 06:39:24 2018
+#&gt; Date of summary: Fri Sep 14 06:39:24 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 35 model solutions performed in 0.075 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.081 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 9d9404e5..dd44a450 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -76,7 +76,7 @@ Compare also the code in the example section to see the degradation models." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 5b683283..f9032c84 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 1b94d319..a31b075e 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -69,7 +69,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
</span>
</div>
@@ -198,10 +198,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
<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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.2
+<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.3
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Thu Sep 6 13:35:48 2018
-#&gt; Date of summary: Thu Sep 6 13:35:48 2018
+#&gt; Date of fit: Fri Sep 14 06:39:25 2018
+#&gt; Date of summary: Fri Sep 14 06:39:25 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -209,7 +209,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.619 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.642 s
#&gt;
#&gt; Weighting: none
#&gt;

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