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authorJohannes Ranke <jranke@uni-bremen.de>2018-09-14 11:38:43 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2018-09-14 11:38:43 +0200
commitc4a35c0e141a4bb05ba508914bebdc2884109e76 (patch)
tree81464f3e17e683dfc7614dadf0899850517954f7 /docs/reference
parentdd65f3503e9d091c82aedcf91635fcf40f778bf9 (diff)
Exclude more example code from CRAN checks
to avoid NOTES about long execution times. Static documentation rebuilt by pkgdown with run_dont_run = TRUE
Diffstat (limited to 'docs/reference')
-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-1.pngbin0 -> 18757 bytes
-rw-r--r--docs/reference/SFO.solution.html6
-rw-r--r--docs/reference/SFORB.solution-1.pngbin0 -> 20255 bytes
-rw-r--r--docs/reference/SFORB.solution.html6
-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.html111
-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.html6
-rw-r--r--docs/reference/mkinfit.html836
-rw-r--r--docs/reference/mkinmod.html35
-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-1.pngbin0 -> 97714 bytes
-rw-r--r--docs/reference/mmkin-2.pngbin0 -> 88254 bytes
-rw-r--r--docs/reference/mmkin-3.pngbin0 -> 85755 bytes
-rw-r--r--docs/reference/mmkin-4.pngbin0 -> 63345 bytes
-rw-r--r--docs/reference/mmkin-5.pngbin0 -> 57629 bytes
-rw-r--r--docs/reference/mmkin.html43
-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-1.pngbin0 -> 55656 bytes
-rw-r--r--docs/reference/schaefer07_complex_case.html24
-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.html11
-rw-r--r--docs/reference/test_data_from_UBA_2014-1.pngbin0 -> 53543 bytes
-rw-r--r--docs/reference/test_data_from_UBA_2014-2.pngbin0 -> 69982 bytes
-rw-r--r--docs/reference/test_data_from_UBA_2014.html62
-rw-r--r--docs/reference/transform_odeparms.html245
51 files changed, 1286 insertions, 187 deletions
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index 22709123..2f714f2c 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 94c4d336..922479a1 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
@@ -278,7 +278,7 @@
#&gt;
#&gt; $time
#&gt; User System verstrichen
-#&gt; 0.165 0.000 0.165
+#&gt; 0.164 0.000 0.164
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -467,8 +467,8 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555bd36378&gt;
-#&gt; &lt;environment: 0x55555bd42bc8&gt;
+#&gt; &lt;bytecode: 0x55555bd535f0&gt;
+#&gt; &lt;environment: 0x55555bd1c770&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -490,8 +490,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555c995188&gt;
-#&gt; &lt;environment: 0x55555bd42bc8&gt;
+#&gt; &lt;bytecode: 0x55555c9c70f8&gt;
+#&gt; &lt;environment: 0x55555bd1c770&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -558,10 +558,10 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] "Fri Sep 14 06:38:57 2018"
+#&gt; [1] "Fri Sep 14 11:34:38 2018"
#&gt;
#&gt; $version
-#&gt; [1] "0.9.47.3"
+#&gt; [1] "0.9.47.4"
#&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 2b6886ff..bea35e09 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</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 73b2450b..9122a546 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</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 e5621863..3d5677e8 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</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 872d68a9..524fbd79 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 232be6f3..a0bcc65d 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index c4f3158d..10f33260 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 8f1ff8de..cb9eb353 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index ae09fcf7..23f82d13 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/SFO.solution-1.png b/docs/reference/SFO.solution-1.png
new file mode 100644
index 00000000..9e6bd786
--- /dev/null
+++ b/docs/reference/SFO.solution-1.png
Binary files differ
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index f4e8eb42..087ff46f 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
@@ -160,9 +160,7 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> </div><span class='co'># NOT RUN {</span>
-<span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFO.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)
-<span class='co'># }</span></pre>
+ <pre class="examples"><div class='input'> </div><div class='input'><span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFO.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFO.solution-1.png' alt='' width='700' height='433' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/SFORB.solution-1.png b/docs/reference/SFORB.solution-1.png
new file mode 100644
index 00000000..6739fe6b
--- /dev/null
+++ b/docs/reference/SFORB.solution-1.png
Binary files differ
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index e568bd5a..61989c40 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
@@ -177,9 +177,7 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> </div><span class='co'># NOT RUN {</span>
-<span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFORB.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.5</span>, <span class='fl'>2</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)
-<span class='co'># }</span></pre>
+ <pre class="examples"><div class='input'> </div><div class='input'><span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFORB.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.5</span>, <span class='fl'>2</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFORB.solution-1.png' alt='' width='700' height='433' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index 99871884..b3324064 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index e39d1c15..fdf465a5 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index a5c63aeb..bddbab1a 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index ec49468a..e780d26b 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index af7642e6..185991d6 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index 8d31b0d2..ef7209bf 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index cea92155..ac2adf1e 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
@@ -155,19 +155,11 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</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'>"phenol"</span>),
<span class='kw'>phenol</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'>"anisole"</span>),
- <span class='kw'>anisole</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'> </div><span class='co'># NOT RUN {</span>
- <span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>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'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-
-<span class='co'># }</span><div class='input'> <span class='co'># No convergence, no covariance matrix ...</span>
- <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span>
- <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: 0.9.47.3
+ <span class='kw'>anisole</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'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>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'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.4
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 06:39:07 2018
-#&gt; Date of summary: Fri Sep 14 06:39:07 2018
+#&gt; Date of fit: Fri Sep 14 11:34:50 2018
+#&gt; Date of summary: Fri Sep 14 11:34:50 2018
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -177,7 +169,96 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.423 s
+#&gt; Fitted with method Port using 574 model solutions performed in 3.33 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; T245_0 100.9000 state
+#&gt; k_T245_sink 0.1000 deparm
+#&gt; k_T245_phenol 0.1001 deparm
+#&gt; k_phenol_sink 0.1002 deparm
+#&gt; k_phenol_anisole 0.1003 deparm
+#&gt; k_anisole_sink 0.1004 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; T245_0 100.900000 -Inf Inf
+#&gt; log_k_T245_sink -2.302585 -Inf Inf
+#&gt; log_k_T245_phenol -2.301586 -Inf Inf
+#&gt; log_k_phenol_sink -2.300587 -Inf Inf
+#&gt; log_k_phenol_anisole -2.299590 -Inf Inf
+#&gt; log_k_anisole_sink -2.298593 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; phenol_0 0 state
+#&gt; anisole_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; T245_0 103.9000 NA NA NA
+#&gt; log_k_T245_sink -4.1130 NA NA NA
+#&gt; log_k_T245_phenol -3.6120 NA NA NA
+#&gt; log_k_phenol_sink -25.0800 NA NA NA
+#&gt; log_k_phenol_anisole -0.9037 NA NA NA
+#&gt; log_k_anisole_sink -5.0090 NA NA NA
+#&gt;
+#&gt; Parameter correlation:</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not estimate covariance matrix; singular system:</span></div><div class='output co'>#&gt; Could not estimate covariance matrix; singular system:
+#&gt;
+#&gt; Residual standard error: 2.78 on 18 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; T245_0 1.039e+02 4.282e+01 7.236e-20 NA NA
+#&gt; k_T245_sink 1.636e-02 8.901e-01 1.926e-01 NA NA
+#&gt; k_T245_phenol 2.701e-02 1.504e+00 7.498e-02 NA NA
+#&gt; k_phenol_sink 1.286e-11 4.575e-11 5.000e-01 NA NA
+#&gt; k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02 NA NA
+#&gt; k_anisole_sink 6.679e-03 8.146e+00 9.469e-08 NA NA
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 10.070 6 16
+#&gt; T245 7.908 3 5
+#&gt; phenol 106.445 2 5
+#&gt; anisole 5.379 1 6
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; T245_sink 3.772e-01
+#&gt; T245_phenol 6.228e-01
+#&gt; phenol_sink 3.175e-11
+#&gt; phenol_anisole 1.000e+00
+#&gt; anisole_sink 1.000e+00
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; T245 15.982 53.091
+#&gt; phenol 1.711 5.685
+#&gt; anisole 103.784 344.763</div><div class='input'> <span class='co'># No convergence, no covariance matrix ...</span>
+ <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span>
+ <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: 0.9.47.4
+#&gt; R version used for fitting: 3.5.1
+#&gt; Date of fit: Fri Sep 14 11:34:51 2018
+#&gt; Date of summary: Fri Sep 14 11:34:51 2018
+#&gt;
+#&gt; Equations:
+#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
+#&gt; d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol -
+#&gt; k_phenol_anisole * phenol
+#&gt; d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 246 model solutions performed in 1.417 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -257,7 +338,7 @@
#&gt; DT50 DT90
#&gt; T245 15.982 53.091
#&gt; phenol 1.711 5.685
-#&gt; anisole 103.784 344.763</div></pre>
+#&gt; anisole 103.784 344.763</div><div class='input'> </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index 8d53bc1b..b83287ff 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index e7342cee..e2b4ef61 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index 16086f3e..c77945b9 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index c8fd8272..a18b226e 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
@@ -178,8 +178,8 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p>
<span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_D</span>), <span class='fl'>4</span>)</div><div class='output co'>#&gt; err.min n.optim df
#&gt; All data 0.0640 4 15
#&gt; parent 0.0646 2 7
-#&gt; m1 0.0469 2 8</div><div class='input'><span class='no'>fit_FOCUS_E</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_E</span>), <span class='fl'>4</span>)</div><div class='output co'>#&gt; err.min n.optim df
+#&gt; m1 0.0469 2 8</div><div class='input'> <span class='no'>fit_FOCUS_E</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_E</span>), <span class='fl'>4</span>)</div><div class='output co'>#&gt; err.min n.optim df
#&gt; All data 0.1544 4 13
#&gt; parent 0.1659 2 7
#&gt; m1 0.1095 2 6</div></pre>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index b1c42168..13029e91 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
@@ -432,17 +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: 0.9.47.3
+<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.4
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 06:39:09 2018
-#&gt; Date of summary: Fri Sep 14 06:39:09 2018
+#&gt; Date of fit: Fri Sep 14 11:34:54 2018
+#&gt; Date of summary: Fri Sep 14 11:34:54 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 0.157 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.141 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -511,7 +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; 0.892 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; 0.906 0.000 0.907 </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
@@ -523,19 +523,86 @@
#&gt; DT50 DT90
#&gt; parent 7.022929 23.32967
#&gt; m1 131.760712 437.69961
-#&gt; </div><span class='co'># NOT RUN {</span>
-<span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</span>
+#&gt; </div><div class='input'><span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</span>
<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit.deSolve</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'>"deSolve"</span>)))
-<span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)
-<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)
-<span class='co'># }</span><div class='input'>
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#&gt; Model cost at call 1 : 18915.53
+#&gt; Model cost at call 2 : 18915.53
+#&gt; Model cost at call 6 : 11424.02
+#&gt; Model cost at call 10 : 11424
+#&gt; Model cost at call 12 : 4094.396
+#&gt; Model cost at call 16 : 4094.396
+#&gt; Model cost at call 19 : 1340.595
+#&gt; Model cost at call 20 : 1340.593
+#&gt; Model cost at call 25 : 1072.239
+#&gt; Model cost at call 28 : 1072.236
+#&gt; Model cost at call 30 : 874.2615
+#&gt; Model cost at call 33 : 874.2611
+#&gt; Model cost at call 35 : 616.2377
+#&gt; Model cost at call 37 : 616.2372
+#&gt; Model cost at call 40 : 467.4386
+#&gt; Model cost at call 42 : 467.4381
+#&gt; Model cost at call 46 : 398.2914
+#&gt; Model cost at call 48 : 398.2914
+#&gt; Model cost at call 49 : 398.2913
+#&gt; Model cost at call 51 : 395.0712
+#&gt; Model cost at call 54 : 395.0711
+#&gt; Model cost at call 56 : 378.3298
+#&gt; Model cost at call 59 : 378.3298
+#&gt; Model cost at call 62 : 376.9812
+#&gt; Model cost at call 64 : 376.9811
+#&gt; Model cost at call 67 : 375.2085
+#&gt; Model cost at call 69 : 375.2085
+#&gt; Model cost at call 70 : 375.2085
+#&gt; Model cost at call 71 : 375.2085
+#&gt; Model cost at call 72 : 374.5723
+#&gt; Model cost at call 74 : 374.5723
+#&gt; Model cost at call 77 : 374.0075
+#&gt; Model cost at call 79 : 374.0075
+#&gt; Model cost at call 80 : 374.0075
+#&gt; Model cost at call 82 : 373.1711
+#&gt; Model cost at call 84 : 373.1711
+#&gt; Model cost at call 87 : 372.6445
+#&gt; Model cost at call 88 : 372.1614
+#&gt; Model cost at call 90 : 372.1614
+#&gt; Model cost at call 91 : 372.1614
+#&gt; Model cost at call 94 : 371.6464
+#&gt; Model cost at call 99 : 371.4299
+#&gt; Model cost at call 101 : 371.4299
+#&gt; Model cost at call 104 : 371.4071
+#&gt; Model cost at call 106 : 371.4071
+#&gt; Model cost at call 107 : 371.4071
+#&gt; Model cost at call 109 : 371.2524
+#&gt; Model cost at call 113 : 371.2524
+#&gt; Model cost at call 114 : 371.2136
+#&gt; Model cost at call 115 : 371.2136
+#&gt; Model cost at call 116 : 371.2136
+#&gt; Model cost at call 119 : 371.2134
+#&gt; Model cost at call 120 : 371.2134
+#&gt; Model cost at call 122 : 371.2134
+#&gt; Model cost at call 123 : 371.2134
+#&gt; Model cost at call 125 : 371.2134
+#&gt; Model cost at call 126 : 371.2134
+#&gt; Model cost at call 135 : 371.2134
+#&gt; Model cost at call 146 : 371.2134
+#&gt; Optimisation by method Port successfully terminated.
+#&gt; User System verstrichen
+#&gt; 0.714 0.000 0.715 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
+#&gt; parent_sink parent_m1 m1_sink
+#&gt; 0.485524 0.514476 1.000000
+#&gt;
+#&gt; $SFORB
+#&gt; logical(0)
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90
+#&gt; parent 7.022929 23.32967
+#&gt; m1 131.760711 437.69961
+#&gt; </div><div class='input'>
# Use stepwise fitting, using optimised parameters from parent only fit, FOMC
-</div><span class='co'># NOT RUN {</span>
-<span class='no'>FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
+</div><div class='input'><span class='no'>FOMC_SFO</span> <span class='kw'>&lt;-</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'>"FOMC"</span>, <span class='st'>"m1"</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))
-<span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</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.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_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='co'># Use starting parameters from parent only FOMC fit</span>
<span class='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
@@ -545,40 +612,733 @@
<span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span>
<span class='no'>SFORB_SFO</span> <span class='kw'>&lt;-</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'>"SFORB"</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>))
-<span class='co'># Fit the model to the FOCUS example dataset D using defaults</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.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_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='no'>fit.SFORB_SFO.deSolve</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>,
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='co'># Use starting parameters from parent only SFORB fit (not really needed in this case)</span>
<span class='no'>fit.SFORB</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='co'># }</span><div class='input'>
-</div><span class='co'># NOT RUN {</span>
-<span class='co'># Weighted fits, including IRLS</span>
+<span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='input'>
+</div><div class='input'><span class='co'># Weighted fits, including IRLS</span>
<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</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='st'>"m1"</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)
-<span class='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)
-<span class='no'>f.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.irls</span>)
-<span class='no'>f.w.mean</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)
-<span class='no'>f.w.value</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>,
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.4
+#&gt; R version used for fitting: 3.5.1
+#&gt; Date of fit: Fri Sep 14 11:35:05 2018
+#&gt; Date of summary: Fri Sep 14 11:35:05 2018
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 186 model solutions performed in 0.763 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt; f_parent_to_m1 0.5000 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.60000 1.61400 96.3300 102.9000
+#&gt; log_k_parent -2.31600 0.04187 -2.4010 -2.2310
+#&gt; log_k_m1 -5.24800 0.13610 -5.5230 -4.9720
+#&gt; f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; parent_0 1.0000 0.5178 -0.1701 -0.5489
+#&gt; log_k_parent 0.5178 1.0000 -0.3285 -0.5451
+#&gt; log_k_m1 -0.1701 -0.3285 1.0000 0.7466
+#&gt; f_parent_ilr_1 -0.5489 -0.5451 0.7466 1.0000
+#&gt;
+#&gt; Residual standard error: 3.211 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
+#&gt; k_parent 0.098700 23.880 5.700e-24 0.090660 1.074e-01
+#&gt; k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03
+#&gt; f_parent_to_m1 0.514500 22.490 4.375e-23 0.468100 5.606e-01
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.398 4 15
+#&gt; parent 6.459 2 7
+#&gt; m1 4.690 2 8
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_m1 0.5145
+#&gt; parent_sink 0.4855
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 7.023 23.33
+#&gt; m1 131.761 437.70
+#&gt;
+#&gt; Data:
+#&gt; time variable observed predicted residual
+#&gt; 0 parent 99.46 99.59848 -1.385e-01
+#&gt; 0 parent 102.04 99.59848 2.442e+00
+#&gt; 1 parent 93.50 90.23787 3.262e+00
+#&gt; 1 parent 92.50 90.23787 2.262e+00
+#&gt; 3 parent 63.23 74.07319 -1.084e+01
+#&gt; 3 parent 68.99 74.07319 -5.083e+00
+#&gt; 7 parent 52.32 49.91206 2.408e+00
+#&gt; 7 parent 55.13 49.91206 5.218e+00
+#&gt; 14 parent 27.27 25.01257 2.257e+00
+#&gt; 14 parent 26.64 25.01257 1.627e+00
+#&gt; 21 parent 11.50 12.53462 -1.035e+00
+#&gt; 21 parent 11.64 12.53462 -8.946e-01
+#&gt; 35 parent 2.85 3.14787 -2.979e-01
+#&gt; 35 parent 2.91 3.14787 -2.379e-01
+#&gt; 50 parent 0.69 0.71624 -2.624e-02
+#&gt; 50 parent 0.63 0.71624 -8.624e-02
+#&gt; 75 parent 0.05 0.06074 -1.074e-02
+#&gt; 75 parent 0.06 0.06074 -7.381e-04
+#&gt; 0 m1 0.00 0.00000 0.000e+00
+#&gt; 0 m1 0.00 0.00000 0.000e+00
+#&gt; 1 m1 4.84 4.80296 3.704e-02
+#&gt; 1 m1 5.64 4.80296 8.370e-01
+#&gt; 3 m1 12.91 13.02400 -1.140e-01
+#&gt; 3 m1 12.96 13.02400 -6.400e-02
+#&gt; 7 m1 22.97 25.04476 -2.075e+00
+#&gt; 7 m1 24.47 25.04476 -5.748e-01
+#&gt; 14 m1 41.69 36.69002 5.000e+00
+#&gt; 14 m1 33.21 36.69002 -3.480e+00
+#&gt; 21 m1 44.37 41.65310 2.717e+00
+#&gt; 21 m1 46.44 41.65310 4.787e+00
+#&gt; 35 m1 41.22 43.31312 -2.093e+00
+#&gt; 35 m1 37.95 43.31312 -5.363e+00
+#&gt; 50 m1 41.19 41.21831 -2.831e-02
+#&gt; 50 m1 40.01 41.21831 -1.208e+00
+#&gt; 75 m1 40.09 36.44703 3.643e+00
+#&gt; 75 m1 33.85 36.44703 -2.597e+00
+#&gt; 100 m1 31.04 31.98163 -9.416e-01
+#&gt; 100 m1 33.13 31.98163 1.148e+00
+#&gt; 120 m1 25.15 28.78984 -3.640e+00
+#&gt; 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.4
+#&gt; R version used for fitting: 3.5.1
+#&gt; Date of fit: Fri Sep 14 11:35:07 2018
+#&gt; Date of summary: Fri Sep 14 11:35:07 2018
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 551 model solutions performed in 2.297 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Iterative reweighting with method obs
+#&gt; Final mean squared residuals of observed variables:
+#&gt; parent m1
+#&gt; 11.573407 7.407845
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt; f_parent_to_m1 0.5000 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.67000 1.79200 96.04000 103.300
+#&gt; log_k_parent -2.31200 0.04560 -2.40400 -2.219
+#&gt; log_k_m1 -5.25100 0.12510 -5.50500 -4.998
+#&gt; f_parent_ilr_1 0.03785 0.06318 -0.09027 0.166
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; parent_0 1.0000 0.5083 -0.1979 -0.6148
+#&gt; log_k_parent 0.5083 1.0000 -0.3894 -0.6062
+#&gt; log_k_m1 -0.1979 -0.3894 1.0000 0.7417
+#&gt; f_parent_ilr_1 -0.6148 -0.6062 0.7417 1.0000
+#&gt;
+#&gt; Residual standard error: 1.054 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.67000 55.630 8.185e-37 96.040000 1.033e+02
+#&gt; k_parent 0.09906 21.930 1.016e-22 0.090310 1.087e-01
+#&gt; k_m1 0.00524 7.996 8.486e-10 0.004066 6.753e-03
+#&gt; f_parent_to_m1 0.51340 23.000 2.038e-23 0.468100 5.584e-01
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.399 4 15
+#&gt; parent 6.466 2 7
+#&gt; m1 4.679 2 8
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_m1 0.5134
+#&gt; parent_sink 0.4866
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 6.997 23.24
+#&gt; m1 132.282 439.43
+#&gt;
+#&gt; Data:
+#&gt; time variable observed predicted residual err
+#&gt; 0 parent 99.46 99.67218 -2.122e-01 3.402
+#&gt; 0 parent 102.04 99.67218 2.368e+00 3.402
+#&gt; 1 parent 93.50 90.27153 3.228e+00 3.402
+#&gt; 1 parent 92.50 90.27153 2.228e+00 3.402
+#&gt; 3 parent 63.23 74.04648 -1.082e+01 3.402
+#&gt; 3 parent 68.99 74.04648 -5.056e+00 3.402
+#&gt; 7 parent 52.32 49.82092 2.499e+00 3.402
+#&gt; 7 parent 55.13 49.82092 5.309e+00 3.402
+#&gt; 14 parent 27.27 24.90288 2.367e+00 3.402
+#&gt; 14 parent 26.64 24.90288 1.737e+00 3.402
+#&gt; 21 parent 11.50 12.44765 -9.476e-01 3.402
+#&gt; 21 parent 11.64 12.44765 -8.076e-01 3.402
+#&gt; 35 parent 2.85 3.11002 -2.600e-01 3.402
+#&gt; 35 parent 2.91 3.11002 -2.000e-01 3.402
+#&gt; 50 parent 0.69 0.70374 -1.374e-02 3.402
+#&gt; 50 parent 0.63 0.70374 -7.374e-02 3.402
+#&gt; 75 parent 0.05 0.05913 -9.134e-03 3.402
+#&gt; 75 parent 0.06 0.05913 8.662e-04 3.402
+#&gt; 0 m1 0.00 0.00000 0.000e+00 2.722
+#&gt; 0 m1 0.00 0.00000 0.000e+00 2.722
+#&gt; 1 m1 4.84 4.81328 2.672e-02 2.722
+#&gt; 1 m1 5.64 4.81328 8.267e-01 2.722
+#&gt; 3 m1 12.91 13.04779 -1.378e-01 2.722
+#&gt; 3 m1 12.96 13.04779 -8.779e-02 2.722
+#&gt; 7 m1 22.97 25.07615 -2.106e+00 2.722
+#&gt; 7 m1 24.47 25.07615 -6.062e-01 2.722
+#&gt; 14 m1 41.69 36.70729 4.983e+00 2.722
+#&gt; 14 m1 33.21 36.70729 -3.497e+00 2.722
+#&gt; 21 m1 44.37 41.65050 2.720e+00 2.722
+#&gt; 21 m1 46.44 41.65050 4.790e+00 2.722
+#&gt; 35 m1 41.22 43.28866 -2.069e+00 2.722
+#&gt; 35 m1 37.95 43.28866 -5.339e+00 2.722
+#&gt; 50 m1 41.19 41.19339 -3.386e-03 2.722
+#&gt; 50 m1 40.01 41.19339 -1.183e+00 2.722
+#&gt; 75 m1 40.09 36.43820 3.652e+00 2.722
+#&gt; 75 m1 33.85 36.43820 -2.588e+00 2.722
+#&gt; 100 m1 31.04 31.98971 -9.497e-01 2.722
+#&gt; 100 m1 33.13 31.98971 1.140e+00 2.722
+#&gt; 120 m1 25.15 28.80898 -3.659e+00 2.722
+#&gt; 120 m1 33.31 28.80898 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.4
+#&gt; R version used for fitting: 3.5.1
+#&gt; Date of fit: Fri Sep 14 11:35:08 2018
+#&gt; Date of summary: Fri Sep 14 11:35:08 2018
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 155 model solutions performed in 0.618 s
+#&gt;
+#&gt; Weighting: mean
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt; f_parent_to_m1 0.5000 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.7300 1.93200 95.81000 103.6000
+#&gt; log_k_parent -2.3090 0.04837 -2.40700 -2.2110
+#&gt; log_k_m1 -5.2550 0.12070 -5.49900 -5.0100
+#&gt; f_parent_ilr_1 0.0354 0.06344 -0.09327 0.1641
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; parent_0 1.0000 0.5004 -0.2143 -0.6514
+#&gt; log_k_parent 0.5004 1.0000 -0.4282 -0.6383
+#&gt; log_k_m1 -0.2143 -0.4282 1.0000 0.7390
+#&gt; f_parent_ilr_1 -0.6514 -0.6383 0.7390 1.0000
+#&gt;
+#&gt; Residual standard error: 0.09829 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.730000 51.630 1.166e-35 95.81000 1.036e+02
+#&gt; k_parent 0.099360 20.670 7.304e-22 0.09007 1.096e-01
+#&gt; k_m1 0.005224 8.287 3.649e-10 0.00409 6.672e-03
+#&gt; f_parent_to_m1 0.512500 22.860 2.497e-23 0.46710 5.578e-01
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.401 4 15
+#&gt; parent 6.473 2 7
+#&gt; m1 4.671 2 8
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_m1 0.5125
+#&gt; parent_sink 0.4875
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 6.976 23.18
+#&gt; m1 132.696 440.81
+#&gt;
+#&gt; Data:
+#&gt; time variable observed predicted residual
+#&gt; 0 parent 99.46 99.73057 -0.270570
+#&gt; 0 parent 102.04 99.73057 2.309430
+#&gt; 1 parent 93.50 90.29805 3.201945
+#&gt; 1 parent 92.50 90.29805 2.201945
+#&gt; 3 parent 63.23 74.02503 -10.795028
+#&gt; 3 parent 68.99 74.02503 -5.035028
+#&gt; 7 parent 52.32 49.74838 2.571618
+#&gt; 7 parent 55.13 49.74838 5.381618
+#&gt; 14 parent 27.27 24.81588 2.454124
+#&gt; 14 parent 26.64 24.81588 1.824124
+#&gt; 21 parent 11.50 12.37885 -0.878849
+#&gt; 21 parent 11.64 12.37885 -0.738849
+#&gt; 35 parent 2.85 3.08022 -0.230219
+#&gt; 35 parent 2.91 3.08022 -0.170219
+#&gt; 50 parent 0.69 0.69396 -0.003958
+#&gt; 50 parent 0.63 0.69396 -0.063958
+#&gt; 75 parent 0.05 0.05789 -0.007888
+#&gt; 75 parent 0.06 0.05789 0.002112
+#&gt; 0 m1 0.00 0.00000 0.000000
+#&gt; 0 m1 0.00 0.00000 0.000000
+#&gt; 1 m1 4.84 4.82149 0.018512
+#&gt; 1 m1 5.64 4.82149 0.818512
+#&gt; 3 m1 12.91 13.06669 -0.156692
+#&gt; 3 m1 12.96 13.06669 -0.106692
+#&gt; 7 m1 22.97 25.10106 -2.131058
+#&gt; 7 m1 24.47 25.10106 -0.631058
+#&gt; 14 m1 41.69 36.72092 4.969077
+#&gt; 14 m1 33.21 36.72092 -3.510923
+#&gt; 21 m1 44.37 41.64835 2.721647
+#&gt; 21 m1 46.44 41.64835 4.791647
+#&gt; 35 m1 41.22 43.26923 -2.049225
+#&gt; 35 m1 37.95 43.26923 -5.319225
+#&gt; 50 m1 41.19 41.17364 0.016361
+#&gt; 50 m1 40.01 41.17364 -1.163639
+#&gt; 75 m1 40.09 36.43122 3.658776
+#&gt; 75 m1 33.85 36.43122 -2.581224
+#&gt; 100 m1 31.04 31.99612 -0.956124
+#&gt; 100 m1 33.13 31.99612 1.133876
+#&gt; 120 m1 25.15 28.82413 -3.674128
+#&gt; 120 m1 33.31 28.82413 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>,
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)
-<span class='co'># }</span><div class='input'>
-</div><span class='co'># NOT RUN {</span>
-<span class='co'># Manual weighting</span>
+<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.4
+#&gt; R version used for fitting: 3.5.1
+#&gt; Date of fit: Fri Sep 14 11:35:09 2018
+#&gt; Date of summary: Fri Sep 14 11:35:09 2018
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 174 model solutions performed in 0.704 s
+#&gt;
+#&gt; Weighting: manual
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt; f_parent_to_m1 0.5000 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.6600 2.712000 94.14000 105.2000
+#&gt; log_k_parent -2.2980 0.008118 -2.31500 -2.2820
+#&gt; log_k_m1 -5.2410 0.096690 -5.43800 -5.0450
+#&gt; f_parent_ilr_1 0.0231 0.057990 -0.09474 0.1409
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; parent_0 1.00000 0.6843 -0.08687 -0.7564
+#&gt; log_k_parent 0.68435 1.0000 -0.12695 -0.5812
+#&gt; log_k_m1 -0.08687 -0.1269 1.00000 0.5195
+#&gt; f_parent_ilr_1 -0.75644 -0.5812 0.51952 1.0000
+#&gt;
+#&gt; Residual standard error: 0.08396 on 34 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.660000 36.75 2.957e-29 94.14000 1.052e+02
+#&gt; k_parent 0.100400 123.20 5.927e-47 0.09878 1.021e-01
+#&gt; k_m1 0.005295 10.34 2.447e-12 0.00435 6.444e-03
+#&gt; f_parent_to_m1 0.508200 24.79 1.184e-23 0.46660 5.497e-01
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.461 4 15
+#&gt; parent 6.520 2 7
+#&gt; m1 4.744 2 8
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_m1 0.5082
+#&gt; parent_sink 0.4918
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 6.902 22.93
+#&gt; m1 130.916 434.89
+#&gt;
+#&gt; Data:
+#&gt; time variable observed predicted residual err
+#&gt; 0 parent 99.46 99.65571 -0.195715 99.46
+#&gt; 0 parent 102.04 99.65571 2.384285 102.04
+#&gt; 1 parent 93.50 90.13383 3.366170 93.50
+#&gt; 1 parent 92.50 90.13383 2.366170 92.50
+#&gt; 3 parent 63.23 73.73252 -10.502518 63.23
+#&gt; 3 parent 68.99 73.73252 -4.742518 68.99
+#&gt; 7 parent 52.32 49.34027 2.979728 52.32
+#&gt; 7 parent 55.13 49.34027 5.789728 55.13
+#&gt; 14 parent 27.27 24.42873 2.841271 27.27
+#&gt; 14 parent 26.64 24.42873 2.211271 26.64
+#&gt; 21 parent 11.50 12.09484 -0.594842 11.50
+#&gt; 21 parent 11.64 12.09484 -0.454842 11.64
+#&gt; 35 parent 2.85 2.96482 -0.114824 2.85
+#&gt; 35 parent 2.91 2.96482 -0.054824 2.91
+#&gt; 50 parent 0.69 0.65733 0.032670 0.69
+#&gt; 50 parent 0.63 0.65733 -0.027330 0.63
+#&gt; 75 parent 0.05 0.05339 -0.003386 0.05
+#&gt; 75 parent 0.06 0.05339 0.006614 0.06
+#&gt; 1 m1 4.84 4.82570 0.014301 4.84
+#&gt; 1 m1 5.64 4.82570 0.814301 5.64
+#&gt; 3 m1 12.91 13.06402 -0.154020 12.91
+#&gt; 3 m1 12.96 13.06402 -0.104020 12.96
+#&gt; 7 m1 22.97 25.04656 -2.076564 22.97
+#&gt; 7 m1 24.47 25.04656 -0.576564 24.47
+#&gt; 14 m1 41.69 36.53601 5.153988 41.69
+#&gt; 14 m1 33.21 36.53601 -3.326012 33.21
+#&gt; 21 m1 44.37 41.34639 3.023609 44.37
+#&gt; 21 m1 46.44 41.34639 5.093609 46.44
+#&gt; 35 m1 41.22 42.82669 -1.606690 41.22
+#&gt; 35 m1 37.95 42.82669 -4.876690 37.95
+#&gt; 50 m1 41.19 40.67342 0.516578 41.19
+#&gt; 50 m1 40.01 40.67342 -0.663422 40.01
+#&gt; 75 m1 40.09 35.91105 4.178947 40.09
+#&gt; 75 m1 33.85 35.91105 -2.061053 33.85
+#&gt; 100 m1 31.04 31.48161 -0.441612 31.04
+#&gt; 100 m1 33.13 31.48161 1.648388 33.13
+#&gt; 120 m1 25.15 28.32018 -3.170181 25.15
+#&gt; 120 m1 33.31 28.32018 4.989819 33.31</div><div class='input'>
+</div><div class='input'><span class='co'># Manual weighting</span>
<span class='no'>dw</span> <span class='kw'>&lt;-</span> <span class='no'>FOCUS_2006_D</span>
<span class='no'>errors</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>1</span>)
<span class='no'>dw</span>$<span class='no'>err.man</span> <span class='kw'>&lt;-</span> <span class='no'>errors</span>[<span class='no'>FOCUS_2006_D</span>$<span class='no'>name</span>]
<span class='no'>f.w.man</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)
-<span class='no'>f.w.man.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.4
+#&gt; R version used for fitting: 3.5.1
+#&gt; Date of fit: Fri Sep 14 11:35:10 2018
+#&gt; Date of summary: Fri Sep 14 11:35:10 2018
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 270 model solutions performed in 1.109 s
+#&gt;
+#&gt; Weighting: manual
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt; f_parent_to_m1 0.5000 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.49000 1.33200 96.7800 102.2000
+#&gt; log_k_parent -2.32100 0.03550 -2.3930 -2.2490
+#&gt; log_k_m1 -5.24100 0.21280 -5.6730 -4.8100
+#&gt; f_parent_ilr_1 0.04571 0.08966 -0.1361 0.2275
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; parent_0 1.00000 0.5312 -0.09456 -0.3351
+#&gt; log_k_parent 0.53123 1.0000 -0.17800 -0.3360
+#&gt; log_k_m1 -0.09456 -0.1780 1.00000 0.7616
+#&gt; f_parent_ilr_1 -0.33514 -0.3360 0.76156 1.0000
+#&gt;
+#&gt; Residual standard error: 2.628 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.490000 74.69 2.221e-41 96.780000 1.022e+02
+#&gt; k_parent 0.098140 28.17 2.012e-26 0.091320 1.055e-01
+#&gt; k_m1 0.005292 4.70 1.873e-05 0.003437 8.148e-03
+#&gt; f_parent_to_m1 0.516200 16.30 1.686e-18 0.452000 5.798e-01
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.400 4 15
+#&gt; parent 6.454 2 7
+#&gt; m1 4.708 2 8
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_m1 0.5162
+#&gt; parent_sink 0.4838
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 7.063 23.46
+#&gt; m1 130.971 435.08
+#&gt;
+#&gt; Data:
+#&gt; time variable observed predicted residual err
+#&gt; 0 parent 99.46 99.48598 -0.025979 1
+#&gt; 0 parent 102.04 99.48598 2.554021 1
+#&gt; 1 parent 93.50 90.18612 3.313880 1
+#&gt; 1 parent 92.50 90.18612 2.313880 1
+#&gt; 3 parent 63.23 74.11316 -10.883163 1
+#&gt; 3 parent 68.99 74.11316 -5.123163 1
+#&gt; 7 parent 52.32 50.05030 2.269705 1
+#&gt; 7 parent 55.13 50.05030 5.079705 1
+#&gt; 14 parent 27.27 25.17975 2.090250 1
+#&gt; 14 parent 26.64 25.17975 1.460250 1
+#&gt; 21 parent 11.50 12.66765 -1.167654 1
+#&gt; 21 parent 11.64 12.66765 -1.027654 1
+#&gt; 35 parent 2.85 3.20616 -0.356164 1
+#&gt; 35 parent 2.91 3.20616 -0.296164 1
+#&gt; 50 parent 0.69 0.73562 -0.045619 1
+#&gt; 50 parent 0.63 0.73562 -0.105619 1
+#&gt; 75 parent 0.05 0.06326 -0.013256 1
+#&gt; 75 parent 0.06 0.06326 -0.003256 1
+#&gt; 0 m1 0.00 0.00000 0.000000 2
+#&gt; 0 m1 0.00 0.00000 0.000000 2
+#&gt; 1 m1 4.84 4.78729 0.052713 2
+#&gt; 1 m1 5.64 4.78729 0.852713 2
+#&gt; 3 m1 12.91 12.98785 -0.077848 2
+#&gt; 3 m1 12.96 12.98785 -0.027848 2
+#&gt; 7 m1 22.97 24.99695 -2.026946 2
+#&gt; 7 m1 24.47 24.99695 -0.526946 2
+#&gt; 14 m1 41.69 36.66353 5.026472 2
+#&gt; 14 m1 33.21 36.66353 -3.453528 2
+#&gt; 21 m1 44.37 41.65681 2.713186 2
+#&gt; 21 m1 46.44 41.65681 4.783186 2
+#&gt; 35 m1 41.22 43.35031 -2.130314 2
+#&gt; 35 m1 37.95 43.35031 -5.400314 2
+#&gt; 50 m1 41.19 41.25637 -0.066368 2
+#&gt; 50 m1 40.01 41.25637 -1.246368 2
+#&gt; 75 m1 40.09 36.46057 3.629429 2
+#&gt; 75 m1 33.85 36.46057 -2.610571 2
+#&gt; 100 m1 31.04 31.96929 -0.929293 2
+#&gt; 100 m1 33.13 31.96929 1.160707 2
+#&gt; 120 m1 25.15 28.76062 -3.610621 2
+#&gt; 120 m1 33.31 28.76062 4.549379 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)
-<span class='co'># }</span></pre>
+<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.4
+#&gt; R version used for fitting: 3.5.1
+#&gt; Date of fit: Fri Sep 14 11:35:13 2018
+#&gt; Date of summary: Fri Sep 14 11:35:13 2018
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 692 model solutions performed in 2.903 s
+#&gt;
+#&gt; Weighting: manual
+#&gt;
+#&gt; Iterative reweighting with method obs
+#&gt; Final mean squared residuals of observed variables:
+#&gt; parent m1
+#&gt; 11.573406 7.407846
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt; f_parent_to_m1 0.5000 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.67000 1.79200 96.04000 103.300
+#&gt; log_k_parent -2.31200 0.04560 -2.40400 -2.220
+#&gt; log_k_m1 -5.25100 0.12510 -5.50500 -4.998
+#&gt; f_parent_ilr_1 0.03785 0.06318 -0.09027 0.166
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; parent_0 1.0000 0.5083 -0.1979 -0.6148
+#&gt; log_k_parent 0.5083 1.0000 -0.3894 -0.6062
+#&gt; log_k_m1 -0.1979 -0.3894 1.0000 0.7417
+#&gt; f_parent_ilr_1 -0.6148 -0.6062 0.7417 1.0000
+#&gt;
+#&gt; Residual standard error: 1.054 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.67000 55.630 8.185e-37 96.040000 1.033e+02
+#&gt; k_parent 0.09906 21.930 1.016e-22 0.090310 1.087e-01
+#&gt; k_m1 0.00524 7.996 8.486e-10 0.004066 6.753e-03
+#&gt; f_parent_to_m1 0.51340 23.000 2.039e-23 0.468100 5.584e-01
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.399 4 15
+#&gt; parent 6.466 2 7
+#&gt; m1 4.679 2 8
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_m1 0.5134
+#&gt; parent_sink 0.4866
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 6.997 23.24
+#&gt; m1 132.282 439.43
+#&gt;
+#&gt; Data:
+#&gt; time variable observed predicted residual err.ini err
+#&gt; 0 parent 99.46 99.67217 -2.122e-01 1 3.402
+#&gt; 0 parent 102.04 99.67217 2.368e+00 1 3.402
+#&gt; 1 parent 93.50 90.27152 3.228e+00 1 3.402
+#&gt; 1 parent 92.50 90.27152 2.228e+00 1 3.402
+#&gt; 3 parent 63.23 74.04648 -1.082e+01 1 3.402
+#&gt; 3 parent 68.99 74.04648 -5.056e+00 1 3.402
+#&gt; 7 parent 52.32 49.82092 2.499e+00 1 3.402
+#&gt; 7 parent 55.13 49.82092 5.309e+00 1 3.402
+#&gt; 14 parent 27.27 24.90288 2.367e+00 1 3.402
+#&gt; 14 parent 26.64 24.90288 1.737e+00 1 3.402
+#&gt; 21 parent 11.50 12.44765 -9.477e-01 1 3.402
+#&gt; 21 parent 11.64 12.44765 -8.077e-01 1 3.402
+#&gt; 35 parent 2.85 3.11002 -2.600e-01 1 3.402
+#&gt; 35 parent 2.91 3.11002 -2.000e-01 1 3.402
+#&gt; 50 parent 0.69 0.70375 -1.375e-02 1 3.402
+#&gt; 50 parent 0.63 0.70375 -7.375e-02 1 3.402
+#&gt; 75 parent 0.05 0.05913 -9.134e-03 1 3.402
+#&gt; 75 parent 0.06 0.05913 8.661e-04 1 3.402
+#&gt; 0 m1 0.00 0.00000 0.000e+00 2 2.722
+#&gt; 0 m1 0.00 0.00000 0.000e+00 2 2.722
+#&gt; 1 m1 4.84 4.81328 2.672e-02 2 2.722
+#&gt; 1 m1 5.64 4.81328 8.267e-01 2 2.722
+#&gt; 3 m1 12.91 13.04779 -1.378e-01 2 2.722
+#&gt; 3 m1 12.96 13.04779 -8.779e-02 2 2.722
+#&gt; 7 m1 22.97 25.07615 -2.106e+00 2 2.722
+#&gt; 7 m1 24.47 25.07615 -6.062e-01 2 2.722
+#&gt; 14 m1 41.69 36.70729 4.983e+00 2 2.722
+#&gt; 14 m1 33.21 36.70729 -3.497e+00 2 2.722
+#&gt; 21 m1 44.37 41.65050 2.719e+00 2 2.722
+#&gt; 21 m1 46.44 41.65050 4.789e+00 2 2.722
+#&gt; 35 m1 41.22 43.28866 -2.069e+00 2 2.722
+#&gt; 35 m1 37.95 43.28866 -5.339e+00 2 2.722
+#&gt; 50 m1 41.19 41.19339 -3.387e-03 2 2.722
+#&gt; 50 m1 40.01 41.19339 -1.183e+00 2 2.722
+#&gt; 75 m1 40.09 36.43820 3.652e+00 2 2.722
+#&gt; 75 m1 33.85 36.43820 -2.588e+00 2 2.722
+#&gt; 100 m1 31.04 31.98971 -9.497e-01 2 2.722
+#&gt; 100 m1 33.13 31.98971 1.140e+00 2 2.722
+#&gt; 120 m1 25.15 28.80897 -3.659e+00 2 2.722
+#&gt; 120 m1 33.31 28.80897 4.501e+00 2 2.722</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index a0eade3b..857e0c74 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
@@ -221,17 +221,35 @@ For the definition of model types and their parameters, the equations given
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-</div><span class='co'># NOT RUN {</span>
-<span class='co'># The above model used to be specified like this, before the advent of mkinsub()</span>
+</div><div class='input'><span class='co'># The above model used to be specified like this, before the advent of mkinsub()</span>
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>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'>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>))
-
+ <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'># Show details of creating the C function</span>
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; Compilation argument:
+#&gt; /usr/lib/R/bin/R CMD SHLIB file3c104e6e45e4.c 2&gt; file3c104e6e45e4.c.err.txt
+#&gt; Program source:
+#&gt; 1: #include &lt;R.h&gt;
+#&gt; 2:
+#&gt; 3:
+#&gt; 4: static double parms [3];
+#&gt; 5: #define k_parent_sink parms[0]
+#&gt; 6: #define k_parent_m1 parms[1]
+#&gt; 7: #define k_m1_sink parms[2]
+#&gt; 8:
+#&gt; 9: void initpar(void (* odeparms)(int *, double *)) {
+#&gt; 10: int N = 3;
+#&gt; 11: odeparms(&amp;N, parms);
+#&gt; 12: }
+#&gt; 13:
+#&gt; 14:
+#&gt; 15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {
+#&gt; 16:
+#&gt; 17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0];
+#&gt; 18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1];
+#&gt; 19: }</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'># If we have several parallel metabolites </span>
<span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
<span class='no'>m_synth_DFOP_par</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
@@ -241,8 +259,7 @@ For the definition of model types and their parameters, the equations given
<span class='no'>fit_DFOP_par_c</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>,
<span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>,
- <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='co'># }</span></pre>
+ <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 75d22288..adcd2a3b 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 6aa67e5b..2d878175 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 6c2ba992..ffd6e89f 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</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; 0.004 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.003 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; 0.001 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.002 0.000 0.001 </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; 0.035 0.000 0.036 </div></pre>
+#&gt; 0.035 0.000 0.035 </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 4ba540b2..b4e1e747 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 65de0664..a34f1dae 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png
new file mode 100644
index 00000000..6f24b369
--- /dev/null
+++ b/docs/reference/mmkin-1.png
Binary files differ
diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png
new file mode 100644
index 00000000..1ed2b216
--- /dev/null
+++ b/docs/reference/mmkin-2.png
Binary files differ
diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png
new file mode 100644
index 00000000..952e6af3
--- /dev/null
+++ b/docs/reference/mmkin-3.png
Binary files differ
diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png
new file mode 100644
index 00000000..cad6ee11
--- /dev/null
+++ b/docs/reference/mmkin-4.png
Binary files differ
diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png
new file mode 100644
index 00000000..7ab171d1
--- /dev/null
+++ b/docs/reference/mmkin-5.png
Binary files differ
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 557da0d7..621571c1 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
@@ -175,15 +175,12 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><span class='co'># NOT RUN {</span>
-<span class='no'>m_synth_SFO_lin</span> <span class='kw'>&lt;-</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='st'>"M1"</span>),
+ <pre class="examples"><div class='input'><span class='no'>m_synth_SFO_lin</span> <span class='kw'>&lt;-</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='st'>"M1"</span>),
<span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M2"</span>),
- <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)
-
+ <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>m_synth_FOMC_lin</span> <span class='kw'>&lt;-</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'>"FOMC"</span>, <span class='st'>"M1"</span>),
<span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M2"</span>),
- <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)
-
+ <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>models</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='kw'>SFO_lin</span> <span class='kw'>=</span> <span class='no'>m_synth_SFO_lin</span>, <span class='kw'>FOMC_lin</span> <span class='kw'>=</span> <span class='no'>m_synth_FOMC_lin</span>)
<span class='no'>datasets</span> <span class='kw'>&lt;-</span> <span class='fu'>lapply</span>(<span class='no'>synthetic_data_for_UBA_2014</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>)
<span class='fu'>names</span>(<span class='no'>datasets</span>) <span class='kw'>&lt;-</span> <span class='fu'>paste</span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)
@@ -191,23 +188,29 @@
<span class='no'>time_default</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</span>(<span class='no'>fits.0</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
-<span class='no'>time_default</span>
-<span class='no'>time_1</span>
-
-<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])
-
+<span class='no'>time_default</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 0.046 0.033 6.654 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 20.150 0.000 20.163 </div><div class='input'>
+<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
+#&gt; parent_M1 parent_sink M1_M2 M1_sink
+#&gt; 0.7340480 0.2659520 0.7505686 0.2494314
+#&gt;
+#&gt; $SFORB
+#&gt; logical(0)
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90
+#&gt; parent 0.8777689 2.915885
+#&gt; M1 2.3257453 7.725959
+#&gt; M2 33.7200874 112.015706
+#&gt; </div><div class='input'>
<span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span>
-<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])
-<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))
-<span class='fu'>plot</span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])
-<span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span>
+<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><div class='img'><img src='mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><div class='img'><img src='mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span>
<span class='co'># by plot.mkinfit and can be plotted using plot_sep</span>
-<span class='fu'>plot</span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]], <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]])
+<span class='fu'>plot</span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]], <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]])
<span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span>
<span class='co'># allow to plot the observed variables separately</span>
-<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])
-<span class='co'># }</span></pre>
+<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 765f1628..4fec74c9 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 0599907d..478a5682 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index 86bb58e5..f59325f9 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index bc4c644a..299fdfbb 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/schaefer07_complex_case-1.png b/docs/reference/schaefer07_complex_case-1.png
new file mode 100644
index 00000000..6a621369
--- /dev/null
+++ b/docs/reference/schaefer07_complex_case-1.png
Binary files differ
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index b212aa53..9fd60805 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
@@ -159,12 +159,22 @@
<span class='kw'>A1</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'>"A2"</span>),
<span class='kw'>B1</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'>C1</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'>A2</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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><span class='co'># NOT RUN {</span>
- <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'>plot</span>(<span class='no'>fit</span>)
- <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)
-
-<span class='co'># }</span><div class='input'> <span class='co'># Compare with the results obtained in the original publication</span>
+ <span class='kw'>A2</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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='fu'>plot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></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_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink
+#&gt; 0.3809621 0.1954665 0.4235714 0.0000000 0.4479674 0.5520326
+#&gt;
+#&gt; $SFORB
+#&gt; logical(0)
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90
+#&gt; parent 13.95078 46.34350
+#&gt; A1 49.75342 165.27728
+#&gt; B1 37.26913 123.80536
+#&gt; C1 11.23133 37.30968
+#&gt; A2 28.50591 94.69457
+#&gt; </div><div class='input'> </div><div class='input'> <span class='co'># Compare with the results obtained in the original publication</span>
<span class='fu'>print</span>(<span class='no'>schaefer07_complex_results</span>)</div><div class='output co'>#&gt; compound parameter KinGUI ModelMaker deviation
#&gt; 1 parent degradation rate 0.0496 0.0506 2.0
#&gt; 2 parent DT50 13.9900 13.6900 2.2
diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html
index c8000ae5..6db7d74c 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 28447e64..1d0a7c52 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</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: 0.9.47.3
+ <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: 0.9.47.4
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 06:39:24 2018
-#&gt; Date of summary: Fri Sep 14 06:39:24 2018
+#&gt; Date of fit: Fri Sep 14 11:35:59 2018
+#&gt; Date of summary: Fri Sep 14 11:35:59 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 0.081 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.076 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 dd44a450..25cfc012 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
@@ -176,8 +176,7 @@ Compare also the code in the example section to see the degradation models." />
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"># NOT RUN {
-# The data have been generated using the following kinetic models
+ <pre class="examples"><div class='input'># The data have been generated using the following kinetic models
m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
M1 = list(type = "SFO", to = "M2"),
M2 = list(type = "SFO"), use_of_ff = "max")
@@ -275,8 +274,10 @@ fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data,
quiet = TRUE)
plot_sep(fit)
summary(fit)
-# }
-</pre>
+</div><div class='output co'>#&gt; <span class='error'>Error: &lt;text&gt;:67:43: Unerwartete(s) SPECIAL</span>
+#&gt; <span class='error'>66: </span>
+#&gt; <span class='error'>67: d_rep[d_rep$time == 0 &amp; d_rep$name &lt;!-- %in%</span>
+#&gt; <span class='error'> ^</span></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png
new file mode 100644
index 00000000..47670389
--- /dev/null
+++ b/docs/reference/test_data_from_UBA_2014-1.png
Binary files differ
diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png
new file mode 100644
index 00000000..8d282842
--- /dev/null
+++ b/docs/reference/test_data_from_UBA_2014-2.png
Binary files differ
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index f9032c84..a30161a2 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
@@ -146,35 +146,63 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> </div><span class='co'># NOT RUN {</span>
- <span class='co'># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span>
+ <pre class="examples"><div class='input'> </div><div class='input'> <span class='co'># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span>
<span class='co'># guidance. Due to the strong correlation of the parameter estimates, the</span>
<span class='co'># covariance matrix is not returned. Note that level P-II evaluations are</span>
<span class='co'># generally considered deprecated due to the frequent occurrence of such</span>
<span class='co'># large parameter correlations, among other reasons (e.g. the adequacy of the</span>
<span class='co'># model).</span>
<span class='no'>m_ws</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent_w</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span>),
- <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span>))
- <span class='no'>f_river</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)
-
- <span class='fu'>summary</span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span>
- <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)
-
+ <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>f_river</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'>
+ <span class='fu'>summary</span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
+#&gt; parent_w_0 9.598567e+01 2.33959800 4.102657e+01 9.568967e-19 NA
+#&gt; k_parent_w_sink 3.603743e-01 0.03497750 1.030303e+01 4.989002e-09 NA
+#&gt; k_parent_w_parent_s 6.031371e-02 0.01746024 3.454346e+00 1.514723e-03 NA
+#&gt; k_parent_s_sink 5.108539e-11 0.10382001 4.920572e-10 5.000000e-01 NA
+#&gt; k_parent_s_parent_w 7.419672e-02 0.11338240 6.543936e-01 2.608069e-01 NA
+#&gt; Upper
+#&gt; parent_w_0 NA
+#&gt; k_parent_w_sink NA
+#&gt; k_parent_w_parent_s NA
+#&gt; k_parent_s_sink NA
+#&gt; k_parent_s_parent_w NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#&gt; err.min n.optim df
+#&gt; All data 0.09246946 5 6
+#&gt; parent_w 0.06377096 3 3
+#&gt; parent_s 0.20882324 2 3</div><div class='input'>
<span class='co'># This is the evaluation used for the validation of software packages</span>
<span class='co'># in the expertise from 2014</span>
<span class='no'>m_soil</span> <span class='kw'>&lt;-</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='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
<span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>),
<span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>),
<span class='kw'>M3</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
- <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)
-
+ <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>f_soil</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))
- <span class='fu'>summary</span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span>
- <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)
-
-<span class='co'># }</span></pre>
+ <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'>summary</span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
+#&gt; parent_0 76.55425584 0.943443794 81.1434198 4.422336e-30 74.602593773
+#&gt; k_parent 0.12081956 0.004815515 25.0896457 1.639665e-18 0.111257517
+#&gt; k_M1 0.84258651 0.930121548 0.9058886 1.871938e-01 0.085876516
+#&gt; k_M2 0.04210878 0.013729902 3.0669396 2.729137e-03 0.021450630
+#&gt; k_M3 0.01122919 0.008044865 1.3958206 8.804912e-02 0.002550984
+#&gt; f_parent_to_M1 0.32240199 0.278620579 1.1571363 1.295467e-01 NA
+#&gt; f_parent_to_M2 0.16099854 0.030548888 5.2701931 1.196190e-05 NA
+#&gt; f_M1_to_M3 0.27921500 0.314732842 0.8871492 1.920908e-01 0.015016983
+#&gt; f_M2_to_M3 0.55641333 0.650246995 0.8556954 2.004966e-01 0.005360555
+#&gt; Upper
+#&gt; parent_0 78.50591790
+#&gt; k_parent 0.13120341
+#&gt; k_M1 8.26712661
+#&gt; k_M2 0.08266188
+#&gt; k_M3 0.04942981
+#&gt; f_parent_to_M1 NA
+#&gt; f_parent_to_M2 NA
+#&gt; f_M1_to_M3 0.90777163
+#&gt; f_M2_to_M3 0.99658633</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#&gt; err.min n.optim df
+#&gt; All data 0.09649963 9 20
+#&gt; parent 0.04721283 2 6
+#&gt; M1 0.26551209 2 5
+#&gt; M2 0.20327575 2 5
+#&gt; M3 0.05196549 3 4</div><div class='input'> </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index a31b075e..c0ca534c 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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</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: 0.9.47.3
+<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: 0.9.47.4
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 06:39:25 2018
-#&gt; Date of summary: Fri Sep 14 06:39:25 2018
+#&gt; Date of fit: Fri Sep 14 11:36:07 2018
+#&gt; Date of summary: Fri Sep 14 11:36:07 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 0.642 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.627 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -273,10 +273,82 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt; DT50 DT90
#&gt; parent 7.023 23.33
#&gt; m1 131.761 437.70</div><div class='input'>
-</div><span class='co'># NOT RUN {</span>
-<span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)
-<span class='co'># }</span><div class='input'>
+</div><div class='input'><span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>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: 0.9.47.4
+#&gt; R version used for fitting: 3.5.1
+#&gt; Date of fit: Fri Sep 14 11:36:08 2018
+#&gt; Date of summary: Fri Sep 14 11:36:08 2018
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
+#&gt; d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 350 model solutions performed in 1.437 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent_sink 0.1000 deparm
+#&gt; k_parent_m1 0.1001 deparm
+#&gt; k_m1_sink 0.1002 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.7500 -Inf Inf
+#&gt; k_parent_sink 0.1000 0 Inf
+#&gt; k_parent_m1 0.1001 0 Inf
+#&gt; k_m1_sink 0.1002 0 Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.600000 1.6140000 96.330000 1.029e+02
+#&gt; k_parent_sink 0.047920 0.0037500 0.040310 5.553e-02
+#&gt; k_parent_m1 0.050780 0.0020940 0.046530 5.502e-02
+#&gt; k_m1_sink 0.005261 0.0007159 0.003809 6.713e-03
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 k_parent_sink k_parent_m1 k_m1_sink
+#&gt; parent_0 1.00000 0.6075 -0.06625 -0.1701
+#&gt; k_parent_sink 0.60752 1.0000 -0.08740 -0.6253
+#&gt; k_parent_m1 -0.06625 -0.0874 1.00000 0.4716
+#&gt; k_m1_sink -0.17006 -0.6253 0.47164 1.0000
+#&gt;
+#&gt; Residual standard error: 3.211 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
+#&gt; k_parent_sink 0.047920 12.780 3.050e-15 0.040310 5.553e-02
+#&gt; k_parent_m1 0.050780 24.250 3.407e-24 0.046530 5.502e-02
+#&gt; k_m1_sink 0.005261 7.349 5.758e-09 0.003809 6.713e-03
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.398 4 15
+#&gt; parent 6.827 3 6
+#&gt; m1 4.490 1 9
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_sink 0.4855
+#&gt; parent_m1 0.5145
+#&gt; m1_sink 1.0000
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 7.023 23.33
+#&gt; m1 131.761 437.70</div><div class='input'>
<span class='no'>initials</span> <span class='kw'>&lt;-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span>
<span class='fu'>names</span>(<span class='no'>initials</span>) <span class='kw'>&lt;-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start</span>)
<span class='no'>transformed</span> <span class='kw'>&lt;-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span>
@@ -284,29 +356,160 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt; parent_0 k_parent_sink k_parent_m1 k_m1_sink
#&gt; 100.7500 0.1000 0.1001 0.1002 </div><div class='input'>
-</div><span class='co'># NOT RUN {</span>
-<span class='co'># The case of formation fractions</span>
+</div><div class='input'><span class='co'># The case of formation fractions</span>
<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</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='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>),
- <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)
-
+ <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>fit.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-<span class='no'>initials</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)
+<span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.4
+#&gt; R version used for fitting: 3.5.1
+#&gt; Date of fit: Fri Sep 14 11:36:09 2018
+#&gt; Date of summary: Fri Sep 14 11:36:09 2018
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 186 model solutions performed in 0.773 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt; f_parent_to_m1 0.5000 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.60000 1.61400 96.3300 102.9000
+#&gt; log_k_parent -2.31600 0.04187 -2.4010 -2.2310
+#&gt; log_k_m1 -5.24800 0.13610 -5.5230 -4.9720
+#&gt; f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; parent_0 1.0000 0.5178 -0.1701 -0.5489
+#&gt; log_k_parent 0.5178 1.0000 -0.3285 -0.5451
+#&gt; log_k_m1 -0.1701 -0.3285 1.0000 0.7466
+#&gt; f_parent_ilr_1 -0.5489 -0.5451 0.7466 1.0000
+#&gt;
+#&gt; Residual standard error: 3.211 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
+#&gt; k_parent 0.098700 23.880 5.700e-24 0.090660 1.074e-01
+#&gt; k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03
+#&gt; f_parent_to_m1 0.514500 22.490 4.375e-23 0.468100 5.606e-01
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.398 4 15
+#&gt; parent 6.459 2 7
+#&gt; m1 4.690 2 8
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_m1 0.5145
+#&gt; parent_sink 0.4855
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 7.023 23.33
+#&gt; m1 131.761 437.70</div><div class='input'><span class='no'>initials</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)
<span class='no'>transformed</span> <span class='kw'>&lt;-</span> <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO.ff</span>)
-<span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO.ff</span>)
-
+<span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO.ff</span>)</div><div class='output co'>#&gt; f_parent_to_m1
+#&gt; 0.5 </div><div class='input'>
<span class='co'># And without sink</span>
<span class='no'>SFO_SFO.ff.2</span> <span class='kw'>&lt;-</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</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>),
- <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)
-
+ <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>fit.ff.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-<span class='co'># }</span></pre>
+<span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.4
+#&gt; R version used for fitting: 3.5.1
+#&gt; Date of fit: Fri Sep 14 11:36:10 2018
+#&gt; Date of summary: Fri Sep 14 11:36:10 2018
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 104 model solutions performed in 0.424 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 84.790 2.96500 78.78 90.800
+#&gt; log_k_parent -2.756 0.08088 -2.92 -2.593
+#&gt; log_k_m1 -4.214 0.11150 -4.44 -3.988
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1
+#&gt; parent_0 1.0000 0.11058 0.46156
+#&gt; log_k_parent 0.1106 1.00000 0.06274
+#&gt; log_k_m1 0.4616 0.06274 1.00000
+#&gt;
+#&gt; Residual standard error: 8.333 on 37 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 84.79000 28.600 3.939e-27 78.78000 90.80000
+#&gt; k_parent 0.06352 12.360 5.237e-15 0.05392 0.07483
+#&gt; k_m1 0.01478 8.966 4.114e-11 0.01179 0.01853
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 19.66 3 16
+#&gt; parent 17.56 2 7
+#&gt; m1 18.71 1 9
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 10.91 36.25
+#&gt; m1 46.89 155.75</div></pre>
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