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authorJohannes Ranke <jranke@uni-bremen.de>2018-03-01 14:32:46 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2018-03-01 14:32:46 +0100
commit6653ff2507f45eae909f491a9af3f1eb5358a600 (patch)
tree03a43f9cf86cc1d675eba1c6f9c5e31da9c2acdd /docs/reference
parenta767013f407f7495492af6a1ceba4cf2b8aae839 (diff)
Static documentation rebuilt using current pkgdown::build_site()
Diffstat (limited to 'docs/reference')
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-rw-r--r--docs/reference/DFOP.solution.html24
-rw-r--r--docs/reference/Extract.mmkin.html57
-rw-r--r--docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html25
-rw-r--r--docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html25
-rw-r--r--docs/reference/FOCUS_2006_HS_ref_A_to_F.html25
-rw-r--r--docs/reference/FOCUS_2006_SFO_ref_A_to_F.html25
-rw-r--r--docs/reference/FOCUS_2006_datasets.html21
-rw-r--r--docs/reference/FOMC.solution-1.pngbin0 -> 17331 bytes
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-rw-r--r--docs/reference/FOMC.solution.html29
-rw-r--r--docs/reference/HS.solution-1.pngbin0 -> 17211 bytes
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-rw-r--r--docs/reference/HS.solution.html24
-rw-r--r--docs/reference/IORE.solution-1.pngbin0 -> 16988 bytes
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-rw-r--r--docs/reference/IORE.solution.html19
-rw-r--r--docs/reference/SFO.solution-2.pngbin6779 -> 0 bytes
-rw-r--r--docs/reference/SFO.solution.html25
-rw-r--r--docs/reference/SFORB.solution-2.pngbin7164 -> 0 bytes
-rw-r--r--docs/reference/SFORB.solution.html29
-rw-r--r--docs/reference/add_err-1.pngbin0 -> 83052 bytes
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-rw-r--r--docs/reference/add_err.html19
-rw-r--r--docs/reference/endpoints.html19
-rw-r--r--docs/reference/geometric_mean.html16
-rw-r--r--docs/reference/ilr.html16
-rw-r--r--docs/reference/index.html8
-rw-r--r--docs/reference/max_twa_parent.html22
-rw-r--r--docs/reference/mccall81_245T.html124
-rw-r--r--docs/reference/mkin_long_to_wide.html18
-rw-r--r--docs/reference/mkin_wide_to_long.html17
-rw-r--r--docs/reference/mkinds.html16
-rw-r--r--docs/reference/mkinerrmin.html22
-rw-r--r--docs/reference/mkinfit.html859
-rw-r--r--docs/reference/mkinmod.html58
-rw-r--r--docs/reference/mkinparplot-1.pngbin0 -> 15186 bytes
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-rw-r--r--docs/reference/mkinparplot.html19
-rw-r--r--docs/reference/mkinplot.html16
-rw-r--r--docs/reference/mkinpredict.html27
-rw-r--r--docs/reference/mkinresplot-1.pngbin0 -> 13625 bytes
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-rw-r--r--docs/reference/mkinsub.html17
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-rw-r--r--docs/reference/plot.mkinfit-1.pngbin0 -> 42225 bytes
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-rw-r--r--docs/reference/plot.mkinfit-2.pngbin0 -> 50584 bytes
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-rw-r--r--docs/reference/plot.mkinfit.html27
-rw-r--r--docs/reference/plot.mmkin-1.pngbin0 -> 31636 bytes
-rw-r--r--docs/reference/plot.mmkin-2.pngbin11215 -> 31920 bytes
-rw-r--r--docs/reference/plot.mmkin-3.pngbin0 -> 24031 bytes
-rw-r--r--docs/reference/plot.mmkin-4.pngbin11308 -> 0 bytes
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-rw-r--r--docs/reference/plot.mmkin.html24
-rw-r--r--docs/reference/print.mkinds.html16
-rw-r--r--docs/reference/print.mkinmod.html16
-rw-r--r--docs/reference/schaefer07_complex_case-4.pngbin18729 -> 0 bytes
-rw-r--r--docs/reference/schaefer07_complex_case.html40
-rw-r--r--docs/reference/sigma_rl.html13
-rw-r--r--docs/reference/summary.mkinfit.html34
-rw-r--r--docs/reference/synthetic_data_for_UBA.html30
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-rw-r--r--docs/reference/test_data_from_UBA_2014.html70
-rw-r--r--docs/reference/transform_odeparms.html272
-rw-r--r--docs/reference/twa.html179
90 files changed, 699 insertions, 1730 deletions
diff --git a/docs/reference/DFOP.solution-1.png b/docs/reference/DFOP.solution-1.png
new file mode 100644
index 00000000..1549a73b
--- /dev/null
+++ b/docs/reference/DFOP.solution-1.png
Binary files differ
diff --git a/docs/reference/DFOP.solution-2.png b/docs/reference/DFOP.solution-2.png
deleted file mode 100644
index 0902b9df..00000000
--- a/docs/reference/DFOP.solution-2.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index 30b9d057..ff1ad823 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -18,12 +18,20 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Double First-Order in Parallel kinetics — DFOP.solution" />
+<meta property="og:description" content="Function describing decline from a defined starting value using the sum
+ of two exponential decline functions." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +78,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +94,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -146,11 +152,11 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>DFOP.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>5</span>, <span class='fl'>0.5</span>, <span class='fl'>0.3</span>), <span class='fl'>0</span>, <span class='fl'>4</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><img src='DFOP.solution-2.png' alt='' width='540' height='400' /></pre>
+ <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>DFOP.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>5</span>, <span class='fl'>0.5</span>, <span class='fl'>0.3</span>), <span class='fl'>0</span>, <span class='fl'>4</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='DFOP.solution-1.png' alt='' width='700' height='432.632880098887' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -173,7 +179,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 5d4eca29..11738484 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -18,12 +18,19 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Subsetting method for mmkin objects — [.mmkin" />
+<meta property="og:description" content="Subsetting method for mmkin objects." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +77,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +93,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -147,16 +152,16 @@
<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'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#&gt; dataset
#&gt; model B C
-#&gt; FOMC List,42 List,42
+#&gt; FOMC List,45 List,45
#&gt; attr(,"class")
#&gt; [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#&gt; dataset
#&gt; model B
-#&gt; SFO List,42
-#&gt; FOMC List,42
+#&gt; SFO List,45
+#&gt; FOMC List,45
#&gt; attr(,"class")
#&gt; [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#&gt; dataset
#&gt; model B
-#&gt; SFO List,42
+#&gt; SFO List,45
#&gt; attr(,"class")
#&gt; [1] "mmkin"</div><div class='input'>
<span class='fu'>head</span>(
@@ -164,7 +169,7 @@
<span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span>]]
)</div><div class='output co'>#&gt; $par
#&gt; parent_0 log_alpha log_beta
-#&gt; 99.666192 2.549849 5.050586
+#&gt; 99.666193 2.549849 5.050586
#&gt;
#&gt; $ssr
#&gt; [1] 28.58291
@@ -180,7 +185,7 @@
#&gt; 25 78
#&gt;
#&gt; $counts
-#&gt; [1] "both X-convergence and relative convergence (5)"
+#&gt; [1] "relative convergence (4)"
#&gt; </div><div class='input'>
<span class='fu'>head</span>(
<span class='co'># The same can be achieved by</span>
@@ -258,7 +263,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.064 0.000 0.063
+#&gt; 0.058 0.000 0.057
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -398,7 +403,7 @@
#&gt; {
#&gt; assign("calls", calls + 1, inherits = TRUE)
#&gt; if (trace_parms)
-#&gt; cat(P, "\\n")
+#&gt; cat(P, "\n")
#&gt; if (length(state.ini.optim) &gt; 0) {
#&gt; odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
#&gt; names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
@@ -420,7 +425,7 @@
#&gt; if (mC$model &lt; cost.old) {
#&gt; if (!quiet)
#&gt; cat("Model cost at call ", calls, ": ", mC$model,
-#&gt; "\\n")
+#&gt; "\n")
#&gt; if (plot) {
#&gt; outtimes_plot = seq(min(observed$time), max(observed$time),
#&gt; length.out = 100)
@@ -447,8 +452,8 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x560110508c60&gt;
-#&gt; &lt;environment: 0x56010f8d8c30&gt;
+#&gt; &lt;bytecode: 0x55555ad80908&gt;
+#&gt; &lt;environment: 0x55555b1b4b90&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -470,8 +475,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x56010fede550&gt;
-#&gt; &lt;environment: 0x56010f8d8c30&gt;
+#&gt; &lt;bytecode: 0x55555b174428&gt;
+#&gt; &lt;environment: 0x55555b1b4b90&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -512,6 +517,10 @@
#&gt; $weight.ini
#&gt; [1] "none"
#&gt;
+#&gt; $tc.ini
+#&gt; sigma_low rsd_high
+#&gt; 0.50 0.07
+#&gt;
#&gt; $reweight.tol
#&gt; [1] 1e-08
#&gt;
@@ -534,7 +543,13 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] "Sat Jul 29 15:14:04 2017"
+#&gt; [1] "Thu Mar 1 14:26:09 2018"
+#&gt;
+#&gt; $version
+#&gt; [1] "0.9.47.1"
+#&gt;
+#&gt; $Rversion
+#&gt; [1] "3.4.3"
#&gt;
#&gt; attr(,"class")
#&gt; [1] "mkinfit" "modFit"
@@ -563,7 +578,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
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 d79aaff6..5fb3ccfe 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -18,12 +18,23 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B" />
+<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values
+generated with different software packages. Taken directly from FOCUS (2006).
+The results from fitting the data with the Topfit software was removed, as
+the initial concentration of the parent compound was fixed to a value of 100
+in this fit." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +81,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +97,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -132,7 +141,7 @@ in this fit.</p>
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -158,7 +167,7 @@ in this fit.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
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 e0da5a8d..c1665dee 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -18,12 +18,23 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F" />
+<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values
+generated with different software packages. Taken directly from FOCUS (2006).
+The results from fitting the data with the Topfit software was removed, as
+the initial concentration of the parent compound was fixed to a value of 100
+in this fit." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +81,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +97,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -131,7 +140,7 @@ in this fit.</p>
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -157,7 +166,7 @@ in this fit.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
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 720073f2..db3d228d 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -18,12 +18,23 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F" />
+<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values
+generated with different software packages. Taken directly from FOCUS (2006).
+The results from fitting the data with the Topfit software was removed, as
+the initial concentration of the parent compound was fixed to a value of 100
+in this fit." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +81,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +97,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -132,7 +141,7 @@ in this fit.</p>
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -158,7 +167,7 @@ in this fit.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
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 b12abf8c..cc4fcb1d 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -18,12 +18,23 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F" />
+<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values
+generated with different software packages. Taken directly from FOCUS (2006).
+The results from fitting the data with the Topfit software was removed, as
+the initial concentration of the parent compound was fixed to a value of 100
+in this fit." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +81,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +97,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -130,7 +139,7 @@ in this fit.</p>
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -156,7 +165,7 @@ in this fit.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 65bc572a..4548c983 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -18,12 +18,19 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets" />
+<meta property="og:description" content="Data taken from FOCUS (2006), p. 258." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +77,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +93,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -123,7 +128,7 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -158,7 +163,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/FOMC.solution-1.png b/docs/reference/FOMC.solution-1.png
new file mode 100644
index 00000000..58178df5
--- /dev/null
+++ b/docs/reference/FOMC.solution-1.png
Binary files differ
diff --git a/docs/reference/FOMC.solution-2.png b/docs/reference/FOMC.solution-2.png
deleted file mode 100644
index a673bc0e..00000000
--- a/docs/reference/FOMC.solution-2.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index 9af30b7a..810b0eba 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -18,12 +18,23 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
+
+
+<meta property="og:title" content="First-Order Multi-Compartment kinetics — FOMC.solution" />
+
+<meta property="og:description" content="Function describing exponential decline from a defined starting value, with
+ a decreasing rate constant.
+The form given here differs slightly from the original reference by Gustafson
+ and Holden (1990). The parameter beta corresponds to 1/beta in the
+ original equation." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +81,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +97,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -152,14 +161,14 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<p>Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A
new model based on spatial variability. <em>Environmental Science and
Technology</em> <b>24</b>, 1032-1038</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>FOMC.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>10</span>, <span class='fl'>2</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><img src='FOMC.solution-2.png' alt='' width='540' height='400' /></pre>
+ <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>FOMC.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>10</span>, <span class='fl'>2</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='FOMC.solution-1.png' alt='' width='700' height='432.632880098887' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -184,7 +193,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/HS.solution-1.png b/docs/reference/HS.solution-1.png
new file mode 100644
index 00000000..e259134e
--- /dev/null
+++ b/docs/reference/HS.solution-1.png
Binary files differ
diff --git a/docs/reference/HS.solution-2.png b/docs/reference/HS.solution-2.png
deleted file mode 100644
index 2e516447..00000000
--- a/docs/reference/HS.solution-2.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 8f6bbbe2..79358efb 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -18,12 +18,20 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Hockey-Stick kinetics — HS.solution" />
+<meta property="og:description" content="Function describing two exponential decline functions with a break point
+ between them." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +78,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +94,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -147,11 +153,11 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>HS.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>2</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><img src='HS.solution-2.png' alt='' width='540' height='400' /></pre>
+ <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>HS.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>2</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='HS.solution-1.png' alt='' width='700' height='432.632880098887' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -174,7 +180,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/IORE.solution-1.png b/docs/reference/IORE.solution-1.png
new file mode 100644
index 00000000..674c25d3
--- /dev/null
+++ b/docs/reference/IORE.solution-1.png
Binary files differ
diff --git a/docs/reference/IORE.solution-2.png b/docs/reference/IORE.solution-2.png
deleted file mode 100644
index a83d49c7..00000000
--- a/docs/reference/IORE.solution-2.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index 45e090c0..f705ab2f 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -18,12 +18,20 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Indeterminate order rate equation kinetics — IORE.solution" />
+<meta property="og:description" content="Function describing exponential decline from a defined starting value, with
+ a concentration dependent rate constant." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +94,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -154,7 +157,7 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>IORE.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.2</span>, <span class='fl'>1.3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>,
- <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><img src='IORE.solution-2.png' alt='' width='540' height='400' /><div class='input'> <span class='no'>fit.fomc</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='IORE.solution-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> <span class='no'>fit.fomc</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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='no'>fit.iore</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>fit.iore.deS</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</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>)
@@ -191,7 +194,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/SFO.solution-2.png b/docs/reference/SFO.solution-2.png
deleted file mode 100644
index 9626091f..00000000
--- a/docs/reference/SFO.solution-2.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index ef9b8eb7..a7934a35 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -18,12 +18,19 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Single First-Order kinetics — SFO.solution" />
+<meta property="og:description" content="Function describing exponential decline from a defined starting value." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +77,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +93,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -136,11 +141,13 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><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><img src='SFO.solution-2.png' alt='' width='540' height='400' /></pre>
+ <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>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -163,7 +170,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/SFORB.solution-2.png b/docs/reference/SFORB.solution-2.png
deleted file mode 100644
index 63a50bf9..00000000
--- a/docs/reference/SFORB.solution-2.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index ebe67733..aaae7cdd 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -18,12 +18,23 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Single First-Order Reversible Binding kinetics — SFORB.solution" />
+<meta property="og:description" content="Function describing the solution of the differential equations describing
+ the kinetic model with first-order terms for a two-way transfer from a free
+ to a bound fraction, and a first-order degradation term for the free
+ fraction. The initial condition is a defined amount in the free fraction and
+ no substance in the bound fraction." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +81,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +97,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -149,11 +158,13 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><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><img src='SFORB.solution-2.png' alt='' width='540' height='400' /></pre>
+ <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>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -176,7 +187,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png
new file mode 100644
index 00000000..4f9b1534
--- /dev/null
+++ b/docs/reference/add_err-1.png
Binary files differ
diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png
new file mode 100644
index 00000000..8fcf4625
--- /dev/null
+++ b/docs/reference/add_err-2.png
Binary files differ
diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png
new file mode 100644
index 00000000..e44839a6
--- /dev/null
+++ b/docs/reference/add_err-3.png
Binary files differ
diff --git a/docs/reference/add_err-4.png b/docs/reference/add_err-4.png
deleted file mode 100644
index 8bbd1758..00000000
--- a/docs/reference/add_err-4.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/add_err-6.png b/docs/reference/add_err-6.png
deleted file mode 100644
index 2a4fe33f..00000000
--- a/docs/reference/add_err-6.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/add_err-8.png b/docs/reference/add_err-8.png
deleted file mode 100644
index 49c4a5f0..00000000
--- a/docs/reference/add_err-8.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index d56a8728..42bec993 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -18,12 +18,21 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
+
+
+<meta property="og:title" content="Add normally distributed errors to simulated kinetic degradation data — add_err" />
+
+<meta property="og:description" content="Normally distributed errors are added to data predicted for a specific
+ degradation model using mkinpredict. The variance of the error
+ may depend on the predicted value and is specified as a standard deviation." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -195,14 +204,14 @@
<span class='no'>d_SFO_SFO_err</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='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>)
-<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>)</div><img src='add_err-4.png' alt='' width='540' height='400' /><div class='input'>
+<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>)</div><div class='img'><img src='add_err-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'>
<span class='co'># We would like to inspect the fit for dataset 3 more closely</span>
<span class='co'># Using double brackets makes the returned object an mkinfit object</span>
<span class='co'># instead of a list of mkinfit objects, so plot.mkinfit is used</span>
-<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span><span class='kw'>[[</span><span class='fl'>3</span>]], <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='add_err-6.png' alt='' width='540' height='400' /><div class='input'>
+<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span><span class='kw'>[[</span><span class='fl'>3</span>]], <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='add_err-2.png' alt='' width='700' height='432.632880098887' /></div><div class='input'>
<span class='co'># If we use single brackets, we should give two indices (model and dataset),</span>
<span class='co'># and plot.mmkin is used</span>
-<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><img src='add_err-8.png' alt='' width='540' height='400' /><div class='input'>
+<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><div class='img'><img src='add_err-3.png' alt='' width='700' height='432.632880098887' /></div><div class='input'>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -230,7 +239,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index ed235a47..c45a0b7c 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -18,12 +18,22 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints" />
+<meta property="og:description" content="This function calculates DT50 and DT90 values as well as formation fractions from kinetic models
+fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites,
+the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but
+with the advantage that the SFORB model can also be used for metabolites." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +96,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -171,7 +176,7 @@ with the advantage that the SFORB model can also be used for metabolites.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index 4af50f48..2d46b4de 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -18,12 +18,19 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Calculate the geometric mean — geometric_mean" />
+<meta property="og:description" content="Function calculating the geometric mean of numeric vectors" />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +93,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -152,7 +154,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 6c3979c5..2c51001f 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -18,12 +18,19 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Function to perform isometric log-ratio transformation — ilr" />
+<meta property="og:description" content="This implementation is a special case of the class of isometric log-ratio transformations." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +93,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -176,7 +178,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 4675748c..218194ad 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -18,12 +18,16 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
+
+
+<meta property="og:title" content="Function reference" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -442,7 +446,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index 0e99e579..5d6baf6a 100644
--- a/docs/reference/max_twa_parent.html
+++ b/docs/reference/max_twa_parent.html
@@ -18,12 +18,23 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit — max_twa_parent" />
+<meta property="og:description" content="This function calculates maximum moving window time weighted average concentrations
+(TWAs) for kinetic models fitted with mkinfit. Currently, only
+calculations for the parent are implemented for the SFO, FOMC and DFOP models,
+using the analytical formulas given in the PEC soil section of the FOCUS
+guidance." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +97,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -139,7 +145,7 @@ guidance.</p>
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -172,7 +178,7 @@ guidance.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 0111deb3..ec7f8ccd 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -18,12 +18,21 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T" />
+<meta property="og:description" content="Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding
+ 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether
+ extracts." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +79,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +95,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -127,108 +134,25 @@
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107
- <a href = 'http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p>
+ <a href='http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p>
<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'>
+ <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>)</div><div class='output co'>#&gt; mkin version: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:14:14 2017
-#&gt; Date of summary: Sat Jul 29 15:14:14 2017
-#&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 612 model solutions performed in 3.558 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 -26.8400 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 7.499e-02 NA NA
-#&gt; k_phenol_sink 2.212e-12 7.870e-12 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 5.462e-12
-#&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='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: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:14:15 2017
-#&gt; Date of summary: Sat Jul 29 15:14:15 2017
+ <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: 0.9.47.1
+#&gt; R version used for fitting: 3.4.3
+#&gt; Date of fit: Thu Mar 1 14:26:15 2018
+#&gt; Date of summary: Thu Mar 1 14:26:15 2018
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -238,7 +162,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.431 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.359 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -340,7 +264,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index 042bdced..a5432dac 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -18,12 +18,21 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Convert a dataframe from long to wide format — mkin_long_to_wide" />
+<meta property="og:description" content="This function takes a dataframe in the long form as required by modCost
+ and converts it into a dataframe with one independent variable and several
+ dependent variables as columns." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +95,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -186,7 +190,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index ddf28dd9..6798efa6 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -18,12 +18,20 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Convert a dataframe with observations over time into long format — mkin_wide_to_long" />
+<meta property="og:description" content="This function simply takes a dataframe with one independent variable and several
+ dependent variable and converts it into the long form as required by modCost." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +94,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -165,7 +168,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index 2d8d64a5..ab06e903 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -18,12 +18,19 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="A dataset class for mkin — mkinds" />
+<meta property="og:description" content="A dataset class for mkin" />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +93,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -154,7 +156,7 @@ in order to be compatible with mkinfit</p></dd>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index 67b7a35e..496cce15 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -18,12 +18,20 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Calculate the minimum error to assume in order to pass the variance test — mkinerrmin" />
+<meta property="og:description" content="This function finds the smallest relative error still resulting in passing the
+chi-squared test as defined in the FOCUS kinetics report from 2006." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +78,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +94,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -146,7 +152,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p>
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -186,7 +192,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 0102aecb..4fb5ef9a 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -18,12 +18,29 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Fit a kinetic model to data with one or more state variables — mkinfit" />
+<meta property="og:description" content="This function uses the Flexible Modelling Environment package
+ FME to create a function calculating the model cost, i.e. the
+ deviation between the kinetic model and the observed data. This model cost is
+ then minimised using the Port algorithm nlminb,
+ using the specified initial or fixed parameters and starting values.
+ Per default, parameters in the kinetic models are internally transformed in order
+ to better satisfy the assumption of a normal distribution of their estimators.
+ In each step of the optimsation, the kinetic model is solved using the
+ function mkinpredict. The variance of the residuals for each
+ observed variable can optionally be iteratively reweighted until convergence
+ using the argument reweight.method = "obs"." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -395,17 +412,17 @@
<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: 0.9.47.1
-#&gt; R version: 3.4.3
-#&gt; Date of fit: Tue Jan 30 10:05:48 2018
-#&gt; Date of summary: Tue Jan 30 10:05:48 2018
+<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.1
+#&gt; R version used for fitting: 3.4.3
+#&gt; Date of fit: Thu Mar 1 14:26:18 2018
+#&gt; Date of summary: Thu Mar 1 14:26:18 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 0.31 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.135 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -474,7 +491,7 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; user system elapsed
-#&gt; 1.196 0.000 1.195 </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; 0.84 0.00 0.84 </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
@@ -486,92 +503,19 @@
#&gt; DT50 DT90
#&gt; parent 7.022929 23.32967
#&gt; m1 131.760712 437.69961
-#&gt; </div><div class='input'>
+#&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>
<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>)))</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 : 874.2614
-#&gt; Model cost at call 33 : 874.2611
-#&gt; Model cost at call 35 : 616.2379
-#&gt; Model cost at call 37 : 616.2374
-#&gt; Model cost at call 40 : 467.4387
-#&gt; Model cost at call 42 : 467.4382
-#&gt; Model cost at call 46 : 398.2913
-#&gt; Model cost at call 48 : 398.2912
-#&gt; Model cost at call 49 : 398.2911
-#&gt; Model cost at call 51 : 395.0711
-#&gt; Model cost at call 54 : 395.071
-#&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 147 : 371.2134
-#&gt; Model cost at call 151 : 371.2134
-#&gt; Model cost at call 152 : 371.2134
-#&gt; Model cost at call 153 : 371.2134
-#&gt; Optimisation by method Port successfully terminated.
-#&gt; user system elapsed
-#&gt; 1.008 0.000 1.006 </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 131.760712 437.69961
-#&gt; </div><div class='input'>
-
-<span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC</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'>
+# 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>(
<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>))</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='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='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>)
@@ -581,739 +525,40 @@
<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>))</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='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='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'>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>)</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: 0.9.47.1
-#&gt; R version: 3.4.3
-#&gt; Date of fit: Tue Jan 30 10:06:00 2018
-#&gt; Date of summary: Tue Jan 30 10:06:00 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 185 model solutions performed in 0.739 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 5.701e-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 4.374e-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: 0.9.47.1
-#&gt; R version: 3.4.3
-#&gt; Date of fit: Tue Jan 30 10:06:02 2018
-#&gt; Date of summary: Tue Jan 30 10:06:02 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 523 model solutions performed in 2.151 s
-#&gt;
-#&gt; Weighting: none
-#&gt;
-#&gt; Iterative reweighting with method obs
-#&gt; Final mean squared residuals of observed variables:
-#&gt; parent m1
-#&gt; 11.573408 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 8.184e-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 24.90287 2.367e+00 3.402
-#&gt; 14 parent 26.64 24.90287 1.737e+00 3.402
-#&gt; 21 parent 11.50 12.44764 -9.476e-01 3.402
-#&gt; 21 parent 11.64 12.44764 -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 41.19338 -3.383e-03 2.722
-#&gt; 50 m1 40.01 41.19338 -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 28.80897 -3.659e+00 2.722
-#&gt; 120 m1 33.31 28.80897 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: 0.9.47.1
-#&gt; R version: 3.4.3
-#&gt; Date of fit: Tue Jan 30 10:06:03 2018
-#&gt; Date of summary: Tue Jan 30 10:06:03 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 0.675 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 7.303e-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'>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'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version: 0.9.47.1
-#&gt; R version: 3.4.3
-#&gt; Date of fit: Tue Jan 30 10:06:04 2018
-#&gt; Date of summary: Tue Jan 30 10:06:04 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 0.68 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 0.6844 -0.08687 -0.7564
-#&gt; log_k_parent 0.68435 1.0000 -0.12694 -0.5812
-#&gt; log_k_m1 -0.08687 -0.1269 1.00000 0.5195
-#&gt; f_parent_ilr_1 -0.75644 -0.5812 0.51951 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 -0.195714 99.46
-#&gt; 0 parent 102.04 99.65571 2.384286 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'>
-
-
+<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='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>)</div><div class='output co'>#&gt; mkin version: 0.9.47.1
-#&gt; R version: 3.4.3
-#&gt; Date of fit: Tue Jan 30 10:06:05 2018
-#&gt; Date of summary: Tue Jan 30 10:06:05 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 297 model solutions performed in 1.178 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 -0.025976 1
-#&gt; 0 parent 102.04 99.48598 2.554024 1
-#&gt; 1 parent 93.50 90.18612 3.313883 1
-#&gt; 1 parent 92.50 90.18612 2.313883 1
-#&gt; 3 parent 63.23 74.11316 -10.883162 1
-#&gt; 3 parent 68.99 74.11316 -5.123162 1
-#&gt; 7 parent 52.32 50.05029 2.269705 1
-#&gt; 7 parent 55.13 50.05029 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 -2.026945 2
-#&gt; 7 m1 24.47 24.99695 -0.526945 2
-#&gt; 14 m1 41.69 36.66353 5.026473 2
-#&gt; 14 m1 33.21 36.66353 -3.453527 2
-#&gt; 21 m1 44.37 41.65681 2.713187 2
-#&gt; 21 m1 46.44 41.65681 4.783187 2
-#&gt; 35 m1 41.22 43.35031 -2.130312 2
-#&gt; 35 m1 37.95 43.35031 -5.400312 2
-#&gt; 50 m1 41.19 41.25637 -0.066365 2
-#&gt; 50 m1 40.01 41.25637 -1.246365 2
-#&gt; 75 m1 40.09 36.46057 3.629433 2
-#&gt; 75 m1 33.85 36.46057 -2.610567 2
-#&gt; 100 m1 31.04 31.96929 -0.929288 2
-#&gt; 100 m1 33.13 31.96929 1.160712 2
-#&gt; 120 m1 25.15 28.76062 -3.610616 2
-#&gt; 120 m1 33.31 28.76062 4.549384 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='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='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>)</div><div class='output co'>#&gt; mkin version: 0.9.47.1
-#&gt; R version: 3.4.3
-#&gt; Date of fit: Tue Jan 30 10:06:08 2018
-#&gt; Date of summary: Tue Jan 30 10:06:08 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 692 model solutions performed in 2.733 s
-#&gt;
-#&gt; Weighting: manual
-#&gt;
-#&gt; Iterative reweighting with method obs
-#&gt; Final mean squared residuals of observed variables:
-#&gt; parent m1
-#&gt; 11.573407 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 -2.220
-#&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 8.184e-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.ini err
-#&gt; 0 parent 99.46 99.67218 -2.122e-01 1 3.402
-#&gt; 0 parent 102.04 99.67218 2.368e+00 1 3.402
-#&gt; 1 parent 93.50 90.27153 3.228e+00 1 3.402
-#&gt; 1 parent 92.50 90.27153 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 -9.476e-01 1 3.402
-#&gt; 21 parent 11.64 12.44765 -8.076e-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 8.662e-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 2.720e+00 2 2.722
-#&gt; 21 m1 46.44 41.65050 4.790e+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 -3.386e-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><div class='input'>
-</div></pre>
+<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)
+<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -1346,7 +591,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 5703b188..c1287905 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -18,12 +18,24 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Function to set up a kinetic model with one or more state variables — mkinmod" />
+<meta property="og:description" content="The function usually takes several expressions, each assigning a compound name to
+ a list, specifying the kinetic model type and reaction or transfer to other
+ observed compartments. Instead of specifying several expressions, a list
+ of lists can be given in the speclist argument.
+For the definition of model types and their parameters, the equations given
+ in the FOCUS and NAFTA guidance documents are used." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +82,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +98,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -182,7 +192,7 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for
Evaluating and Calculating Degradation Kinetics in Environmental
Media</p>
@@ -196,36 +206,17 @@
<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>
<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>))</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='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'># 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>)</div><div class='output co'>#&gt; Compilation argument:
-#&gt; /usr/lib/R/bin/R CMD SHLIB file519167a14b3a.c 2&gt; file519167a14b3a.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='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='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>)),
@@ -235,7 +226,8 @@
<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>)</div></pre>
+ <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -264,7 +256,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png
new file mode 100644
index 00000000..42811535
--- /dev/null
+++ b/docs/reference/mkinparplot-1.png
Binary files differ
diff --git a/docs/reference/mkinparplot-4.png b/docs/reference/mkinparplot-4.png
deleted file mode 100644
index c9f4aadb..00000000
--- a/docs/reference/mkinparplot-4.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 67ba6052..30954168 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -18,12 +18,20 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Function to plot the confidence intervals obtained using mkinfit — mkinparplot" />
+<meta property="og:description" content="This function plots the confidence intervals for the parameters
+ fitted using mkinfit." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +94,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -132,7 +135,7 @@
<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"phenol"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
<span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"anisole"</span>)),
<span class='kw'>anisole</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'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</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'>mkinparplot</span>(<span class='no'>fit</span>)</div><img src='mkinparplot-4.png' alt='' width='540' height='400' /></pre>
+<span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='432.632880098887' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -157,7 +160,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 7c875ebe..5df3f872 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -18,12 +18,19 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — mkinplot" />
+<meta property="og:description" content="Deprecated function. It now only calls the plot method plot.mkinfit." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +93,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -152,7 +154,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index b3453e6c..df6316e1 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -18,12 +18,21 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Produce predictions from a kinetic model using specific parameters — mkinpredict" />
+<meta property="og:description" content="This function produces a time series for all the observed variables in a
+ kinetic model as specified by mkinmod, using a specific set of
+ kinetic parameters and initial values for the state variables." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +79,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +95,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -299,17 +306,17 @@
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.004 0.000 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 elapsed
-#&gt; 0.000 0.000 0.001 </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 elapsed
-#&gt; 0.032 0.000 0.032 </div></pre>
+#&gt; 0.031 0.000 0.031 </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -334,7 +341,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png
new file mode 100644
index 00000000..8636baf2
--- /dev/null
+++ b/docs/reference/mkinresplot-1.png
Binary files differ
diff --git a/docs/reference/mkinresplot-4.png b/docs/reference/mkinresplot-4.png
deleted file mode 100644
index 5f3a65e3..00000000
--- a/docs/reference/mkinresplot-4.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index 5cb9fa96..036917f1 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -18,12 +18,22 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Function to plot residuals stored in an mkin object — mkinresplot" />
+<meta property="og:description" content="This function plots the residuals for the specified subset of the
+ observed variables from an mkinfit object. A combined plot of the fitted
+ model and the residuals can be obtained using plot.mkinfit
+ using the argument show_residuals = TRUE." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +96,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -175,7 +180,7 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>model</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>))</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</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</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'>mkinresplot</span>(<span class='no'>fit</span>, <span class='st'>"m1"</span>)</div><img src='mkinresplot-4.png' alt='' width='540' height='400' /></pre>
+<span class='fu'>mkinresplot</span>(<span class='no'>fit</span>, <span class='st'>"m1"</span>)</div><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='432.632880098887' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -202,7 +207,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 257d3f89..7724220f 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -18,12 +18,20 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Function to set up a kinetic submodel for one state variable — mkinsub" />
+<meta property="og:description" content="This is a convenience function to set up the lists used as arguments for
+ mkinmod." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +94,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -182,7 +185,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/mmkin-12.png b/docs/reference/mmkin-12.png
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+++ /dev/null
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+++ /dev/null
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+++ /dev/null
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+++ /dev/null
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+++ /dev/null
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diff --git a/docs/reference/mmkin-19.png b/docs/reference/mmkin-19.png
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+++ /dev/null
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diff --git a/docs/reference/mmkin-23.png b/docs/reference/mmkin-23.png
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+++ /dev/null
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diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index d649563f..e97e3f81 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -18,12 +18,20 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin" />
+<meta property="og:description" content="This function calls mkinfit on all combinations of models and datasets
+ specified in its first two arguments." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +78,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +94,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -152,45 +158,39 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'>
+ <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>),
<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>)</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='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='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>)</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='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='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>)
<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>))</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation by method Port did not converge.</span>
-#&gt; <span class='warning'>Convergence code is 1</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation by method Port did not converge.</span>
-#&gt; <span class='warning'>Convergence code is 1</span></div><div class='input'>
-<span class='no'>time_default</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 15.992 0.188 11.440 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 24.576 0.000 24.578 </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; 0.7340479 0.2659521 0.7505687 0.2494313
-#&gt;
-#&gt; $SFORB
-#&gt; logical(0)
-#&gt;
-#&gt; $distimes
-#&gt; DT50 DT90
-#&gt; parent 0.8777689 2.915885
-#&gt; M1 2.3257456 7.725960
-#&gt; M2 33.7200862 112.015702
-#&gt; </div><div class='input'>
+<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='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>, ])</div><img src='mmkin-15.png' alt='' width='540' height='400' /><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><img src='mmkin-17.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><img src='mmkin-19.png' alt='' width='540' height='400' /><div class='input'><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>, ])
+<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='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>)</div><img src='mmkin-21.png' alt='' width='540' height='400' /><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='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='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>])</div><img src='mmkin-23.png' alt='' width='540' height='400' /><div class='input'>
-</div></pre>
+<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>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -217,7 +217,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png
new file mode 100644
index 00000000..2bb8f5dd
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+++ /dev/null
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diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png
new file mode 100644
index 00000000..22a3f8b0
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new file mode 100644
index 00000000..93e859c7
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index cb52d4ac..27edd6f3 100644
--- a/docs/reference/plot.mkinfit-4.png
+++ b/docs/reference/plot.mkinfit-4.png
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deleted file mode 100644
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+++ /dev/null
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diff --git a/docs/reference/plot.mkinfit-8.png b/docs/reference/plot.mkinfit-8.png
deleted file mode 100644
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--- a/docs/reference/plot.mkinfit-8.png
+++ /dev/null
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diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 0af2bbf6..4bdad93f 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -18,12 +18,24 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit" />
+<meta property="og:description" content="Solves the differential equations with the optimised and fixed parameters
+ from a previous successful call to mkinfit and plots
+ the observed data together with the solution of the fitted model.
+If the current plot device is a tikz device,
+ then latex is being used for the formatting of the chi2 error level,
+ if show_errmin = TRUE." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +98,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -237,12 +244,12 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, &#8230
<span class='co'># parent to sink included, use Levenberg-Marquardt for speed</span>
<span class='no'>SFO_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'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</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'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</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</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='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>)
-<span class='fu'>plot</span>(<span class='no'>fit</span>)</div><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='plot.mkinfit-6.png' alt='' width='540' height='400' /><div class='input'>
+<span class='fu'>plot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='432.632880098887' /></div><div class='input'>
<span class='co'># Show the observed variables separately</span>
-<span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><img src='plot.mkinfit-8.png' alt='' width='540' height='400' /><div class='input'>
+<span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='432.632880098887' /></div><div class='input'>
<span class='co'># Show the observed variables separately, with residuals</span>
<span class='fu'>plot</span>(<span class='no'>fit</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'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>),
- <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='plot.mkinfit-10.png' alt='' width='540' height='400' /><div class='input'>
+ <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='432.632880098887' /></div><div class='input'>
<span class='co'># The same can be obtained with less typing, using the convenience function plot_sep</span>
<span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div></pre>
</div>
@@ -269,7 +276,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, &#8230
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png
new file mode 100644
index 00000000..2554b68b
--- /dev/null
+++ b/docs/reference/plot.mmkin-1.png
Binary files differ
diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png
index 21af1e7b..9a66294f 100644
--- a/docs/reference/plot.mmkin-2.png
+++ b/docs/reference/plot.mmkin-2.png
Binary files differ
diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png
new file mode 100644
index 00000000..b0f7fa21
--- /dev/null
+++ b/docs/reference/plot.mmkin-3.png
Binary files differ
diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png
deleted file mode 100644
index 3004f48f..00000000
--- a/docs/reference/plot.mmkin-4.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/plot.mmkin-6.png b/docs/reference/plot.mmkin-6.png
deleted file mode 100644
index 02ed2ab1..00000000
--- a/docs/reference/plot.mmkin-6.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index aa3df77a..11da6685 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -18,12 +18,23 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin" />
+<meta property="og:description" content="When x is a row selected from an mmkin object ([.mmkin), the same model
+ fitted for at least one dataset is shown. When it is a column, the fit of at least one model
+ to the same dataset is shown.
+If the current plot device is a tikz device,
+ then latex is being used for the formatting of the chi2 error level." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +97,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -165,11 +171,11 @@
<span class='no'>fits</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>c</span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>),
<span class='fu'>list</span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='co'># named list for titles</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='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>)
- <span class='fu'>plot</span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><img src='plot.mmkin-2.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><img src='plot.mmkin-4.png' alt='' width='540' height='400' /><div class='input'>
+ <span class='fu'>plot</span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='img'><img src='plot.mmkin-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><div class='img'><img src='plot.mmkin-2.png' alt='' width='700' height='432.632880098887' /></div><div class='input'>
<span class='co'># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span>
<span class='co'># height should be smaller than the plot width (this is not possible for the html pages</span>
<span class='co'># generated by pkgdown, as far as I know).</span>
- <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span>]) <span class='co'># same as plot(fits[1, 2])</span></div><img src='plot.mmkin-6.png' alt='' width='540' height='400' /></pre>
+ <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span>]) <span class='co'># same as plot(fits[1, 2])</span></div><div class='img'><img src='plot.mmkin-3.png' alt='' width='700' height='432.632880098887' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -194,7 +200,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index 14342f21..8e0d18b2 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -18,12 +18,19 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Print mkinds objects — print.mkinds" />
+<meta property="og:description" content="Print mkinds objects." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +93,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -143,7 +145,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index 33782b7d..db15cc60 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -18,12 +18,19 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Print mkinmod objects — print.mkinmod" />
+<meta property="og:description" content="Print mkinmod objects in a way that the user finds his way to get to its components." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +93,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -164,7 +166,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/schaefer07_complex_case-4.png b/docs/reference/schaefer07_complex_case-4.png
deleted file mode 100644
index b90185a1..00000000
--- a/docs/reference/schaefer07_complex_case-4.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 605f572e..6c53f805 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -18,12 +18,21 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case" />
+<meta property="og:description" content="This dataset was used for a comparison of KinGUI and ModelMaker to check the
+ software quality of KinGUI in the original publication (Schäfer et al., 2007).
+ The results from the fitting are also included." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -86,12 +95,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -140,24 +144,12 @@
<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'>
+ <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>)</div><img src='schaefer07_complex_case-4.png' alt='' width='540' height='400' /><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; 0.3809618 0.1954667 0.4235715 0.0000000 0.4479596 0.5520404
-#&gt;
-#&gt; $SFORB
-#&gt; logical(0)
-#&gt;
-#&gt; $distimes
-#&gt; DT50 DT90
-#&gt; parent 13.95078 46.34349
-#&gt; A1 49.75345 165.27739
-#&gt; B1 37.26908 123.80521
-#&gt; C1 11.23130 37.30957
-#&gt; A2 28.50652 94.69662
-#&gt; </div><div class='input'>
- <span class='co'># Compare with the results obtained in the original publication</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='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
@@ -194,7 +186,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/sigma_rl.html b/docs/reference/sigma_rl.html
index b7c93961..868c0d4f 100644
--- a/docs/reference/sigma_rl.html
+++ b/docs/reference/sigma_rl.html
@@ -18,12 +18,21 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
+
+
+<meta property="og:title" content="Two component error model of Rocke and Lorenzato — sigma_rl" />
+
+<meta property="og:description" content="Function describing the standard deviation of the measurement error
+ in dependence of the measured value \(y\):
+$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$" />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -157,7 +166,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index f20e3948..977ff8d8 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -18,12 +18,22 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Summary method for class "mkinfit" — summary.mkinfit" />
+<meta property="og:description" content="Lists model equations, the summary as returned by summary.modFit,
+ the chi2 error levels calculated according to FOCUS guidance (2006) as far
+ as defined therein, and optionally the data, consisting of observed, predicted
+ and residual values." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +80,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +96,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -177,21 +185,21 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<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: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:15:30 2017
-#&gt; Date of summary: Sat Jul 29 15:15:30 2017
+ <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: 0.9.47.1
+#&gt; R version used for fitting: 3.4.3
+#&gt; Date of fit: Thu Mar 1 14:26:27 2018
+#&gt; Date of summary: Thu Mar 1 14:26:27 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 0.084 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.076 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -277,7 +285,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index f9603f34..192e8dc2 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -18,12 +18,31 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014" />
+<meta property="og:description" content="The 12 datasets were generated using four different models and three different
+ variance components. The four models are either the SFO or the DFOP model with either
+ two sequential or two parallel metabolites.
+Variance component 'a' is based on a normal distribution with standard deviation of 3,
+ Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7.
+ Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the
+ minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07
+ for the increase of the standard deviation with y.
+Initial concentrations for metabolites and all values where adding the variance component resulted
+ in a value below the assumed limit of detection of 0.1 were set to NA.
+As an example, the first dataset has the title SFO_lin_a and is based on the SFO model
+ with two sequential metabolites (linear pathway), with added variance component 'a'.
+Compare also the code in the example section to see the degradation models." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -136,7 +155,7 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'>
+ <pre class="examples"># NOT RUN {
# 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"),
@@ -235,11 +254,8 @@ fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data,
quiet = TRUE)
plot_sep(fit)
summary(fit)
-
-</div><div class='output co'>#&gt; <span class='error'>Error: &lt;text&gt;:68:43: Unerwartete(s) SPECIAL</span>
-#&gt; <span class='error'>67: </span>
-#&gt; <span class='error'>68: d_rep[d_rep$time == 0 &amp; d_rep$name &lt;!-- %in%</span>
-#&gt; <span class='error'> ^</span></div></pre>
+# }
+</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -261,7 +277,7 @@ summary(fit)
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/synthetic_data_for_UBA_2014-10.png b/docs/reference/synthetic_data_for_UBA_2014-10.png
deleted file mode 100644
index 7e15e1b3..00000000
--- a/docs/reference/synthetic_data_for_UBA_2014-10.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/test_data_from_UBA_2014-12.png b/docs/reference/test_data_from_UBA_2014-12.png
deleted file mode 100644
index 6738f3a0..00000000
--- a/docs/reference/test_data_from_UBA_2014-12.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/test_data_from_UBA_2014-16.png b/docs/reference/test_data_from_UBA_2014-16.png
deleted file mode 100644
index 6738f3a0..00000000
--- a/docs/reference/test_data_from_UBA_2014-16.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/test_data_from_UBA_2014-4.png b/docs/reference/test_data_from_UBA_2014-4.png
deleted file mode 100644
index 8c65e604..00000000
--- a/docs/reference/test_data_from_UBA_2014-4.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/test_data_from_UBA_2014-6.png b/docs/reference/test_data_from_UBA_2014-6.png
deleted file mode 100644
index 8c65e604..00000000
--- a/docs/reference/test_data_from_UBA_2014-6.png
+++ /dev/null
Binary files differ
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index ed2ccd9c..c4292d9c 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -18,12 +18,20 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014" />
+<meta property="og:description" content="The datasets were used for the comparative validation of several kinetic evaluation
+ software packages (Ranke, 2014)." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -123,7 +131,7 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'>
+ <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>
<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>
@@ -131,57 +139,27 @@
<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>))</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><img src='test_data_from_UBA_2014-4.png' alt='' width='540' height='400' /><div class='input'>
- <span class='fu'>summary</span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
-#&gt; parent_w_0 9.598567e+01 2.33959810 4.102657e+01 9.568973e-19 NA
-#&gt; k_parent_w_sink 3.603743e-01 0.03497716 1.030313e+01 4.988281e-09 NA
-#&gt; k_parent_w_parent_s 6.031370e-02 0.01746026 3.454342e+00 1.514738e-03 NA
-#&gt; k_parent_s_sink 5.099834e-11 0.10381939 4.912217e-10 5.000000e-01 NA
-#&gt; k_parent_s_parent_w 7.419672e-02 0.11338174 6.543974e-01 2.608057e-01 NA
-#&gt; Upper
-#&gt; parent_w_0 NA
-#&gt; k_parent_w_sink NA
-#&gt; k_parent_w_parent_s NA
-#&gt; k_parent_s_sink NA
-#&gt; k_parent_s_parent_w NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#&gt; err.min n.optim df
-#&gt; All data 0.09246946 5 6
-#&gt; parent_w 0.06377096 3 3
-#&gt; parent_s 0.20882324 2 3</div><div class='input'>
+ <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span>))
+ <span class='no'>f_river</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<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>)$<span class='no'>bpar</span>
+ <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)
+
<span class='co'># This is the evaluation used for the validation of software packages</span>
<span class='co'># in the expertise from 2014</span>
<span class='no'>m_soil</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
<span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>),
<span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>),
<span class='kw'>M3</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
- <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+ <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)
+
<span class='no'>f_soil</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<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>))</div><img src='test_data_from_UBA_2014-12.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'>summary</span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
-#&gt; parent_0 76.55425583 0.943443834 81.1434164 4.422340e-30 74.602593306
-#&gt; k_parent 0.12081956 0.004815515 25.0896457 1.639665e-18 0.111257526
-#&gt; k_M1 0.84258650 0.930121206 0.9058889 1.871937e-01 0.085876305
-#&gt; k_M2 0.04210878 0.013729902 3.0669396 2.729137e-03 0.021450631
-#&gt; k_M3 0.01122919 0.008044866 1.3958205 8.804914e-02 0.002550985
-#&gt; f_parent_to_M1 0.32240199 0.278620411 1.1571370 1.295466e-01 NA
-#&gt; f_parent_to_M2 0.16099854 0.030548889 5.2701930 1.196191e-05 NA
-#&gt; f_M1_to_M3 0.27921500 0.314732717 0.8871496 1.920907e-01 0.015016888
-#&gt; f_M2_to_M3 0.55641332 0.650247079 0.8556952 2.004966e-01 0.005360551
-#&gt; Upper
-#&gt; parent_0 78.50591836
-#&gt; k_parent 0.13120340
-#&gt; k_M1 8.26714671
-#&gt; k_M2 0.08266187
-#&gt; k_M3 0.04942980
-#&gt; f_parent_to_M1 NA
-#&gt; f_parent_to_M2 NA
-#&gt; f_M1_to_M3 0.90777217
-#&gt; f_M2_to_M3 0.99658634</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#&gt; err.min n.optim df
-#&gt; All data 0.09649963 9 20
-#&gt; parent 0.04721283 2 6
-#&gt; M1 0.26551209 2 5
-#&gt; M2 0.20327575 2 5
-#&gt; M3 0.05196549 3 4</div><div class='input'>
-</div></pre>
+ <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))
+ <span class='fu'>summary</span>(<span class='no'>f_soil</span>)$<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>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -203,7 +181,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index bbf15a41..630a5103 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -18,12 +18,27 @@
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
+
+
+<meta property="og:title" content="Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms" />
+<meta property="og:description" content="The transformations are intended to map parameters that should only take
+ on restricted values to the full scale of real numbers. For kinetic rate
+ constants and other paramters that can only take on positive values, a
+ simple log transformation is used. For compositional parameters, such as
+ the formations fractions that should always sum up to 1 and can not be
+ negative, the ilr transformation is used.
+The transformation of sets of formation fractions is fragile, as it supposes
+ the same ordering of the components in forward and backward transformation.
+ This is no problem for the internal use in mkinfit." />
+<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -70,6 +85,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
+ <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
@@ -83,12 +101,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
- <li>
- <a href="http://github.com/jranke/mkin">
- <span class="fa fa-github fa-lg"></span>
-
- </a>
-</li>
+
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -170,10 +183,10 @@
<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: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:15:35 2017
-#&gt; Date of summary: Sat Jul 29 15:15:35 2017
+<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: 0.9.47.1
+#&gt; R version used for fitting: 3.4.3
+#&gt; Date of fit: Thu Mar 1 14:26:28 2018
+#&gt; Date of summary: Thu Mar 1 14:26:28 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -181,7 +194,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.608 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.571 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -245,84 +258,10 @@
#&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>)</div><div class='output co'>#&gt; mkin version: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:15:36 2017
-#&gt; Date of summary: Sat Jul 29 15:15:36 2017
-#&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 352 model solutions performed in 1.401 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='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'>
<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>
@@ -330,162 +269,29 @@
<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>
<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>)</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='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)
+
<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>)</div><div class='output co'>#&gt; mkin version: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:15:37 2017
-#&gt; Date of summary: Sat Jul 29 15:15:37 2017
-#&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 185 model solutions performed in 0.772 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 5.701e-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 4.374e-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='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='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>)</div><div class='output co'>#&gt; f_parent_to_m1
-#&gt; 0.5 </div><div class='input'>
+<span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO.ff</span>)
+
<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>)</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='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)
+
<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>)</div><div class='output co'>#&gt; mkin version: 0.9.46
-#&gt; R version: 3.4.1
-#&gt; Date of fit: Sat Jul 29 15:15:38 2017
-#&gt; Date of summary: Sat Jul 29 15:15:38 2017
-#&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 0.416 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 0.11059 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 3.938e-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><div class='input'>
-</div></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>)
+<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -510,7 +316,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
diff --git a/docs/reference/twa.html b/docs/reference/twa.html
deleted file mode 100644
index be76b439..00000000
--- a/docs/reference/twa.html
+++ /dev/null
@@ -1,179 +0,0 @@
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- <h1>Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit</h1>
- </div>
-
-
- <p>This function calculates maximum moving window time weighted average concentrations
-(TWAs) for kinetic models fitted with <code><a href='mkinfit.html'>mkinfit</a></code>. Currently, only
-calculations for the parent are implemented for the SFO, FOMC and DFOP models,
-using the analytical formulas given in the PEC soil section of the FOCUS
-guidance.</p>
-
-
- <pre class="usage"><span class='fu'>twa</span>(<span class='no'>fit</span>, <span class='no'>windows</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>fit</th>
- <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
- </tr>
- <tr>
- <th>windows</th>
- <td><p>The width of the time windows for which the TWAs should be calculated.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>A numeric vector, named using the <code>windows</code> argument.</p>
-
- <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
-
- <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence and
- Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
- Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
- EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
-
-
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><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='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'>twa</span>(<span class='no'>fit</span>, <span class='fu'>c</span>(<span class='fl'>7</span>, <span class='fl'>21</span>))</div><div class='output co'>#&gt; 7 21
-#&gt; 34.71343 18.22124 </div></pre>
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
- <h2>Contents</h2>
- <ul class="nav nav-pills nav-stacked">
- <li><a href="#arguments">Arguments</a></li>
-
- <li><a href="#value">Value</a></li>
-
- <li><a href="#references">References</a></li>
-
- <li><a href="#examples">Examples</a></li>
- </ul>
-
- <h2>Author</h2>
-
- Johannes Ranke
-
- </div>
-</div>
-
- <footer>
- <div class="copyright">
- <p>Developed by Johannes Ranke.</p>
-</div>
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