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+ — DFOP.solution • mkin</title>
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+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>Function describing decline from a defined starting value using the sum
+ of two exponential decline functions.</p>
+
+
+ <pre><span class='fu'>DFOP.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>g</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>t</dt>
+ <dd> Time. </dd>
+ <dt>parent.0</dt>
+ <dd> Starting value for the response variable at time zero. </dd>
+ <dt>k1</dt>
+ <dd> First kinetic constant. </dd>
+ <dt>k2</dt>
+ <dd> Second kinetic constant. </dd>
+ <dt>g</dt>
+ <dd> Fraction of the starting value declining according to the
+ first kinetic constant.
+ </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The value of the response variable at time <code>t</code>.</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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</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>
+ </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>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
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+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
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diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
new file mode 100644
index 00000000..4ea16d10
--- /dev/null
+++ b/docs/reference/Extract.mmkin.html
@@ -0,0 +1,1209 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Subsetting method for mmkin objects — [.mmkin • mkin</title>
+
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+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
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+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
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+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Subsetting method for mmkin objects</h1>
+ </div>
+
+
+ <p>Subsetting method for mmkin objects.</p>
+
+
+ <pre># S3 method for mmkin
+[(x, i, j, ..., drop = FALSE)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>x</dt>
+ <dd>An <code><a href='mmkin.html'>mmkin</a> object</code></dd>
+ <dt>i</dt>
+ <dd>Row index selecting the fits for specific models</dd>
+ <dt>j</dt>
+ <dd>Column index selecting the fits to specific datasets</dd>
+ <dt>...</dt>
+ <dd>Not used, only there to satisfy the generic method definition</dd>
+ <dt>drop</dt>
+ <dd>If FALSE, the method always returns an mmkin object, otherwise either
+ a list of mkinfit objects or a single mkinfit object.</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>An object of class <code><a href='mmkin.html'>mmkin</a></code>.</p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'> <span class='co'># Only use one core, to pass R CMD check --as-cran</span>
+ <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'>"SFO"</span>, <span class='st'>"FOMC"</span>), <span class='fu'>list</span>(<span class='kw'>B</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</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'>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; attr(,&quot;class&quot;)
+#&gt; [1] &quot;mmkin&quot;
+#&gt; </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; attr(,&quot;class&quot;)
+#&gt; [1] &quot;mmkin&quot;
+#&gt; </div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]$<span class='no'>FOMC</span></div><div class='output co'>#&gt; $par
+#&gt; parent_0 log_alpha log_beta
+#&gt; 99.666193 2.549849 5.050586
+#&gt;
+#&gt; $ssr
+#&gt; [1] 28.58291
+#&gt;
+#&gt; $convergence
+#&gt; [1] 0
+#&gt;
+#&gt; $iterations
+#&gt; [1] 21
+#&gt;
+#&gt; $evaluations
+#&gt; function gradient
+#&gt; 25 78
+#&gt;
+#&gt; $counts
+#&gt; [1] &quot;both X-convergence and relative convergence (5)&quot;
+#&gt;
+#&gt; $hessian
+#&gt; parent_0 log_alpha log_beta
+#&gt; parent_0 4.123033 -95.69983 93.17699
+#&gt; log_alpha -95.699832 6618.85833 -6352.46648
+#&gt; log_beta 93.176993 -6352.46648 6101.23483
+#&gt;
+#&gt; $residuals
+#&gt; parent parent parent parent parent parent
+#&gt; 1.046192647 -3.322396479 3.655156669 -1.705316770 0.406306255 -0.123734689
+#&gt; parent parent
+#&gt; -0.036886982 -0.006240458
+#&gt;
+#&gt; $ms
+#&gt; [1] 3.572863
+#&gt;
+#&gt; $var_ms
+#&gt; parent
+#&gt; 3.572863
+#&gt;
+#&gt; $var_ms_unscaled
+#&gt; parent
+#&gt; 3.572863
+#&gt;
+#&gt; $var_ms_unweighted
+#&gt; parent
+#&gt; 3.572863
+#&gt;
+#&gt; $rank
+#&gt; [1] 3
+#&gt;
+#&gt; $df.residual
+#&gt; [1] 5
+#&gt;
+#&gt; $solution_type
+#&gt; [1] &quot;analytical&quot;
+#&gt;
+#&gt; $transform_rates
+#&gt; [1] TRUE
+#&gt;
+#&gt; $transform_fractions
+#&gt; [1] TRUE
+#&gt;
+#&gt; $method.modFit
+#&gt; [1] &quot;Port&quot;
+#&gt;
+#&gt; $maxit.modFit
+#&gt; [1] &quot;auto&quot;
+#&gt;
+#&gt; $calls
+#&gt; [1] 111
+#&gt;
+#&gt; $time
+#&gt; user system elapsed
+#&gt; 0.26 0.00 0.26
+#&gt;
+#&gt; $mkinmod
+#&gt; &lt;mkinmod&gt; model generated with
+#&gt; Use of formation fractions $use_of_ff: min
+#&gt; Specification $spec:
+#&gt; $parent
+#&gt; $type: FOMC; $sink: TRUE
+#&gt;
+#&gt; $observed
+#&gt; name time value
+#&gt; 1 parent 0 98.62
+#&gt; 2 parent 3 81.43
+#&gt; 3 parent 7 53.18
+#&gt; 4 parent 14 34.89
+#&gt; 5 parent 30 10.09
+#&gt; 6 parent 62 1.50
+#&gt; 7 parent 90 0.33
+#&gt; 8 parent 118 0.08
+#&gt;
+#&gt; $obs_vars
+#&gt; [1] &quot;parent&quot;
+#&gt;
+#&gt; $predicted
+#&gt; name time value
+#&gt; 1 parent 0.000000 99.66619265
+#&gt; 2 parent 1.191919 90.41690342
+#&gt; 3 parent 2.383838 82.08630014
+#&gt; 4 parent 3.000000 78.10760352
+#&gt; 5 parent 3.575758 74.57722848
+#&gt; 6 parent 4.767677 67.80342415
+#&gt; 7 parent 5.959596 61.68822425
+#&gt; 8 parent 7.000000 56.83515667
+#&gt; 9 parent 7.151515 56.16343898
+#&gt; 10 parent 8.343434 51.16836285
+#&gt; 11 parent 9.535354 46.64890734
+#&gt; 12 parent 10.727273 42.55683931
+#&gt; 13 parent 11.919192 38.84911158
+#&gt; 14 parent 13.111111 35.48727414
+#&gt; 15 parent 14.000000 33.18468323
+#&gt; 16 parent 14.303030 32.43695565
+#&gt; 17 parent 15.494949 29.66740651
+#&gt; 18 parent 16.686869 27.15109578
+#&gt; 19 parent 17.878788 24.86335532
+#&gt; 20 parent 19.070707 22.78206538
+#&gt; 21 parent 20.262626 20.88737647
+#&gt; 22 parent 21.454545 19.16146324
+#&gt; 23 parent 22.646465 17.58830644
+#&gt; 24 parent 23.838384 16.15349953
+#&gt; 25 parent 25.030303 14.84407724
+#&gt; 26 parent 26.222222 13.64836315
+#&gt; 27 parent 27.414141 12.55583436
+#&gt; 28 parent 28.606061 11.55700107
+#&gt; 29 parent 29.797980 10.64329940
+#&gt; 30 parent 30.000000 10.49630626
+#&gt; 31 parent 30.989899 9.80699593
+#&gt; 32 parent 32.181818 9.04110261
+#&gt; 33 parent 33.373737 8.33930082
+#&gt; 34 parent 34.565657 7.69587362
+#&gt; 35 parent 35.757576 7.10564515
+#&gt; 36 parent 36.949495 6.56392657
+#&gt; 37 parent 38.141414 6.06646759
+#&gt; 38 parent 39.333333 5.60941311
+#&gt; 39 parent 40.525253 5.18926438
+#&gt; 40 parent 41.717172 4.80284421
+#&gt; 41 parent 42.909091 4.44726569
+#&gt; 42 parent 44.101010 4.11990420
+#&gt; 43 parent 45.292929 3.81837216
+#&gt; 44 parent 46.484848 3.54049644
+#&gt; 45 parent 47.676768 3.28429799
+#&gt; 46 parent 48.868687 3.04797350
+#&gt; 47 parent 50.060606 2.82987892
+#&gt; 48 parent 51.252525 2.62851456
+#&gt; 49 parent 52.444444 2.44251172
+#&gt; 50 parent 53.636364 2.27062056
+#&gt; 51 parent 54.828283 2.11169922
+#&gt; 52 parent 56.020202 1.96470393
+#&gt; 53 parent 57.212121 1.82868009
+#&gt; 54 parent 58.404040 1.70275424
+#&gt; 55 parent 59.595960 1.58612677
+#&gt; 56 parent 60.787879 1.47806529
+#&gt; 57 parent 61.979798 1.37789865
+#&gt; 58 parent 62.000000 1.37626531
+#&gt; 59 parent 63.171717 1.28501157
+#&gt; 60 parent 64.363636 1.19883967
+#&gt; 61 parent 65.555556 1.11886504
+#&gt; 62 parent 66.747475 1.04461220
+#&gt; 63 parent 67.939394 0.97564441
+#&gt; 64 parent 69.131313 0.91156031
+#&gt; 65 parent 70.323232 0.85199096
+#&gt; 66 parent 71.515152 0.79659697
+#&gt; 67 parent 72.707071 0.74506609
+#&gt; 68 parent 73.898990 0.69711084
+#&gt; 69 parent 75.090909 0.65246649
+#&gt; 70 parent 76.282828 0.61088912
+#&gt; 71 parent 77.474747 0.57215389
+#&gt; 72 parent 78.666667 0.53605348
+#&gt; 73 parent 79.858586 0.50239663
+#&gt; 74 parent 81.050505 0.47100683
+#&gt; 75 parent 82.242424 0.44172111
+#&gt; 76 parent 83.434343 0.41438896
+#&gt; 77 parent 84.626263 0.38887128
+#&gt; 78 parent 85.818182 0.36503953
+#&gt; 79 parent 87.010101 0.34277481
+#&gt; 80 parent 88.202020 0.32196716
+#&gt; 81 parent 89.393939 0.30251479
+#&gt; 82 parent 90.000000 0.29311302
+#&gt; 83 parent 90.585859 0.28432347
+#&gt; 84 parent 91.777778 0.26730596
+#&gt; 85 parent 92.969697 0.25138141
+#&gt; 86 parent 94.161616 0.23647487
+#&gt; 87 parent 95.353535 0.22251689
+#&gt; 88 parent 96.545455 0.20944302
+#&gt; 89 parent 97.737374 0.19719349
+#&gt; 90 parent 98.929293 0.18571281
+#&gt; 91 parent 100.121212 0.17494947
+#&gt; 92 parent 101.313131 0.16485560
+#&gt; 93 parent 102.505051 0.15538676
+#&gt; 94 parent 103.696970 0.14650163
+#&gt; 95 parent 104.888889 0.13816179
+#&gt; 96 parent 106.080808 0.13033150
+#&gt; 97 parent 107.272727 0.12297753
+#&gt; 98 parent 108.464646 0.11606895
+#&gt; 99 parent 109.656566 0.10957695
+#&gt; 100 parent 110.848485 0.10347470
+#&gt; 101 parent 112.040404 0.09773723
+#&gt; 102 parent 113.232323 0.09234125
+#&gt; 103 parent 114.424242 0.08726506
+#&gt; 104 parent 115.616162 0.08248842
+#&gt; 105 parent 116.808081 0.07799245
+#&gt; 106 parent 118.000000 0.07375954
+#&gt;
+#&gt; $cost
+#&gt; function (P)
+#&gt; {
+#&gt; assign(&quot;calls&quot;, calls + 1, inherits = TRUE)
+#&gt; if (trace_parms)
+#&gt; cat(P, &quot;\n&quot;)
+#&gt; if (length(state.ini.optim) &gt; 0) {
+#&gt; odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
+#&gt; names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
+#&gt; }
+#&gt; else {
+#&gt; odeini &lt;- state.ini.fixed
+#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
+#&gt; }
+#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
+#&gt; transparms.fixed)
+#&gt; parms &lt;- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates,
+#&gt; transform_fractions = transform_fractions)
+#&gt; out &lt;- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type,
+#&gt; use_compiled = use_compiled, method.ode = method.ode,
+#&gt; atol = atol, rtol = rtol, ...)
+#&gt; assign(&quot;out_predicted&quot;, out, inherits = TRUE)
+#&gt; mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
+#&gt; scaleVar = scaleVar)
+#&gt; if (mC$model &lt; cost.old) {
+#&gt; if (!quiet)
+#&gt; cat(&quot;Model cost at call &quot;, calls, &quot;: &quot;, mC$model,
+#&gt; &quot;\n&quot;)
+#&gt; if (plot) {
+#&gt; outtimes_plot = seq(min(observed$time), max(observed$time),
+#&gt; length.out = 100)
+#&gt; out_plot &lt;- mkinpredict(mkinmod, parms, odeini, outtimes_plot,
+#&gt; solution_type = solution_type, use_compiled = use_compiled,
+#&gt; method.ode = method.ode, atol = atol, rtol = rtol,
+#&gt; ...)
+#&gt; plot(0, type = &quot;n&quot;, xlim = range(observed$time),
+#&gt; ylim = c(0, max(observed$value, na.rm = TRUE)),
+#&gt; xlab = &quot;Time&quot;, ylab = &quot;Observed&quot;)
+#&gt; col_obs &lt;- pch_obs &lt;- 1:length(obs_vars)
+#&gt; lty_obs &lt;- rep(1, length(obs_vars))
+#&gt; names(col_obs) &lt;- names(pch_obs) &lt;- names(lty_obs) &lt;- obs_vars
+#&gt; for (obs_var in obs_vars) {
+#&gt; points(subset(observed, name == obs_var, c(time,
+#&gt; value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
+#&gt; }
+#&gt; matlines(out_plot$time, out_plot[-1], col = col_obs,
+#&gt; lty = lty_obs)
+#&gt; legend(&quot;topright&quot;, inset = c(0.05, 0.05), legend = obs_vars,
+#&gt; col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
+#&gt; }
+#&gt; assign(&quot;cost.old&quot;, mC$model, inherits = TRUE)
+#&gt; }
+#&gt; return(mC)
+#&gt; }
+#&gt; &lt;environment: 0x5421f48&gt;
+#&gt;
+#&gt; $cost_notrans
+#&gt; function (P)
+#&gt; {
+#&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)
+#&gt; }
+#&gt; else {
+#&gt; odeini &lt;- state.ini.fixed
+#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
+#&gt; }
+#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
+#&gt; parms.fixed)
+#&gt; out &lt;- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type,
+#&gt; use_compiled = use_compiled, method.ode = method.ode,
+#&gt; atol = atol, rtol = rtol, ...)
+#&gt; mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
+#&gt; scaleVar = scaleVar)
+#&gt; return(mC)
+#&gt; }
+#&gt; &lt;environment: 0x5421f48&gt;
+#&gt;
+#&gt; $hessian_notrans
+#&gt; parent_0 alpha beta
+#&gt; parent_0 4.1230329 -7.473531 0.5968527
+#&gt; alpha -7.4735307 40.365690 -3.1777189
+#&gt; beta 0.5968527 -3.177719 0.2503425
+#&gt;
+#&gt; $start
+#&gt; value type
+#&gt; parent_0 98.62 state
+#&gt; alpha 1.00 deparm
+#&gt; beta 10.00 deparm
+#&gt;
+#&gt; $start_transformed
+#&gt; value lower upper
+#&gt; parent_0 98.620000 -Inf Inf
+#&gt; log_alpha 0.000000 -Inf Inf
+#&gt; log_beta 2.302585 -Inf Inf
+#&gt;
+#&gt; $fixed
+#&gt; [1] value type
+#&gt; &lt;0 rows&gt; (or 0-length row.names)
+#&gt;
+#&gt; $data
+#&gt; time variable observed predicted residual
+#&gt; 1 0 parent 98.62 99.66619265 -1.046192647
+#&gt; 2 3 parent 81.43 78.10760352 3.322396479
+#&gt; 3 7 parent 53.18 56.83515667 -3.655156669
+#&gt; 4 14 parent 34.89 33.18468323 1.705316770
+#&gt; 5 30 parent 10.09 10.49630626 -0.406306255
+#&gt; 6 62 parent 1.50 1.37626531 0.123734689
+#&gt; 7 90 parent 0.33 0.29311302 0.036886982
+#&gt; 8 118 parent 0.08 0.07375954 0.006240458
+#&gt;
+#&gt; $atol
+#&gt; [1] 1e-08
+#&gt;
+#&gt; $rtol
+#&gt; [1] 1e-10
+#&gt;
+#&gt; $weight.ini
+#&gt; [1] &quot;none&quot;
+#&gt;
+#&gt; $reweight.tol
+#&gt; [1] 1e-08
+#&gt;
+#&gt; $reweight.max.iter
+#&gt; [1] 10
+#&gt;
+#&gt; $bparms.optim
+#&gt; parent_0 alpha beta
+#&gt; 99.66619 12.80517 156.11390
+#&gt;
+#&gt; $bparms.fixed
+#&gt; numeric(0)
+#&gt;
+#&gt; $bparms.ode
+#&gt; alpha beta
+#&gt; 12.80517 156.11390
+#&gt;
+#&gt; $bparms.state
+#&gt; parent
+#&gt; 99.66619
+#&gt;
+#&gt; $date
+#&gt; [1] &quot;Wed Oct 26 23:50:33 2016&quot;
+#&gt;
+#&gt; attr(,&quot;class&quot;)
+#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot;
+#&gt; </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; attr(,&quot;class&quot;)
+#&gt; [1] &quot;mmkin&quot;
+#&gt; </div><div class='input'> <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"SFO"</span>, <span class='st'>"B"</span>]] <span class='co'># This is equivalent to</span></div><div class='output co'>#&gt; $par
+#&gt; parent_0 log_k_parent_sink
+#&gt; 99.174072 -2.549028
+#&gt;
+#&gt; $ssr
+#&gt; [1] 30.65564
+#&gt;
+#&gt; $convergence
+#&gt; [1] 0
+#&gt;
+#&gt; $iterations
+#&gt; [1] 5
+#&gt;
+#&gt; $evaluations
+#&gt; function gradient
+#&gt; 8 15
+#&gt;
+#&gt; $counts
+#&gt; [1] &quot;relative convergence (4)&quot;
+#&gt;
+#&gt; $hessian
+#&gt; parent_0 log_k_parent_sink
+#&gt; parent_0 4.163631 -94.09343
+#&gt; log_k_parent_sink -94.093431 6311.34610
+#&gt;
+#&gt; $residuals
+#&gt; parent parent parent parent parent parent
+#&gt; 0.55407218 -2.98452128 4.20445742 -1.68599939 -0.58185357 -0.72033730
+#&gt; parent parent
+#&gt; -0.24260405 -0.07020339
+#&gt;
+#&gt; $ms
+#&gt; [1] 3.831956
+#&gt;
+#&gt; $var_ms
+#&gt; parent
+#&gt; 3.831956
+#&gt;
+#&gt; $var_ms_unscaled
+#&gt; parent
+#&gt; 3.831956
+#&gt;
+#&gt; $var_ms_unweighted
+#&gt; parent
+#&gt; 3.831956
+#&gt;
+#&gt; $rank
+#&gt; [1] 2
+#&gt;
+#&gt; $df.residual
+#&gt; [1] 6
+#&gt;
+#&gt; $solution_type
+#&gt; [1] &quot;analytical&quot;
+#&gt;
+#&gt; $transform_rates
+#&gt; [1] TRUE
+#&gt;
+#&gt; $transform_fractions
+#&gt; [1] TRUE
+#&gt;
+#&gt; $method.modFit
+#&gt; [1] &quot;Port&quot;
+#&gt;
+#&gt; $maxit.modFit
+#&gt; [1] &quot;auto&quot;
+#&gt;
+#&gt; $calls
+#&gt; [1] 29
+#&gt;
+#&gt; $time
+#&gt; user system elapsed
+#&gt; 0.068 0.000 0.070
+#&gt;
+#&gt; $mkinmod
+#&gt; &lt;mkinmod&gt; model generated with
+#&gt; Use of formation fractions $use_of_ff: min
+#&gt; Specification $spec:
+#&gt; $parent
+#&gt; $type: SFO; $sink: TRUE
+#&gt; Coefficient matrix $coefmat available
+#&gt;
+#&gt; $observed
+#&gt; name time value
+#&gt; 1 parent 0 98.62
+#&gt; 2 parent 3 81.43
+#&gt; 3 parent 7 53.18
+#&gt; 4 parent 14 34.89
+#&gt; 5 parent 30 10.09
+#&gt; 6 parent 62 1.50
+#&gt; 7 parent 90 0.33
+#&gt; 8 parent 118 0.08
+#&gt;
+#&gt; $obs_vars
+#&gt; [1] &quot;parent&quot;
+#&gt;
+#&gt; $predicted
+#&gt; name time value
+#&gt; 1 parent 0.000000 99.17407218
+#&gt; 2 parent 1.191919 90.35253561
+#&gt; 3 parent 2.383838 82.31567498
+#&gt; 4 parent 3.000000 78.44547872
+#&gt; 5 parent 3.575758 74.99369333
+#&gt; 6 parent 4.767677 68.32300215
+#&gt; 7 parent 5.959596 62.24566915
+#&gt; 8 parent 7.000000 57.38445742
+#&gt; 9 parent 7.151515 56.70891509
+#&gt; 10 parent 8.343434 51.66465547
+#&gt; 11 parent 9.535354 47.06908288
+#&gt; 12 parent 10.727273 42.88228661
+#&gt; 13 parent 11.919192 39.06790599
+#&gt; 14 parent 13.111111 35.59281463
+#&gt; 15 parent 14.000000 33.20400061
+#&gt; 16 parent 14.303030 32.42683275
+#&gt; 17 parent 15.494949 29.54246504
+#&gt; 18 parent 16.686869 26.91466193
+#&gt; 19 parent 17.878788 24.52060198
+#&gt; 20 parent 19.070707 22.33949373
+#&gt; 21 parent 20.262626 20.35239512
+#&gt; 22 parent 21.454545 18.54204899
+#&gt; 23 parent 22.646465 16.89273320
+#&gt; 24 parent 23.838384 15.39012410
+#&gt; 25 parent 25.030303 14.02117212
+#&gt; 26 parent 26.222222 12.77398846
+#&gt; 27 parent 27.414141 11.63774182
+#&gt; 28 parent 28.606061 10.60256435
+#&gt; 29 parent 29.797980 9.65946594
+#&gt; 30 parent 30.000000 9.50814643
+#&gt; 31 parent 30.989899 8.80025617
+#&gt; 32 parent 32.181818 8.01747313
+#&gt; 33 parent 33.373737 7.30431867
+#&gt; 34 parent 34.565657 6.65459931
+#&gt; 35 parent 35.757576 6.06267251
+#&gt; 36 parent 36.949495 5.52339762
+#&gt; 37 parent 38.141414 5.03209124
+#&gt; 38 parent 39.333333 4.58448658
+#&gt; 39 parent 40.525253 4.17669637
+#&gt; 40 parent 41.717172 3.80517911
+#&gt; 41 parent 42.909091 3.46670832
+#&gt; 42 parent 44.101010 3.15834451
+#&gt; 43 parent 45.292929 2.87740968
+#&gt; 44 parent 46.484848 2.62146400
+#&gt; 45 parent 47.676768 2.38828471
+#&gt; 46 parent 48.868687 2.17584671
+#&gt; 47 parent 50.060606 1.98230508
+#&gt; 48 parent 51.252525 1.80597899
+#&gt; 49 parent 52.444444 1.64533711
+#&gt; 50 parent 53.636364 1.49898432
+#&gt; 51 parent 54.828283 1.36564963
+#&gt; 52 parent 56.020202 1.24417505
+#&gt; 53 parent 57.212121 1.13350565
+#&gt; 54 parent 58.404040 1.03268029
+#&gt; 55 parent 59.595960 0.94082335
+#&gt; 56 parent 60.787879 0.85713708
+#&gt; 57 parent 61.979798 0.78089471
+#&gt; 58 parent 62.000000 0.77966270
+#&gt; 59 parent 63.171717 0.71143411
+#&gt; 60 parent 64.363636 0.64815202
+#&gt; 61 parent 65.555556 0.59049888
+#&gt; 62 parent 66.747475 0.53797399
+#&gt; 63 parent 67.939394 0.49012119
+#&gt; 64 parent 69.131313 0.44652489
+#&gt; 65 parent 70.323232 0.40680649
+#&gt; 66 parent 71.515152 0.37062104
+#&gt; 67 parent 72.707071 0.33765429
+#&gt; 68 parent 73.898990 0.30761993
+#&gt; 69 parent 75.090909 0.28025713
+#&gt; 70 parent 76.282828 0.25532825
+#&gt; 71 parent 77.474747 0.23261679
+#&gt; 72 parent 78.666667 0.21192552
+#&gt; 73 parent 79.858586 0.19307474
+#&gt; 74 parent 81.050505 0.17590074
+#&gt; 75 parent 82.242424 0.16025436
+#&gt; 76 parent 83.434343 0.14599973
+#&gt; 77 parent 84.626263 0.13301305
+#&gt; 78 parent 85.818182 0.12118154
+#&gt; 79 parent 87.010101 0.11040244
+#&gt; 80 parent 88.202020 0.10058214
+#&gt; 81 parent 89.393939 0.09163535
+#&gt; 82 parent 90.000000 0.08739595
+#&gt; 83 parent 90.585859 0.08348439
+#&gt; 84 parent 91.777778 0.07605845
+#&gt; 85 parent 92.969697 0.06929305
+#&gt; 86 parent 94.161616 0.06312943
+#&gt; 87 parent 95.353535 0.05751406
+#&gt; 88 parent 96.545455 0.05239819
+#&gt; 89 parent 97.737374 0.04773737
+#&gt; 90 parent 98.929293 0.04349113
+#&gt; 91 parent 100.121212 0.03962259
+#&gt; 92 parent 101.313131 0.03609816
+#&gt; 93 parent 102.505051 0.03288723
+#&gt; 94 parent 103.696970 0.02996191
+#&gt; 95 parent 104.888889 0.02729679
+#&gt; 96 parent 106.080808 0.02486874
+#&gt; 97 parent 107.272727 0.02265667
+#&gt; 98 parent 108.464646 0.02064136
+#&gt; 99 parent 109.656566 0.01880531
+#&gt; 100 parent 110.848485 0.01713257
+#&gt; 101 parent 112.040404 0.01560863
+#&gt; 102 parent 113.232323 0.01422024
+#&gt; 103 parent 114.424242 0.01295535
+#&gt; 104 parent 115.616162 0.01180297
+#&gt; 105 parent 116.808081 0.01075310
+#&gt; 106 parent 118.000000 0.00979661
+#&gt;
+#&gt; $cost
+#&gt; function (P)
+#&gt; {
+#&gt; assign(&quot;calls&quot;, calls + 1, inherits = TRUE)
+#&gt; if (trace_parms)
+#&gt; cat(P, &quot;\n&quot;)
+#&gt; if (length(state.ini.optim) &gt; 0) {
+#&gt; odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
+#&gt; names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
+#&gt; }
+#&gt; else {
+#&gt; odeini &lt;- state.ini.fixed
+#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
+#&gt; }
+#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
+#&gt; transparms.fixed)
+#&gt; parms &lt;- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates,
+#&gt; transform_fractions = transform_fractions)
+#&gt; out &lt;- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type,
+#&gt; use_compiled = use_compiled, method.ode = method.ode,
+#&gt; atol = atol, rtol = rtol, ...)
+#&gt; assign(&quot;out_predicted&quot;, out, inherits = TRUE)
+#&gt; mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
+#&gt; scaleVar = scaleVar)
+#&gt; if (mC$model &lt; cost.old) {
+#&gt; if (!quiet)
+#&gt; cat(&quot;Model cost at call &quot;, calls, &quot;: &quot;, mC$model,
+#&gt; &quot;\n&quot;)
+#&gt; if (plot) {
+#&gt; outtimes_plot = seq(min(observed$time), max(observed$time),
+#&gt; length.out = 100)
+#&gt; out_plot &lt;- mkinpredict(mkinmod, parms, odeini, outtimes_plot,
+#&gt; solution_type = solution_type, use_compiled = use_compiled,
+#&gt; method.ode = method.ode, atol = atol, rtol = rtol,
+#&gt; ...)
+#&gt; plot(0, type = &quot;n&quot;, xlim = range(observed$time),
+#&gt; ylim = c(0, max(observed$value, na.rm = TRUE)),
+#&gt; xlab = &quot;Time&quot;, ylab = &quot;Observed&quot;)
+#&gt; col_obs &lt;- pch_obs &lt;- 1:length(obs_vars)
+#&gt; lty_obs &lt;- rep(1, length(obs_vars))
+#&gt; names(col_obs) &lt;- names(pch_obs) &lt;- names(lty_obs) &lt;- obs_vars
+#&gt; for (obs_var in obs_vars) {
+#&gt; points(subset(observed, name == obs_var, c(time,
+#&gt; value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
+#&gt; }
+#&gt; matlines(out_plot$time, out_plot[-1], col = col_obs,
+#&gt; lty = lty_obs)
+#&gt; legend(&quot;topright&quot;, inset = c(0.05, 0.05), legend = obs_vars,
+#&gt; col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
+#&gt; }
+#&gt; assign(&quot;cost.old&quot;, mC$model, inherits = TRUE)
+#&gt; }
+#&gt; return(mC)
+#&gt; }
+#&gt; &lt;environment: 0x2b30d68&gt;
+#&gt;
+#&gt; $cost_notrans
+#&gt; function (P)
+#&gt; {
+#&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)
+#&gt; }
+#&gt; else {
+#&gt; odeini &lt;- state.ini.fixed
+#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
+#&gt; }
+#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
+#&gt; parms.fixed)
+#&gt; out &lt;- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type,
+#&gt; use_compiled = use_compiled, method.ode = method.ode,
+#&gt; atol = atol, rtol = rtol, ...)
+#&gt; mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
+#&gt; scaleVar = scaleVar)
+#&gt; return(mC)
+#&gt; }
+#&gt; &lt;environment: 0x2b30d68&gt;
+#&gt;
+#&gt; $hessian_notrans
+#&gt; parent_0 k_parent_sink
+#&gt; parent_0 4.163631 -1203.894
+#&gt; k_parent_sink -1203.893702 1033188.753
+#&gt;
+#&gt; $start
+#&gt; value type
+#&gt; parent_0 98.62 state
+#&gt; k_parent_sink 0.10 deparm
+#&gt;
+#&gt; $start_transformed
+#&gt; value lower upper
+#&gt; parent_0 98.620000 -Inf Inf
+#&gt; log_k_parent_sink -2.302585 -Inf Inf
+#&gt;
+#&gt; $fixed
+#&gt; [1] value type
+#&gt; &lt;0 rows&gt; (or 0-length row.names)
+#&gt;
+#&gt; $data
+#&gt; time variable observed predicted residual
+#&gt; 1 0 parent 98.62 99.17407218 -0.55407218
+#&gt; 2 3 parent 81.43 78.44547872 2.98452128
+#&gt; 3 7 parent 53.18 57.38445742 -4.20445742
+#&gt; 4 14 parent 34.89 33.20400061 1.68599939
+#&gt; 5 30 parent 10.09 9.50814643 0.58185357
+#&gt; 6 62 parent 1.50 0.77966270 0.72033730
+#&gt; 7 90 parent 0.33 0.08739595 0.24260405
+#&gt; 8 118 parent 0.08 0.00979661 0.07020339
+#&gt;
+#&gt; $atol
+#&gt; [1] 1e-08
+#&gt;
+#&gt; $rtol
+#&gt; [1] 1e-10
+#&gt;
+#&gt; $weight.ini
+#&gt; [1] &quot;none&quot;
+#&gt;
+#&gt; $reweight.tol
+#&gt; [1] 1e-08
+#&gt;
+#&gt; $reweight.max.iter
+#&gt; [1] 10
+#&gt;
+#&gt; $bparms.optim
+#&gt; parent_0 k_parent_sink
+#&gt; 99.17407218 0.07815759
+#&gt;
+#&gt; $bparms.fixed
+#&gt; numeric(0)
+#&gt;
+#&gt; $bparms.ode
+#&gt; k_parent_sink
+#&gt; 0.07815759
+#&gt;
+#&gt; $bparms.state
+#&gt; parent
+#&gt; 99.17407
+#&gt;
+#&gt; $date
+#&gt; [1] &quot;Wed Oct 26 23:50:32 2016&quot;
+#&gt;
+#&gt; attr(,&quot;class&quot;)
+#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot;
+#&gt; </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#&gt; [[1]]
+#&gt; $par
+#&gt; parent_0 log_k_parent_sink
+#&gt; 99.174072 -2.549028
+#&gt;
+#&gt; $ssr
+#&gt; [1] 30.65564
+#&gt;
+#&gt; $convergence
+#&gt; [1] 0
+#&gt;
+#&gt; $iterations
+#&gt; [1] 5
+#&gt;
+#&gt; $evaluations
+#&gt; function gradient
+#&gt; 8 15
+#&gt;
+#&gt; $counts
+#&gt; [1] &quot;relative convergence (4)&quot;
+#&gt;
+#&gt; $hessian
+#&gt; parent_0 log_k_parent_sink
+#&gt; parent_0 4.163631 -94.09343
+#&gt; log_k_parent_sink -94.093431 6311.34610
+#&gt;
+#&gt; $residuals
+#&gt; parent parent parent parent parent parent
+#&gt; 0.55407218 -2.98452128 4.20445742 -1.68599939 -0.58185357 -0.72033730
+#&gt; parent parent
+#&gt; -0.24260405 -0.07020339
+#&gt;
+#&gt; $ms
+#&gt; [1] 3.831956
+#&gt;
+#&gt; $var_ms
+#&gt; parent
+#&gt; 3.831956
+#&gt;
+#&gt; $var_ms_unscaled
+#&gt; parent
+#&gt; 3.831956
+#&gt;
+#&gt; $var_ms_unweighted
+#&gt; parent
+#&gt; 3.831956
+#&gt;
+#&gt; $rank
+#&gt; [1] 2
+#&gt;
+#&gt; $df.residual
+#&gt; [1] 6
+#&gt;
+#&gt; $solution_type
+#&gt; [1] &quot;analytical&quot;
+#&gt;
+#&gt; $transform_rates
+#&gt; [1] TRUE
+#&gt;
+#&gt; $transform_fractions
+#&gt; [1] TRUE
+#&gt;
+#&gt; $method.modFit
+#&gt; [1] &quot;Port&quot;
+#&gt;
+#&gt; $maxit.modFit
+#&gt; [1] &quot;auto&quot;
+#&gt;
+#&gt; $calls
+#&gt; [1] 29
+#&gt;
+#&gt; $time
+#&gt; user system elapsed
+#&gt; 0.068 0.000 0.070
+#&gt;
+#&gt; $mkinmod
+#&gt; &lt;mkinmod&gt; model generated with
+#&gt; Use of formation fractions $use_of_ff: min
+#&gt; Specification $spec:
+#&gt; $parent
+#&gt; $type: SFO; $sink: TRUE
+#&gt; Coefficient matrix $coefmat available
+#&gt;
+#&gt; $observed
+#&gt; name time value
+#&gt; 1 parent 0 98.62
+#&gt; 2 parent 3 81.43
+#&gt; 3 parent 7 53.18
+#&gt; 4 parent 14 34.89
+#&gt; 5 parent 30 10.09
+#&gt; 6 parent 62 1.50
+#&gt; 7 parent 90 0.33
+#&gt; 8 parent 118 0.08
+#&gt;
+#&gt; $obs_vars
+#&gt; [1] &quot;parent&quot;
+#&gt;
+#&gt; $predicted
+#&gt; name time value
+#&gt; 1 parent 0.000000 99.17407218
+#&gt; 2 parent 1.191919 90.35253561
+#&gt; 3 parent 2.383838 82.31567498
+#&gt; 4 parent 3.000000 78.44547872
+#&gt; 5 parent 3.575758 74.99369333
+#&gt; 6 parent 4.767677 68.32300215
+#&gt; 7 parent 5.959596 62.24566915
+#&gt; 8 parent 7.000000 57.38445742
+#&gt; 9 parent 7.151515 56.70891509
+#&gt; 10 parent 8.343434 51.66465547
+#&gt; 11 parent 9.535354 47.06908288
+#&gt; 12 parent 10.727273 42.88228661
+#&gt; 13 parent 11.919192 39.06790599
+#&gt; 14 parent 13.111111 35.59281463
+#&gt; 15 parent 14.000000 33.20400061
+#&gt; 16 parent 14.303030 32.42683275
+#&gt; 17 parent 15.494949 29.54246504
+#&gt; 18 parent 16.686869 26.91466193
+#&gt; 19 parent 17.878788 24.52060198
+#&gt; 20 parent 19.070707 22.33949373
+#&gt; 21 parent 20.262626 20.35239512
+#&gt; 22 parent 21.454545 18.54204899
+#&gt; 23 parent 22.646465 16.89273320
+#&gt; 24 parent 23.838384 15.39012410
+#&gt; 25 parent 25.030303 14.02117212
+#&gt; 26 parent 26.222222 12.77398846
+#&gt; 27 parent 27.414141 11.63774182
+#&gt; 28 parent 28.606061 10.60256435
+#&gt; 29 parent 29.797980 9.65946594
+#&gt; 30 parent 30.000000 9.50814643
+#&gt; 31 parent 30.989899 8.80025617
+#&gt; 32 parent 32.181818 8.01747313
+#&gt; 33 parent 33.373737 7.30431867
+#&gt; 34 parent 34.565657 6.65459931
+#&gt; 35 parent 35.757576 6.06267251
+#&gt; 36 parent 36.949495 5.52339762
+#&gt; 37 parent 38.141414 5.03209124
+#&gt; 38 parent 39.333333 4.58448658
+#&gt; 39 parent 40.525253 4.17669637
+#&gt; 40 parent 41.717172 3.80517911
+#&gt; 41 parent 42.909091 3.46670832
+#&gt; 42 parent 44.101010 3.15834451
+#&gt; 43 parent 45.292929 2.87740968
+#&gt; 44 parent 46.484848 2.62146400
+#&gt; 45 parent 47.676768 2.38828471
+#&gt; 46 parent 48.868687 2.17584671
+#&gt; 47 parent 50.060606 1.98230508
+#&gt; 48 parent 51.252525 1.80597899
+#&gt; 49 parent 52.444444 1.64533711
+#&gt; 50 parent 53.636364 1.49898432
+#&gt; 51 parent 54.828283 1.36564963
+#&gt; 52 parent 56.020202 1.24417505
+#&gt; 53 parent 57.212121 1.13350565
+#&gt; 54 parent 58.404040 1.03268029
+#&gt; 55 parent 59.595960 0.94082335
+#&gt; 56 parent 60.787879 0.85713708
+#&gt; 57 parent 61.979798 0.78089471
+#&gt; 58 parent 62.000000 0.77966270
+#&gt; 59 parent 63.171717 0.71143411
+#&gt; 60 parent 64.363636 0.64815202
+#&gt; 61 parent 65.555556 0.59049888
+#&gt; 62 parent 66.747475 0.53797399
+#&gt; 63 parent 67.939394 0.49012119
+#&gt; 64 parent 69.131313 0.44652489
+#&gt; 65 parent 70.323232 0.40680649
+#&gt; 66 parent 71.515152 0.37062104
+#&gt; 67 parent 72.707071 0.33765429
+#&gt; 68 parent 73.898990 0.30761993
+#&gt; 69 parent 75.090909 0.28025713
+#&gt; 70 parent 76.282828 0.25532825
+#&gt; 71 parent 77.474747 0.23261679
+#&gt; 72 parent 78.666667 0.21192552
+#&gt; 73 parent 79.858586 0.19307474
+#&gt; 74 parent 81.050505 0.17590074
+#&gt; 75 parent 82.242424 0.16025436
+#&gt; 76 parent 83.434343 0.14599973
+#&gt; 77 parent 84.626263 0.13301305
+#&gt; 78 parent 85.818182 0.12118154
+#&gt; 79 parent 87.010101 0.11040244
+#&gt; 80 parent 88.202020 0.10058214
+#&gt; 81 parent 89.393939 0.09163535
+#&gt; 82 parent 90.000000 0.08739595
+#&gt; 83 parent 90.585859 0.08348439
+#&gt; 84 parent 91.777778 0.07605845
+#&gt; 85 parent 92.969697 0.06929305
+#&gt; 86 parent 94.161616 0.06312943
+#&gt; 87 parent 95.353535 0.05751406
+#&gt; 88 parent 96.545455 0.05239819
+#&gt; 89 parent 97.737374 0.04773737
+#&gt; 90 parent 98.929293 0.04349113
+#&gt; 91 parent 100.121212 0.03962259
+#&gt; 92 parent 101.313131 0.03609816
+#&gt; 93 parent 102.505051 0.03288723
+#&gt; 94 parent 103.696970 0.02996191
+#&gt; 95 parent 104.888889 0.02729679
+#&gt; 96 parent 106.080808 0.02486874
+#&gt; 97 parent 107.272727 0.02265667
+#&gt; 98 parent 108.464646 0.02064136
+#&gt; 99 parent 109.656566 0.01880531
+#&gt; 100 parent 110.848485 0.01713257
+#&gt; 101 parent 112.040404 0.01560863
+#&gt; 102 parent 113.232323 0.01422024
+#&gt; 103 parent 114.424242 0.01295535
+#&gt; 104 parent 115.616162 0.01180297
+#&gt; 105 parent 116.808081 0.01075310
+#&gt; 106 parent 118.000000 0.00979661
+#&gt;
+#&gt; $cost
+#&gt; function (P)
+#&gt; {
+#&gt; assign(&quot;calls&quot;, calls + 1, inherits = TRUE)
+#&gt; if (trace_parms)
+#&gt; cat(P, &quot;\n&quot;)
+#&gt; if (length(state.ini.optim) &gt; 0) {
+#&gt; odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
+#&gt; names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
+#&gt; }
+#&gt; else {
+#&gt; odeini &lt;- state.ini.fixed
+#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
+#&gt; }
+#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
+#&gt; transparms.fixed)
+#&gt; parms &lt;- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates,
+#&gt; transform_fractions = transform_fractions)
+#&gt; out &lt;- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type,
+#&gt; use_compiled = use_compiled, method.ode = method.ode,
+#&gt; atol = atol, rtol = rtol, ...)
+#&gt; assign(&quot;out_predicted&quot;, out, inherits = TRUE)
+#&gt; mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
+#&gt; scaleVar = scaleVar)
+#&gt; if (mC$model &lt; cost.old) {
+#&gt; if (!quiet)
+#&gt; cat(&quot;Model cost at call &quot;, calls, &quot;: &quot;, mC$model,
+#&gt; &quot;\n&quot;)
+#&gt; if (plot) {
+#&gt; outtimes_plot = seq(min(observed$time), max(observed$time),
+#&gt; length.out = 100)
+#&gt; out_plot &lt;- mkinpredict(mkinmod, parms, odeini, outtimes_plot,
+#&gt; solution_type = solution_type, use_compiled = use_compiled,
+#&gt; method.ode = method.ode, atol = atol, rtol = rtol,
+#&gt; ...)
+#&gt; plot(0, type = &quot;n&quot;, xlim = range(observed$time),
+#&gt; ylim = c(0, max(observed$value, na.rm = TRUE)),
+#&gt; xlab = &quot;Time&quot;, ylab = &quot;Observed&quot;)
+#&gt; col_obs &lt;- pch_obs &lt;- 1:length(obs_vars)
+#&gt; lty_obs &lt;- rep(1, length(obs_vars))
+#&gt; names(col_obs) &lt;- names(pch_obs) &lt;- names(lty_obs) &lt;- obs_vars
+#&gt; for (obs_var in obs_vars) {
+#&gt; points(subset(observed, name == obs_var, c(time,
+#&gt; value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
+#&gt; }
+#&gt; matlines(out_plot$time, out_plot[-1], col = col_obs,
+#&gt; lty = lty_obs)
+#&gt; legend(&quot;topright&quot;, inset = c(0.05, 0.05), legend = obs_vars,
+#&gt; col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
+#&gt; }
+#&gt; assign(&quot;cost.old&quot;, mC$model, inherits = TRUE)
+#&gt; }
+#&gt; return(mC)
+#&gt; }
+#&gt; &lt;environment: 0x2b30d68&gt;
+#&gt;
+#&gt; $cost_notrans
+#&gt; function (P)
+#&gt; {
+#&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)
+#&gt; }
+#&gt; else {
+#&gt; odeini &lt;- state.ini.fixed
+#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
+#&gt; }
+#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
+#&gt; parms.fixed)
+#&gt; out &lt;- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type,
+#&gt; use_compiled = use_compiled, method.ode = method.ode,
+#&gt; atol = atol, rtol = rtol, ...)
+#&gt; mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
+#&gt; scaleVar = scaleVar)
+#&gt; return(mC)
+#&gt; }
+#&gt; &lt;environment: 0x2b30d68&gt;
+#&gt;
+#&gt; $hessian_notrans
+#&gt; parent_0 k_parent_sink
+#&gt; parent_0 4.163631 -1203.894
+#&gt; k_parent_sink -1203.893702 1033188.753
+#&gt;
+#&gt; $start
+#&gt; value type
+#&gt; parent_0 98.62 state
+#&gt; k_parent_sink 0.10 deparm
+#&gt;
+#&gt; $start_transformed
+#&gt; value lower upper
+#&gt; parent_0 98.620000 -Inf Inf
+#&gt; log_k_parent_sink -2.302585 -Inf Inf
+#&gt;
+#&gt; $fixed
+#&gt; [1] value type
+#&gt; &lt;0 rows&gt; (or 0-length row.names)
+#&gt;
+#&gt; $data
+#&gt; time variable observed predicted residual
+#&gt; 1 0 parent 98.62 99.17407218 -0.55407218
+#&gt; 2 3 parent 81.43 78.44547872 2.98452128
+#&gt; 3 7 parent 53.18 57.38445742 -4.20445742
+#&gt; 4 14 parent 34.89 33.20400061 1.68599939
+#&gt; 5 30 parent 10.09 9.50814643 0.58185357
+#&gt; 6 62 parent 1.50 0.77966270 0.72033730
+#&gt; 7 90 parent 0.33 0.08739595 0.24260405
+#&gt; 8 118 parent 0.08 0.00979661 0.07020339
+#&gt;
+#&gt; $atol
+#&gt; [1] 1e-08
+#&gt;
+#&gt; $rtol
+#&gt; [1] 1e-10
+#&gt;
+#&gt; $weight.ini
+#&gt; [1] &quot;none&quot;
+#&gt;
+#&gt; $reweight.tol
+#&gt; [1] 1e-08
+#&gt;
+#&gt; $reweight.max.iter
+#&gt; [1] 10
+#&gt;
+#&gt; $bparms.optim
+#&gt; parent_0 k_parent_sink
+#&gt; 99.17407218 0.07815759
+#&gt;
+#&gt; $bparms.fixed
+#&gt; numeric(0)
+#&gt;
+#&gt; $bparms.ode
+#&gt; k_parent_sink
+#&gt; 0.07815759
+#&gt;
+#&gt; $bparms.state
+#&gt; parent
+#&gt; 99.17407
+#&gt;
+#&gt; $date
+#&gt; [1] &quot;Wed Oct 26 23:50:32 2016&quot;
+#&gt;
+#&gt; attr(,&quot;class&quot;)
+#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot;
+#&gt;
+#&gt; </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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
new file mode 100644
index 00000000..6f071674
--- /dev/null
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -0,0 +1,146 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+ — FOCUS_2006_DFOP_ref_A_to_B • mkin</title>
+
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+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+
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+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
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+<!-- mathjax -->
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+</li>
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+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>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.</p>
+
+
+ <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span>)</pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>A data frame containing the following variables.
+ <dl class='dl-horizontal'>
+ <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd>
+ <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd>
+ <dt><code>f</code></dt><dd>The fitted f parameter</dd>
+ <dt><code>k1</code></dt><dd>The fitted k1 parameter</dd>
+ <dt><code>k2</code></dt><dd>The fitted k2 parameter</dd>
+ <dt><code>DT50</code></dt><dd>The resulting half-life of the parent compound</dd>
+ <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd>
+ <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd>
+ </dl></p>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span>)</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="#format">Format</a></li>
+
+ <li><a href="#source">Source</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
new file mode 100644
index 00000000..d721b2d9
--- /dev/null
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -0,0 +1,145 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
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+ — FOCUS_2006_FOMC_ref_A_to_F • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- 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">
+
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+ <div class="navbar-header">
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+ <span class="icon-bar"></span>
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+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
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+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
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+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>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.</p>
+
+
+ <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span>)</pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>A data frame containing the following variables.
+ <dl class='dl-horizontal'>
+ <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd>
+ <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd>
+ <dt><code>alpha</code></dt><dd>The fitted alpha parameter</dd>
+ <dt><code>beta</code></dt><dd>The fitted beta parameter</dd>
+ <dt><code>DT50</code></dt><dd>The resulting half-life of the parent compound</dd>
+ <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd>
+ <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd>
+ </dl></p>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span>)</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="#format">Format</a></li>
+
+ <li><a href="#source">Source</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
new file mode 100644
index 00000000..11fcea7c
--- /dev/null
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -0,0 +1,146 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>
+ — FOCUS_2006_HS_ref_A_to_F • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- 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">
+
+
+<!-- pkgdown -->
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+<script src="../pkgdown.js"></script>
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+
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
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+
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+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>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.</p>
+
+
+ <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_HS_ref_A_to_F</span>)</pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>A data frame containing the following variables.
+ <dl class='dl-horizontal'>
+ <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd>
+ <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd>
+ <dt><code>tb</code></dt><dd>The fitted tb parameter</dd>
+ <dt><code>k1</code></dt><dd>The fitted k1 parameter</dd>
+ <dt><code>k2</code></dt><dd>The fitted k2 parameter</dd>
+ <dt><code>DT50</code></dt><dd>The resulting half-life of the parent compound</dd>
+ <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd>
+ <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd>
+ </dl></p>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_HS_ref_A_to_F</span>)</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="#format">Format</a></li>
+
+ <li><a href="#source">Source</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
new file mode 100644
index 00000000..17c34f0f
--- /dev/null
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -0,0 +1,144 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>
+ — FOCUS_2006_SFO_ref_A_to_F • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- 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">
+
+
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+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>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.</p>
+
+
+ <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_SFO_ref_A_to_F</span>)</pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>A data frame containing the following variables.
+ <dl class='dl-horizontal'>
+ <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd>
+ <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd>
+ <dt><code>k</code></dt><dd>The fitted first-order degradation rate constant</dd>
+ <dt><code>DT50</code></dt><dd>The resulting half-life of the parent compound</dd>
+ <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd>
+ <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd>
+ </dl></p>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_SFO_ref_A_to_F</span>)</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="#format">Format</a></li>
+
+ <li><a href="#source">Source</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
new file mode 100644
index 00000000..c5bdae8b
--- /dev/null
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+ <h1>
+</h1>
+ </div>
+
+
+ <p>Data taken from FOCUS (2006), p. 258.</p>
+
+
+ <pre><span class='no'>FOCUS_2006_datasets</span></pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>6 datasets with observations on the following variables.
+ <dl class='dl-horizontal'>
+ <dt><code>name</code></dt><dd>a factor containing the name of the observed variable</dd>
+ <dt><code>time</code></dt><dd>a numeric vector containing time points</dd>
+ <dt><code>value</code></dt><dd>a numeric vector containing concentrations in percent of applied radioactivity</dd>
+ </dl></p>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='no'>FOCUS_2006_C</span></div><div class='output co'>#&gt; name time value
+#&gt; 1 parent 0 85.1
+#&gt; 2 parent 1 57.9
+#&gt; 3 parent 3 29.9
+#&gt; 4 parent 7 14.6
+#&gt; 5 parent 14 9.7
+#&gt; 6 parent 28 6.6
+#&gt; 7 parent 63 4.0
+#&gt; 8 parent 91 3.9
+#&gt; 9 parent 119 0.6
+#&gt; </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="#format">Format</a></li>
+
+ <li><a href="#source">Source</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
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+</div>
+
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diff --git a/docs/reference/FOMC.solution-2.png b/docs/reference/FOMC.solution-2.png
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+ <div class="page-header">
+ <h1> First-Order Multi-Compartment kinetics </h1>
+ </div>
+
+
+ <p>Function describing exponential decline from a defined starting value, with
+ a decreasing rate constant.</p>
+
+ <p>The form given here differs slightly from the original reference by Gustafson
+ and Holden (1990). The parameter <code>beta</code> corresponds to 1/beta in the
+ original equation.</p>
+
+
+ <pre><span class='fu'>FOMC.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>alpha</span>, <span class='no'>beta</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>t</dt>
+ <dd> Time. </dd>
+ <dt>parent.0</dt>
+ <dd> Starting value for the response variable at time zero. </dd>
+ <dt>alpha</dt>
+ <dd>
+ Shape parameter determined by coefficient of variation of rate constant
+ values. </dd>
+ <dt>beta</dt>
+ <dd>
+ Location parameter.
+</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+ <p>The solution of the FOMC kinetic model reduces to the
+ <code><a href='SFO.solution.html'>SFO.solution</a></code> for large values of <code>alpha</code> and
+ <code>beta</code> with
+ \(k = \frac{\beta}{\alpha}\).</p>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The value of the response variable at time <code>t</code>.</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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</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>
+ </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="#note">Note</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#references">References</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/HS.solution-2.png b/docs/reference/HS.solution-2.png
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diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
new file mode 100644
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--- /dev/null
+++ b/docs/reference/HS.solution.html
@@ -0,0 +1,148 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
+<title> Hockey-Stick kinetics — HS.solution • mkin</title>
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+ <a href="../reference/index.html">Reference</a>
+</li>
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+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
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+
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+
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+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1> Hockey-Stick kinetics </h1>
+ </div>
+
+
+ <p>Function describing two exponential decline functions with a break point
+ between them.</p>
+
+
+ <pre><span class='fu'>HS.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>tb</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>t</dt>
+ <dd> Time. </dd>
+ <dt>parent.0</dt>
+ <dd> Starting value for the response variable at time zero. </dd>
+ <dt>k1</dt>
+ <dd> First kinetic constant. </dd>
+ <dt>k2</dt>
+ <dd> Second kinetic constant. </dd>
+ <dt>tb</dt>
+ <dd> Break point. Before this time, exponential decline according
+ to <code>k1</code> is calculated, after this time, exponential decline proceeds
+ according to <code>k2</code>. </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The value of the response variable at time <code>t</code>.</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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</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>
+ </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>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
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+
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+</html>
diff --git a/docs/reference/IORE.solution-2.png b/docs/reference/IORE.solution-2.png
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@@ -0,0 +1,166 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
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+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
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+</div><!--/.navbar -->
+
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+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1> Indeterminate order rate equation kinetics </h1>
+ </div>
+
+
+ <p>Function describing exponential decline from a defined starting value, with
+ a concentration dependent rate constant.</p>
+
+
+ <pre><span class='fu'>IORE.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k__iore</span>, <span class='no'>N</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>t</dt>
+ <dd> Time. </dd>
+ <dt>parent.0</dt>
+ <dd> Starting value for the response variable at time zero. </dd>
+ <dt>k__iore</dt>
+ <dd> Rate constant. Note that this depends on the concentration units used. </dd>
+ <dt>N</dt>
+ <dd> Exponent describing the nonlinearity of the rate equation </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+ <p>The solution of the IORE kinetic model reduces to the
+ <code><a href='SFO.solution.html'>SFO.solution</a></code> if N = 1.
+ The parameters of the IORE model can be transformed to equivalent parameters
+ of the FOMC mode - see the NAFTA guidance for details.</p>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The value of the response variable at time <code>t</code>.</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for
+ Evaluating and Calculating Degradation Kinetics in Environmental
+ Media</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'>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='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>)
+
+ <span class='fu'>print</span>(<span class='fu'>data.frame</span>(<span class='fu'>coef</span>(<span class='no'>fit.fomc</span>), <span class='fu'>coef</span>(<span class='no'>fit.iore</span>), <span class='fu'>coef</span>(<span class='no'>fit.iore.deS</span>),
+ <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'>paste</span>(<span class='st'>"model par"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)))</div><div class='output co'>#&gt; coef.fit.fomc. coef.fit.iore. coef.fit.iore.deS.
+#&gt; model par 1 85.87489063 85.874891 85.874890
+#&gt; model par 2 0.05192238 -4.826631 -4.826631
+#&gt; model par 3 0.65096665 1.949403 1.949403
+#&gt; </div><div class='input'> <span class='fu'>print</span>(<span class='fu'>rbind</span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>,
+ <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>))</div><div class='output co'>#&gt; DT50 DT90 DT50back
+#&gt; fomc 1.785233 15.1479 4.559973
+#&gt; iore 1.785233 15.1479 4.559973
+#&gt; iore.deS 1.785233 15.1479 4.559973
+#&gt; </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="#note">Note</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#references">References</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
new file mode 100644
index 00000000..3ce813bf
--- /dev/null
+++ b/docs/reference/SFO.solution.html
@@ -0,0 +1,141 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
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+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1> Single First-Order kinetics </h1>
+ </div>
+
+
+ <p>Function describing exponential decline from a defined starting value.</p>
+
+
+ <pre><span class='fu'>SFO.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>t</dt>
+ <dd> Time. </dd>
+ <dt>parent.0</dt>
+ <dd> Starting value for the response variable at time zero. </dd>
+ <dt>k</dt>
+ <dd> Kinetic constant. </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The value of the response variable at time <code>t</code>.</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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFO.solution(x, 100, 3), 0, 2)</span></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>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
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+
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+</html>
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
new file mode 100644
index 00000000..942fa576
--- /dev/null
+++ b/docs/reference/SFORB.solution.html
@@ -0,0 +1,150 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
+<title> Single First-Order Reversible Binding kinetics — SFORB.solution • mkin</title>
+
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+
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+<li>
+ <a href="../news/index.html">News</a>
+</li>
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+
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+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1> Single First-Order Reversible Binding kinetics </h1>
+ </div>
+
+
+ <p>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.</p>
+
+
+ <pre><span class='fu'>SFORB.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k_12</span>, <span class='no'>k_21</span>, <span class='no'>k_1output</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>t</dt>
+ <dd> Time. </dd>
+ <dt>parent.0</dt>
+ <dd> Starting value for the response variable at time zero. </dd>
+ <dt>k_12</dt>
+ <dd> Kinetic constant describing transfer from free to bound. </dd>
+ <dt>k_21</dt>
+ <dd> Kinetic constant describing transfer from bound to free. </dd>
+ <dt>k_1output</dt>
+ <dd> Kinetic constant describing degradation of the free fraction. </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The value of the response variable, which is the sum of free and bound
+ fractions at time <code>t</code>.</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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)</span></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>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/add_err-4.png b/docs/reference/add_err-4.png
new file mode 100644
index 00000000..f3d04134
--- /dev/null
+++ b/docs/reference/add_err-4.png
Binary files differ
diff --git a/docs/reference/add_err-6.png b/docs/reference/add_err-6.png
new file mode 100644
index 00000000..05b27247
--- /dev/null
+++ b/docs/reference/add_err-6.png
Binary files differ
diff --git a/docs/reference/add_err-8.png b/docs/reference/add_err-8.png
new file mode 100644
index 00000000..b0182d2a
--- /dev/null
+++ b/docs/reference/add_err-8.png
Binary files differ
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
new file mode 100644
index 00000000..2500e092
--- /dev/null
+++ b/docs/reference/add_err.html
@@ -0,0 +1,214 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
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+ — add_err • mkin</title>
+
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+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>Normally distributed errors are added to data predicted for a specific
+ degradation model using <code><a href='mkinpredict.html'>mkinpredict</a></code>. The variance of the error
+ may depend on the predicted value and is specified as a standard deviation.</p>
+
+
+ <pre><span class='fu'>add_err</span>(<span class='no'>prediction</span>, <span class='no'>sdfunc</span>,
+ <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>,
+ <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>prediction</dt>
+ <dd>
+ A prediction from a kinetic model as produced by <code><a href='mkinpredict.html'>mkinpredict</a></code>.
+ </dd>
+ <dt>sdfunc</dt>
+ <dd>
+ A function taking the predicted value as its only argument and returning
+ a standard deviation that should be used for generating the random error
+ terms for this value.
+ </dd>
+ <dt>n</dt>
+ <dd>
+ The number of datasets to be generated.
+ </dd>
+ <dt>LOD</dt>
+ <dd>
+ The limit of detection (LOD). Values that are below the LOD after adding
+ the random error will be set to NA.
+ </dd>
+ <dt>reps</dt>
+ <dd>
+ The number of replicates to be generated within the datasets.
+ </dd>
+ <dt>digits</dt>
+ <dd>
+ The number of digits to which the values will be rounded.
+ </dd>
+ <dt>seed</dt>
+ <dd>
+ The seed used for the generation of random numbers. If NA, the seed
+ is not set.
+ </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A list of datasets compatible with <code><a href='mmkin.html'>mmkin</a></code>, i.e.
+ the components of the list are datasets compatible with
+ <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Ranke J and Lehmann R (2015) To t-test or not to t-test, that is the question. XV Symposium on Pesticide Chemistry 2-4 September 2015, Piacenza, Italy
+ http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='co'># The kinetic model</span>
+<span class='no'>m_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'>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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'>
+<span class='co'># Generate a prediction for a specific set of parameters</span>
+<span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>)
+
+<span class='co'># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span>
+<span class='co'># from 2015</span>
+<span class='no'>d_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_SFO_SFO</span>,
+ <span class='fu'>c</span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
+ <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fu'>log</span>(<span class='fl'>2</span>)/<span class='fl'>1000</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='no'>sampling_times</span>)
+
+<span class='co'># Add an error term with a constant (independent of the value) standard deviation</span>
+<span class='co'># of 10, and generate three datasets</span>
+<span class='no'>d_SFO_SFO_err</span> <span class='kw'>&lt;-</span> <span class='fu'>add_err</span>(<span class='no'>d_SFO_SFO</span>, <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fl'>10</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456789</span> )
+
+<span class='co'># Name the datasets for nicer plotting</span>
+<span class='fu'>names</span>(<span class='no'>d_SFO_SFO_err</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='co'># Name the model in the list of models (with only one member in this case)</span>
+<span class='co'># for nicer plotting later on.</span>
+<span class='co'># Be quiet and use the faster Levenberg-Marquardt algorithm, as the datasets</span>
+<span class='co'># are easy and examples are run often. Use only one core not to offend CRAN</span>
+<span class='co'># checks</span>
+<span class='no'>f_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>list</span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>m_SFO_SFO</span>),
+ <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='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='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'>
+</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, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
new file mode 100644
index 00000000..73d7e746
--- /dev/null
+++ b/docs/reference/endpoints.html
@@ -0,0 +1,137 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
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+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+ — endpoints • mkin</title>
+
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+
+<!-- Font Awesome icons -->
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+
+
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+ <div class="container">
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+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
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+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
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+<li>
+ <a href="../news/index.html">News</a>
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+
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+
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+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>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.</p>
+
+
+ <pre><span class='fu'>endpoints</span>(<span class='no'>fit</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>fit</dt>
+ <dd>
+ An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.
+ </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+ <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A list with the components mentioned above.</p>
+
+
+ </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="#note">Note</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
new file mode 100644
index 00000000..62a9163f
--- /dev/null
+++ b/docs/reference/geometric_mean.html
@@ -0,0 +1,132 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title> Calculate the geometric mean — geometric_mean • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
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+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
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+
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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+
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+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1> Calculate the geometric mean </h1>
+ </div>
+
+
+ <p>Function calculating the geometric mean of numeric vectors</p>
+
+
+ <pre><span class='fu'>geometric_mean</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>x</dt>
+ <dd> A numeric vector </dd>
+ <dt>na.rm</dt>
+ <dd> Should NA values be ignored </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The geometric mean.</p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#&gt; [1] 3
+#&gt; </div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>))</div><div class='output co'>#&gt; [1] NA
+#&gt; </div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>), <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; [1] 1.732051
+#&gt; </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="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
new file mode 100644
index 00000000..82accca4
--- /dev/null
+++ b/docs/reference/ilr.html
@@ -0,0 +1,170 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
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+ — ilr • mkin</title>
+
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+
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+
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+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
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+ <a href="../news/index.html">News</a>
+</li>
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+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>This implementation is a special case of the class of isometric log-ratio transformations.</p>
+
+
+ <pre><span class='fu'>ilr</span>(<span class='no'>x</span>)
+ <span class='fu'>invilr</span>(<span class='no'>x</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>x</dt>
+ <dd>
+ A numeric vector. Naturally, the forward transformation is only sensible for
+ vectors with all elements being greater than zero.
+ </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The result of the forward or backward transformation. The returned components always
+ sum to 1 for the case of the inverse log-ratio transformation.</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Peter Filzmoser, Karel Hron (2008) Outlier Detection for Compositional Data Using Robust Methods. Math Geosci 40 233-248</p>
+
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <p>Another implementation can be found in R package <code>robCompositions</code>.</p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='co'># Order matters</span>
+<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.1</span>, <span class='fl'>1</span>, <span class='fl'>10</span>))</div><div class='output co'>#&gt; [1] -1.628174 -2.820079
+#&gt; </div><div class='input'><span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>10</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>))</div><div class='output co'>#&gt; [1] 1.628174 2.820079
+#&gt; </div><div class='input'><span class='co'># Equal entries give ilr transformations with zeros as elements</span>
+<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>3</span>, <span class='fl'>3</span>, <span class='fl'>3</span>))</div><div class='output co'>#&gt; [1] 0 0
+#&gt; </div><div class='input'><span class='co'># Almost equal entries give small numbers</span>
+<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.3</span>, <span class='fl'>0.4</span>, <span class='fl'>0.3</span>))</div><div class='output co'>#&gt; [1] -0.2034219 0.1174457
+#&gt; </div><div class='input'><span class='co'># Only the ratio between the numbers counts, not their sum</span>
+<span class='fu'>invilr</span>(<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#&gt; [1] 0.70 0.29 0.01
+#&gt; </div><div class='input'><span class='fu'>invilr</span>(<span class='fu'>ilr</span>(<span class='fl'>2.1</span> * <span class='fu'>c</span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#&gt; [1] 0.70 0.29 0.01
+#&gt; </div><div class='input'><span class='co'># Inverse transformation of larger numbers gives unequal elements</span>
+<span class='fu'>invilr</span>(-<span class='fl'>10</span>)</div><div class='output co'>#&gt; [1] 7.213536e-07 9.999993e-01
+#&gt; </div><div class='input'><span class='fu'>invilr</span>(<span class='fu'>c</span>(-<span class='fl'>10</span>, <span class='fl'>0</span>))</div><div class='output co'>#&gt; [1] 7.207415e-07 9.991507e-01 8.486044e-04
+#&gt; </div><div class='input'><span class='co'># The sum of the elements of the inverse ilr is 1</span>
+<span class='fu'>sum</span>(<span class='fu'>invilr</span>(<span class='fu'>c</span>(-<span class='fl'>10</span>, <span class='fl'>0</span>)))</div><div class='output co'>#&gt; [1] 1
+#&gt; </div><div class='input'><span class='co'># This is why we do not need all elements of the inverse transformation to go back:</span>
+<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='fl'>0.1</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>)
+<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'>invilr</span>(<span class='no'>a</span>)
+<span class='fu'>length</span>(<span class='no'>b</span>) <span class='co'># Four elements</span></div><div class='output co'>#&gt; [1] 4
+#&gt; </div><div class='input'><span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'>sum</span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>]))) <span class='co'># Gives c(0.1, 0.3, 0.5)</span></div><div class='output co'>#&gt; [1] 0.1 0.3 0.5
+#&gt; </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="#see-also">See also</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+ René Lehmann and Johannes Ranke
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
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+</html>
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+ <h1>Function reference</h1>
+ <h4>version&nbsp;0.9.44.9000</h4>
+ </div>
+
+ <div class="contents">
+ <h2 id="section-main-functions" class="hasAnchor"><a href="#section-main-functions" class="anchor"></a>Main functions</h2>
+ <p class="section-desc"><p>Essential functionality</p></p>
+
+ <p><a href="mkinfit.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkinfit.html">mkinfit</a></code></li>
+ </ul>
+ <p><a href="mkinmod.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkinmod.html">mkinmod</a></code></li>
+ </ul>
+ <p><a href="mmkin.html">
+</a></p>
+ <ul>
+ <li><code><a href="mmkin.html">mmkin</a></code></li>
+ </ul>
+ <h2 id="section-show-results" class="hasAnchor"><a href="#section-show-results" class="anchor"></a>Show results</h2>
+ <p class="section-desc"><p>Functions working with mkinfit objects</p></p>
+
+ <p><a href="endpoints.html">
+</a></p>
+ <ul>
+ <li><code><a href="endpoints.html">endpoints</a></code></li>
+ </ul>
+ <p><a href="mkinerrmin.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkinerrmin.html">mkinerrmin</a></code></li>
+ </ul>
+ <p><a href="mkinparplot.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkinparplot.html">mkinparplot</a></code></li>
+ </ul>
+ <p><a href="mkinresplot.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkinresplot.html">mkinresplot</a></code></li>
+ </ul>
+ <p><a href="plot.mkinfit.html">
+</a></p>
+ <ul>
+ <li><code><a href="plot.mkinfit.html">plot.mkinfit</a></code></li><li><code><a href="plot.mkinfit.html">plot_sep</a></code></li>
+ </ul>
+ <p><a href="summary.mkinfit.html">
+</a></p>
+ <ul>
+ <li><code><a href="summary.mkinfit.html">summary.mkinfit</a></code></li><li><code><a href="summary.mkinfit.html">print.summary.mkinfit</a></code></li>
+ </ul>
+ <h2 id="section-work-with-mmkin-objects" class="hasAnchor"><a href="#section-work-with-mmkin-objects" class="anchor"></a>Work with mmkin objects</h2>
+ <p class="section-desc"><p>Functions working with aggregated results</p></p>
+
+ <p><a href="Extract.mmkin.html">Subsetting method for mmkin objects</a></p>
+ <ul>
+ <li><code><a href="Extract.mmkin.html">[.mmkin</a></code></li>
+ </ul>
+ <p><a href="plot.mmkin.html">
+</a></p>
+ <ul>
+ <li><code><a href="plot.mmkin.html">plot.mmkin</a></code></li>
+ </ul>
+ <h2 id="section-datasets-and-known-results" class="hasAnchor"><a href="#section-datasets-and-known-results" class="anchor"></a>Datasets and known results</h2>
+ <p class="section-desc"></p>
+
+ <p><a href="FOCUS_2006_DFOP_ref_A_to_B.html">
+</a></p>
+ <ul>
+ <li><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code></li>
+ </ul>
+ <p><a href="FOCUS_2006_FOMC_ref_A_to_F.html">
+</a></p>
+ <ul>
+ <li><code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code></li>
+ </ul>
+ <p><a href="FOCUS_2006_HS_ref_A_to_F.html">
+</a></p>
+ <ul>
+ <li><code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code></li>
+ </ul>
+ <p><a href="FOCUS_2006_SFO_ref_A_to_F.html">
+</a></p>
+ <ul>
+ <li><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code></li>
+ </ul>
+ <p><a href="mccall81_245T.html">
+</a></p>
+ <ul>
+ <li><code><a href="mccall81_245T.html">mccall81_245T</a></code></li>
+ </ul>
+ <p><a href="schaefer07_complex_case.html">
+</a></p>
+ <ul>
+ <li><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code></li><li><code><a href="schaefer07_complex_case.html">schaefer07_complex_results</a></code></li>
+ </ul>
+ <p><a href="synthetic_data_for_UBA.html">
+</a></p>
+ <ul>
+ <li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li>
+ </ul>
+ <h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2>
+ <p class="section-desc"></p>
+
+ <p><a href="geometric_mean.html"> Calculate the geometric mean </a></p>
+ <ul>
+ <li><code><a href="geometric_mean.html">geometric_mean</a></code></li>
+ </ul>
+ <p><a href="ilr.html">
+</a></p>
+ <ul>
+ <li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li>
+ </ul>
+ <p><a href="mkin_long_to_wide.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li>
+ </ul>
+ <p><a href="mkinpredict.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkinpredict.html">mkinpredict</a></code></li>
+ </ul>
+ <p><a href="mkinsub.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkinsub.html">mkinsub</a></code></li>
+ </ul>
+ <p><a href="mkin_wide_to_long.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li>
+ </ul>
+ <p><a href="print.mkinmod.html">
+</a></p>
+ <ul>
+ <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li>
+ </ul>
+ <p><a href="transform_odeparms.html">
+</a></p>
+ <ul>
+ <li><code><a href="transform_odeparms.html">transform_odeparms</a></code></li><li><code><a href="transform_odeparms.html">backtransform_odeparms</a></code></li>
+ </ul>
+ <h2 id="section-analytical-solutions" class="hasAnchor"><a href="#section-analytical-solutions" class="anchor"></a>Analytical solutions</h2>
+ <p class="section-desc"><p>Parent only model solutions</p></p>
+
+ <p><a href="DFOP.solution.html">
+</a></p>
+ <ul>
+ <li><code><a href="DFOP.solution.html">DFOP.solution</a></code></li>
+ </ul>
+ <p><a href="FOMC.solution.html"> First-Order Multi-Compartment kinetics </a></p>
+ <ul>
+ <li><code><a href="FOMC.solution.html">FOMC.solution</a></code></li>
+ </ul>
+ <p><a href="HS.solution.html"> Hockey-Stick kinetics </a></p>
+ <ul>
+ <li><code><a href="HS.solution.html">HS.solution</a></code></li>
+ </ul>
+ <p><a href="IORE.solution.html"> Indeterminate order rate equation kinetics </a></p>
+ <ul>
+ <li><code><a href="IORE.solution.html">IORE.solution</a></code></li>
+ </ul>
+ <p><a href="SFORB.solution.html"> Single First-Order Reversible Binding kinetics </a></p>
+ <ul>
+ <li><code><a href="SFORB.solution.html">SFORB.solution</a></code></li>
+ </ul>
+ <h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2>
+ <p class="section-desc"><p>Functions that have been superseeded</p></p>
+
+ <p><a href="mkinplot.html">
+</a></p>
+ <ul>
+ <li><code><a href="mkinplot.html">mkinplot</a></code></li>
+ </ul>
+
+ </div>
+ </div>
+
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#section-main-functions">Main functions</a></li>
+ <li><a href="#section-show-results">Show results</a></li>
+ <li><a href="#section-work-with-mmkin-objects">Work with mmkin objects</a></li>
+ <li><a href="#section-datasets-and-known-results">Datasets and known results</a></li>
+ <li><a href="#section-helper-functions">Helper functions</a></li>
+ <li><a href="#section-analytical-solutions">Analytical solutions</a></li>
+ <li><a href="#section-deprecated-functions">Deprecated functions</a></li>
+ </ul>
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
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+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
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+</html>
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+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>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.</p>
+
+
+ <pre><span class='no'>mccall81_245T</span></pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>A dataframe containing the following variables.
+ <dl class='dl-horizontal'>
+ <dt><code>name</code></dt><dd>the name of the compound observed. Note that T245 is used as
+ an acronym for 2,4,5-T. T245 is a legitimate object name
+ in R, which is necessary for specifying models using
+ <code><a href='mkinmod.html'>mkinmod</a></code>.</dd>
+ <dt><code>time</code></dt><dd>a numeric vector containing sampling times in days after
+ treatment</dd>
+ <dt><code>value</code></dt><dd>a numeric vector containing concentrations in percent of applied radioactivity</dd>
+ <dt><code>soil</code></dt><dd>a factor containing the name of the soil</dd>
+ </dl></p>
+
+ <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>
+
+
+ <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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'>## Not run: ------------------------------------</span>
+<span class='co'># fit.1 &lt;- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span>
+<span class='co'># summary(fit.1, data = FALSE)</span>
+<span class='co'># </span>
+<span class='co'>## ---------------------------------------------</span>
+ <span class='co'># No covariance matrix and 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: 0.9.44.9000
+#&gt; R version: 3.3.1
+#&gt; Date of fit: Wed Oct 26 23:50:40 2016
+#&gt; Date of summary: Wed Oct 26 23:50:40 2016
+#&gt;
+#&gt; Equations:
+#&gt; d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
+#&gt; d_phenol = + k_T245_phenol * T245 - k_phenol_sink * phenol -
+#&gt; k_phenol_anisole * phenol
+#&gt; d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 246 model solutions performed in 1.43 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_anisole 0.1002 deparm
+#&gt; k_anisole_sink 0.1003 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_anisole -2.300587 -Inf Inf
+#&gt; log_k_anisole_sink -2.299590 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; phenol_0 0 state
+#&gt; anisole_0 0 state
+#&gt; k_phenol_sink 0 deparm
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; T245_0 103.9000 2.35200 98.930 108.8000
+#&gt; log_k_T245_sink -4.1130 0.13250 -4.390 -3.8350
+#&gt; log_k_T245_phenol -3.6120 0.05002 -3.716 -3.5070
+#&gt; log_k_phenol_anisole -0.9037 0.30580 -1.544 -0.2637
+#&gt; log_k_anisole_sink -5.0090 0.11180 -5.243 -4.7750
+#&gt;
+#&gt; Parameter correlation:
+#&gt; T245_0 log_k_T245_sink log_k_T245_phenol
+#&gt; T245_0 1.00000 0.63761 -0.1742
+#&gt; log_k_T245_sink 0.63761 1.00000 -0.3831
+#&gt; log_k_T245_phenol -0.17416 -0.38313 1.0000
+#&gt; log_k_phenol_anisole -0.05948 0.08745 -0.3047
+#&gt; log_k_anisole_sink -0.16208 -0.60469 0.5227
+#&gt; log_k_phenol_anisole log_k_anisole_sink
+#&gt; T245_0 -0.05948 -0.1621
+#&gt; log_k_T245_sink 0.08745 -0.6047
+#&gt; log_k_T245_phenol -0.30470 0.5227
+#&gt; log_k_phenol_anisole 1.00000 -0.1774
+#&gt; log_k_anisole_sink -0.17744 1.0000
+#&gt;
+#&gt; Residual standard error: 2.706 on 19 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 44.160 6.462e-21 98.930000 108.80000
+#&gt; k_T245_sink 1.636e-02 7.545 1.978e-07 0.012400 0.02159
+#&gt; k_T245_phenol 2.701e-02 19.990 1.607e-14 0.024320 0.02999
+#&gt; k_phenol_anisole 4.051e-01 3.270 2.014e-03 0.213600 0.76820
+#&gt; k_anisole_sink 6.679e-03 8.942 1.544e-08 0.005285 0.00844
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 9.831 5 17
+#&gt; T245 7.908 3 5
+#&gt; phenol 99.808 1 6
+#&gt; anisole 5.379 1 6
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; T245_sink 0.3772
+#&gt; T245_phenol 0.6228
+#&gt; phenol_anisole 1.0000
+#&gt; phenol_sink 0.0000
+#&gt; anisole_sink 1.0000
+#&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
+#&gt; </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="#format">Format</a></li>
+
+ <li><a href="#source">Source</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
new file mode 100644
index 00000000..cc50bf7d
--- /dev/null
+++ b/docs/reference/mkin_long_to_wide.html
@@ -0,0 +1,170 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
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+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
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+ <div id="navbar" class="navbar-collapse collapse">
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+ <a href="../reference/index.html">Reference</a>
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+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>This function takes a dataframe in the long form as required by <code>modCost</code>
+ and converts it into a dataframe with one independent variable and several
+ dependent variables as columns.</p>
+
+
+ <pre><span class='fu'>mkin_long_to_wide</span>(<span class='no'>long_data</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>, <span class='kw'>outtime</span> <span class='kw'>=</span> <span class='st'>"time"</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>long_data</dt>
+ <dd>
+ The dataframe must contain one variable called &quot;time&quot; with the time values specified by the
+ <code>time</code> argument, one column called &quot;name&quot; with the grouping of the observed values, and
+ finally one column of observed values called &quot;value&quot;.
+</dd>
+ <dt>time</dt>
+ <dd>
+ The name of the time variable in the long input data.
+</dd>
+ <dt>outtime</dt>
+ <dd>
+ The name of the time variable in the wide output data.
+</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Dataframe in wide format.</p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='fu'>mkin_long_to_wide</span>(<span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; time parent m1
+#&gt; 1 0 99.46 0.00
+#&gt; 2 0 102.04 0.00
+#&gt; 3 1 93.50 4.84
+#&gt; 4 1 92.50 5.64
+#&gt; 5 3 63.23 12.91
+#&gt; 6 3 68.99 12.96
+#&gt; 7 7 52.32 22.97
+#&gt; 8 7 55.13 24.47
+#&gt; 9 14 27.27 41.69
+#&gt; 10 14 26.64 33.21
+#&gt; 11 21 11.50 44.37
+#&gt; 12 21 11.64 46.44
+#&gt; 13 35 2.85 41.22
+#&gt; 14 35 2.91 37.95
+#&gt; 15 50 0.69 41.19
+#&gt; 16 50 0.63 40.01
+#&gt; 17 75 0.05 40.09
+#&gt; 18 75 0.06 33.85
+#&gt; 19 100 NA 31.04
+#&gt; 20 100 NA 33.13
+#&gt; 21 120 NA 25.15
+#&gt; 22 120 NA 33.31
+#&gt; </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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
new file mode 100644
index 00000000..bce6d6a4
--- /dev/null
+++ b/docs/reference/mkin_wide_to_long.html
@@ -0,0 +1,149 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
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+ — mkin_wide_to_long • mkin</title>
+
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+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
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+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
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+
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+
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+ </div><!--/.nav-collapse -->
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+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>This function simply takes a dataframe with one independent variable and several
+ dependent variable and converts it into the long form as required by <code>modCost</code>.</p>
+
+
+ <pre><span class='fu'>mkin_wide_to_long</span>(<span class='no'>wide_data</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"t"</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>wide_data</dt>
+ <dd>
+ The dataframe must contain one variable with the time values specified by the
+ <code>time</code> argument and usually more than one column of observed values.
+</dd>
+ <dt>time</dt>
+ <dd>
+ The name of the time variable.
+</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Dataframe in long format as needed for <code>modCost</code>.</p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='no'>wide</span> <span class='kw'>&lt;-</span> <span class='fu'>data.frame</span>(<span class='kw'>t</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>2</span>,<span class='fl'>3</span>), <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>4</span>,<span class='fl'>7</span>), <span class='kw'>y</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>3</span>,<span class='fl'>4</span>,<span class='fl'>5</span>))
+<span class='fu'>mkin_wide_to_long</span>(<span class='no'>wide</span>)</div><div class='output co'>#&gt; name time value
+#&gt; 1 x 1 1
+#&gt; 2 x 2 4
+#&gt; 3 x 3 7
+#&gt; 4 y 1 3
+#&gt; 5 y 2 4
+#&gt; 6 y 3 5
+#&gt; </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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
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+</html>
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
new file mode 100644
index 00000000..e5d99fd5
--- /dev/null
+++ b/docs/reference/mkinds.html
@@ -0,0 +1,136 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
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+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
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+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>A dataset class for mkin</h1>
+ </div>
+
+
+ <p>A dataset class for mkin</p>
+
+
+ <pre><span class='no'>mkinds</span></pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>An <code>R6Class</code> generator object.</p>
+
+ <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2>
+
+ <p></p>
+ <p><dl class='dl-horizontal'>
+<dt><code>title</code></dt><dd>A full title for the dataset</dd></p>
+ <p><dt><code>sampling</code></dt><dd>times The sampling times</dd></p>
+ <p><dt><code>time_unit</code></dt><dd>The time unit</dd></p>
+ <p><dt><code>observed</code></dt><dd>Names of the observed compounds</dd></p>
+ <p><dt><code>unit</code></dt><dd>The unit of the observations</dd></p>
+ <p><dt><code>replicates</code></dt><dd>The number of replicates</dd></p>
+ <p><dt><code>data</code></dt><dd>A dataframe with at least the columns name, time and value
+in order to be compatible with mkinfit</dd>
+</dl></p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='no'>mds</span> <span class='kw'>&lt;-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>)</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="#format">Format</a></li>
+
+ <li><a href="#fields">Fields</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
new file mode 100644
index 00000000..5b437b08
--- /dev/null
+++ b/docs/reference/mkinerrmin.html
@@ -0,0 +1,168 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>
+ — mkinerrmin • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
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+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+
+<!-- Font Awesome icons -->
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+
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+
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>This function uses <code>optimize</code> in order to iteratively find the
+smallest relative error still resulting in passing the chi-squared test
+as defined in the FOCUS kinetics report from 2006.</p>
+
+
+ <pre><span class='fu'>mkinerrmin</span>(<span class='no'>fit</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>fit</dt>
+ <dd>
+ an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.
+ </dd>
+ <dt>alpha</dt>
+ <dd>
+ The confidence level chosen for the chi-squared test.
+</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A dataframe with the following components:</p>
+ <p>The dataframe has one row for the total dataset and one further row for
+ each observed state variable in the model.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>This function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</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</span> <span class='kw'>=</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'>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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'>
+<span class='no'>fit_FOCUS_D</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_D</span>), <span class='fl'>4</span>)</div><div class='output co'>#&gt; err.min n.optim df
+#&gt; All data 0.0640 4 15
+#&gt; parent 0.0646 2 7
+#&gt; m1 0.0469 2 8
+#&gt; </div><div class='input'><span class='no'>fit_FOCUS_E</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_E</span>), <span class='fl'>4</span>)</div><div class='output co'>#&gt; err.min n.optim df
+#&gt; All data 0.1544 4 13
+#&gt; parent 0.1659 2 7
+#&gt; m1 0.1095 2 6
+#&gt; </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="#details">Details</a></li>
+
+ <li><a href="#references">References</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
new file mode 100644
index 00000000..6bfb9352
--- /dev/null
+++ b/docs/reference/mkinfit.html
@@ -0,0 +1,549 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>
+ — mkinfit • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
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+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- 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">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>This function uses the Flexible Modelling Environment package
+ <code>FME</code> 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 <code>nlminb</code>,
+ 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 <code><a href='mkinpredict.html'>mkinpredict</a></code>. The variance of the residuals for each
+ observed variable can optionally be iteratively reweighted until convergence
+ using the argument <code>reweight.method = &quot;obs&quot;</code>.</p>
+
+
+ <pre><span class='fu'>mkinfit</span>(<span class='no'>mkinmod</span>, <span class='no'>observed</span>,
+ <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>state.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>fixed_initials</span> <span class='kw'>=</span> <span class='fu'>names</span>(<span class='no'>mkinmod</span>$<span class='no'>diffs</span>)[-<span class='fl'>1</span>],
+ <span class='kw'>from_max_mean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"auto"</span>, <span class='st'>"analytical"</span>, <span class='st'>"eigen"</span>, <span class='st'>"deSolve"</span>),
+ <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>,
+ <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Port"</span>, <span class='st'>"Marq"</span>, <span class='st'>"SANN"</span>, <span class='st'>"Nelder-Mead"</span>, <span class='st'>"BFGS"</span>, <span class='st'>"CG"</span>, <span class='st'>"L-BFGS-B"</span>),
+ <span class='kw'>maxit.modFit</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>control.modFit</span> <span class='kw'>=</span> <span class='fu'>list</span>(),
+ <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>plot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"none"</span>,
+ <span class='kw'>scaleVar</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>,
+ <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+ <span class='kw'>reweight.tol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>reweight.max.iter</span> <span class='kw'>=</span> <span class='fl'>10</span>,
+ <span class='kw'>trace_parms</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>mkinmod</dt>
+ <dd>
+ A list of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the kinetic model to be
+ fitted to the data, or one of the shorthand names (&quot;SFO&quot;, &quot;FOMC&quot;, &quot;DFOP&quot;,
+ &quot;HS&quot;, &quot;SFORB&quot;). If a shorthand name is given, a parent only degradation
+ model is generated for the variable with the highest value in
+ <code>observed</code>.
+ </dd>
+ <dt>observed</dt>
+ <dd>
+ The observed data. It has to be in the long format as described in
+ <code>modFit</code>, i.e. the first column called &quot;name&quot; must contain the
+ name of the observed variable for each data point. The second column must
+ contain the times of observation, named &quot;time&quot;. The third column must be
+ named &quot;value&quot; and contain the observed values. Optionally, a further column
+ can contain weights for each data point. Its name must be passed as a
+ further argument named <code>err</code> which is then passed on to
+ <code>modFit</code>.
+ </dd>
+ <dt>parms.ini</dt>
+ <dd>
+ A named vector of initial values for the parameters, including parameters
+ to be optimised and potentially also fixed parameters as indicated by
+ <code>fixed_parms</code>. If set to &quot;auto&quot;, initial values for rate constants
+ are set to default values. Using parameter names that are not in the model
+ gives an error.
+
+ It is possible to only specify a subset of the parameters that the model
+ needs. You can use the parameter lists &quot;bparms.ode&quot; from a previously
+ fitted model, which contains the differential equation parameters from this
+ model. This works nicely if the models are nested. An example is given
+ below.
+ </dd>
+ <dt>state.ini</dt>
+ <dd>
+ A named vector of initial values for the state variables of the model. In
+ case the observed variables are represented by more than one model
+ variable, the names will differ from the names of the observed variables
+ (see <code>map</code> component of <code><a href='mkinmod.html'>mkinmod</a></code>). The default is to set
+ the initial value of the first model variable to the mean of the time zero
+ values for the variable with the maximum observed value, and all others to 0.
+ If this variable has no time zero observations, its initial value is set to 100.
+ </dd>
+ <dt>fixed_parms</dt>
+ <dd>
+ The names of parameters that should not be optimised but rather kept at the
+ values specified in <code>parms.ini</code>.
+ </dd>
+ <dt>fixed_initials</dt>
+ <dd>
+ The names of model variables for which the initial state at time 0 should
+ be excluded from the optimisation. Defaults to all state variables except
+ for the first one.
+ </dd>
+ <dt>from_max_mean</dt>
+ <dd>
+ If this is set to TRUE, and the model has only one observed variable, then
+ data before the time of the maximum observed value (after averaging for each
+ sampling time) are discarded, and this time is subtracted from all
+ remaining time values, so the time of the maximum observed mean value is
+ the new time zero.
+ </dd>
+ <dt>solution_type</dt>
+ <dd>
+ If set to &quot;eigen&quot;, the solution of the system of differential equations is
+ based on the spectral decomposition of the coefficient matrix in cases that
+ this is possible. If set to &quot;deSolve&quot;, a numerical ode solver from package
+ <code>deSolve</code> is used. If set to &quot;analytical&quot;, an analytical
+ solution of the model is used. This is only implemented for simple
+ degradation experiments with only one state variable, i.e. with no
+ metabolites. The default is &quot;auto&quot;, which uses &quot;analytical&quot; if possible,
+ otherwise &quot;eigen&quot; if the model can be expressed using eigenvalues and
+ eigenvectors, and finally &quot;deSolve&quot; for the remaining models (time
+ dependence of degradation rates and metabolites). This argument is passed
+ on to the helper function <code><a href='mkinpredict.html'>mkinpredict</a></code>.
+ </dd>
+ <dt>method.ode</dt>
+ <dd>
+ The solution method passed via <code><a href='mkinpredict.html'>mkinpredict</a></code> to
+ <code>ode</code> in case the solution type is &quot;deSolve&quot;. The default
+ &quot;lsoda&quot; is performant, but sometimes fails to converge.
+ </dd>
+ <dt>use_compiled</dt>
+ <dd>
+ If set to <code>FALSE</code>, no compiled version of the <code><a href='mkinmod.html'>mkinmod</a></code>
+ model is used, in the calls to <code><a href='mkinpredict.html'>mkinpredict</a></code> even if
+ a compiled verion is present.
+ </dd>
+ <dt>method.modFit</dt>
+ <dd>
+ The optimisation method passed to <code>modFit</code>.
+
+ In order to optimally deal with problems where local minima occur, the
+ &quot;Port&quot; algorithm is now used per default as it is less prone to get trapped
+ in local minima and depends less on starting values for parameters than
+ the Levenberg Marquardt variant selected by &quot;Marq&quot;. However, &quot;Port&quot; needs
+ more iterations.
+
+ The former default &quot;Marq&quot; is the Levenberg Marquardt algorithm
+ <code>nls.lm</code> from the package <code>minpack.lm</code> and usually needs
+ the least number of iterations.
+
+ The &quot;Pseudo&quot; algorithm is not included because it needs finite parameter bounds
+ which are currently not supported.
+
+ The &quot;Newton&quot; algorithm is not included because its number of iterations
+ can not be controlled by <code>control.modFit</code> and it does not appear
+ to provide advantages over the other algorithms.
+ </dd>
+ <dt>maxit.modFit</dt>
+ <dd>
+ Maximum number of iterations in the optimisation. If not &quot;auto&quot;, this will
+ be passed to the method called by <code>modFit</code>, overriding
+ what may be specified in the next argument <code>control.modFit</code>.
+ </dd>
+ <dt>control.modFit</dt>
+ <dd>
+ Additional arguments passed to the optimisation method used by
+ <code>modFit</code>.
+ </dd>
+ <dt>transform_rates</dt>
+ <dd>
+ Boolean specifying if kinetic rate constants should be transformed in the
+ model specification used in the fitting for better compliance with the
+ assumption of normal distribution of the estimator. If TRUE, also
+ alpha and beta parameters of the FOMC model are log-transformed, as well
+ as k1 and k2 rate constants for the DFOP and HS models and the break point
+ tb of the HS model.
+ If FALSE, zero is used as a lower bound for the rates in the optimisation.
+ </dd>
+ <dt>transform_fractions</dt>
+ <dd>
+ Boolean specifying if formation fractions constants should be transformed in the
+ model specification used in the fitting for better compliance with the
+ assumption of normal distribution of the estimator. The default (TRUE) is
+ to do transformations. If TRUE, the g parameter of the DFOP and HS
+ models are also transformed, as they can also be seen as compositional
+ data. The transformation used for these transformations is the
+ <code><a href='ilr.html'>ilr</a></code> transformation.
+ </dd>
+ <dt>plot</dt>
+ <dd>
+ Should the observed values and the numerical solutions be plotted at each
+ stage of the optimisation?
+ </dd>
+ <dt>quiet</dt>
+ <dd>
+ Suppress printing out the current model cost after each improvement?
+ </dd>
+ <dt>err </dt>
+ <dd>either <code>NULL</code>, or the name of the column with the
+ <em>error</em> estimates, used to weigh the residuals (see details of
+ <code>modCost</code>); if <code>NULL</code>, then the residuals are not weighed.
+ </dd>
+ <dt>weight</dt>
+ <dd>
+ only if <code>err</code>=<code>NULL</code>: how to weight the residuals, one of &quot;none&quot;,
+ &quot;std&quot;, &quot;mean&quot;, see details of <code>modCost</code>.
+ </dd>
+ <dt>scaleVar</dt>
+ <dd>
+ Will be passed to <code>modCost</code>. Default is not to scale Variables
+ according to the number of observations.
+ </dd>
+ <dt>atol</dt>
+ <dd>
+ Absolute error tolerance, passed to <code>ode</code>. Default is 1e-8,
+ lower than in <code>lsoda</code>.
+ </dd>
+ <dt>rtol</dt>
+ <dd>
+ Absolute error tolerance, passed to <code>ode</code>. Default is 1e-10,
+ much lower than in <code>lsoda</code>.
+ </dd>
+ <dt>n.outtimes</dt>
+ <dd>
+ The length of the dataseries that is produced by the model prediction
+ function <code><a href='mkinpredict.html'>mkinpredict</a></code>. This impacts the accuracy of
+ the numerical solver if that is used (see <code>solution_type</code> argument.
+ The default value is 100.
+ </dd>
+ <dt>reweight.method</dt>
+ <dd>
+ The method used for iteratively reweighting residuals, also known
+ as iteratively reweighted least squares (IRLS). Default is NULL,
+ the other method implemented is called &quot;obs&quot;, meaning that each
+ observed variable is assumed to have its own variance, this is
+ estimated from the fit and used for weighting the residuals
+ in each iteration until convergence of this estimate up to
+ <code>reweight.tol</code> or up to the maximum number of iterations
+ specified by <code>reweight.max.iter</code>.
+ </dd>
+ <dt>reweight.tol</dt>
+ <dd>
+ Tolerance for convergence criterion for the variance components
+ in IRLS fits.
+ </dd>
+ <dt>reweight.max.iter</dt>
+ <dd>
+ Maximum iterations in IRLS fits.
+ </dd>
+ <dt>trace_parms</dt>
+ <dd>
+ Should a trace of the parameter values be listed?
+ </dd>
+ <dt>&amp;#8230;</dt>
+ <dd>
+ Further arguments that will be passed to <code>modFit</code>.
+ </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A list with &quot;mkinfit&quot; and &quot;modFit&quot; in the class attribute.
+ A summary can be obtained by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
+
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and
+ <code><a href='mkinparplot.html'>mkinparplot</a></code>.</p>
+ <p>Fitting of several models to several datasets in a single call to
+ <code><a href='mmkin.html'>mmkin</a></code>.</p>
+
+ <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+ <p>The implementation of iteratively reweighted least squares is inspired by the
+ work of the KinGUII team at Bayer Crop Science (Walter Schmitt and Zhenglei
+ Gao). A similar implemention can also be found in CAKE 2.0, which is the
+ other GUI derivative of mkin, sponsored by Syngenta.</p>
+
+ <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+ <p>When using the &quot;IORE&quot; submodel for metabolites, fitting with
+ &quot;transform_rates = TRUE&quot; (the default) often leads to failures of the
+ numerical ODE solver. In this situation it may help to switch off the
+ internal rate transformation.</p>
+
+
+ <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: 0.9.44.9000
+#&gt; R version: 3.3.1
+#&gt; Date of fit: Wed Oct 26 23:50:42 2016
+#&gt; Date of summary: Wed Oct 26 23:50:42 2016
+#&gt;
+#&gt; Equations:
+#&gt; d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
+#&gt;
+#&gt; Model predictions using solution type analytical
+#&gt;
+#&gt; Fitted with method Port using 64 model solutions performed in 0.168 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 85.1 state
+#&gt; alpha 1.0 deparm
+#&gt; beta 10.0 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 85.100000 -Inf Inf
+#&gt; log_alpha 0.000000 -Inf Inf
+#&gt; log_beta 2.302585 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; None
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 85.87000 2.2460 80.38000 91.3700
+#&gt; log_alpha 0.05192 0.1605 -0.34080 0.4446
+#&gt; log_beta 0.65100 0.2801 -0.03452 1.3360
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_alpha log_beta
+#&gt; parent_0 1.0000 -0.2033 -0.3624
+#&gt; log_alpha -0.2033 1.0000 0.9547
+#&gt; log_beta -0.3624 0.9547 1.0000
+#&gt;
+#&gt; Residual standard error: 2.275 on 6 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 85.870 38.230 1.069e-08 80.3800 91.370
+#&gt; alpha 1.053 6.231 3.953e-04 0.7112 1.560
+#&gt; beta 1.917 3.570 5.895e-03 0.9661 3.806
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.657 3 6
+#&gt; parent 6.657 3 6
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90 DT50back
+#&gt; parent 1.785 15.15 4.56
+#&gt;
+#&gt; Data:
+#&gt; time variable observed predicted residual
+#&gt; 0 parent 85.1 85.875 -0.7749
+#&gt; 1 parent 57.9 55.191 2.7091
+#&gt; 3 parent 29.9 31.845 -1.9452
+#&gt; 7 parent 14.6 17.012 -2.4124
+#&gt; 14 parent 9.7 9.241 0.4590
+#&gt; 28 parent 6.6 4.754 1.8460
+#&gt; 63 parent 4.0 2.102 1.8977
+#&gt; 91 parent 3.9 1.441 2.4590
+#&gt; 119 parent 0.6 1.092 -0.4919
+#&gt; </div><div class='input'>
+<span class='co'># One parent compound, one metabolite, both single first order.</span>
+<span class='co'># Use mkinsub for convenience in model formulation. Pathway to sink included per default.</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'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
+<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; user system elapsed
+#&gt; 1.272 1.204 0.943
+#&gt; </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 99.59848 -3.03822 -2.98030 -5.24750
+#&gt; </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
+#&gt; parent_sink parent_m1 m1_sink
+#&gt; 0.485524 0.514476 1.000000
+#&gt;
+#&gt; $SFORB
+#&gt; logical(0)
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90
+#&gt; parent 7.022929 23.32967
+#&gt; m1 131.760712 437.69961
+#&gt;
+#&gt; </div><div class='input'><span class='co'>## Not run: ------------------------------------</span>
+<span class='co'># # deSolve is slower when no C compiler (gcc) was available during model generation</span>
+<span class='co'># print(system.time(fit.deSolve &lt;- mkinfit(SFO_SFO, FOCUS_2006_D, </span>
+<span class='co'># solution_type = "deSolve")))</span>
+<span class='co'># coef(fit.deSolve)</span>
+<span class='co'># endpoints(fit.deSolve)</span>
+<span class='co'>## ---------------------------------------------</span>
+
+<span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC</span>
+<span class='co'>## Not run: ------------------------------------</span>
+<span class='co'># FOMC_SFO &lt;- mkinmod(</span>
+<span class='co'># parent = mkinsub("FOMC", "m1"),</span>
+<span class='co'># m1 = mkinsub("SFO"))</span>
+<span class='co'># # Fit the model to the FOCUS example dataset D using defaults</span>
+<span class='co'># fit.FOMC_SFO &lt;- mkinfit(FOMC_SFO, FOCUS_2006_D)</span>
+<span class='co'># # Use starting parameters from parent only FOMC fit</span>
+<span class='co'># fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, plot=TRUE)</span>
+<span class='co'># fit.FOMC_SFO &lt;- mkinfit(FOMC_SFO, FOCUS_2006_D, </span>
+<span class='co'># parms.ini = fit.FOMC$bparms.ode, plot=TRUE)</span>
+<span class='co'># </span>
+<span class='co'># # Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span>
+<span class='co'># SFORB_SFO &lt;- mkinmod(</span>
+<span class='co'># parent = list(type = "SFORB", to = "m1", sink = TRUE),</span>
+<span class='co'># m1 = list(type = "SFO"))</span>
+<span class='co'># # Fit the model to the FOCUS example dataset D using defaults</span>
+<span class='co'># fit.SFORB_SFO &lt;- mkinfit(SFORB_SFO, FOCUS_2006_D)</span>
+<span class='co'># fit.SFORB_SFO.deSolve &lt;- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve")</span>
+<span class='co'># # Use starting parameters from parent only SFORB fit (not really needed in this case)</span>
+<span class='co'># fit.SFORB = mkinfit("SFORB", FOCUS_2006_D)</span>
+<span class='co'># fit.SFORB_SFO &lt;- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode)</span>
+<span class='co'>## ---------------------------------------------</span>
+
+<span class='co'>## Not run: ------------------------------------</span>
+<span class='co'># # Weighted fits, including IRLS</span>
+<span class='co'># SFO_SFO.ff &lt;- mkinmod(parent = mkinsub("SFO", "m1"),</span>
+<span class='co'># m1 = mkinsub("SFO"), use_of_ff = "max")</span>
+<span class='co'># f.noweight &lt;- mkinfit(SFO_SFO.ff, FOCUS_2006_D)</span>
+<span class='co'># summary(f.noweight)</span>
+<span class='co'># f.irls &lt;- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs")</span>
+<span class='co'># summary(f.irls)</span>
+<span class='co'># f.w.mean &lt;- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean")</span>
+<span class='co'># summary(f.w.mean)</span>
+<span class='co'># f.w.value &lt;- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value")</span>
+<span class='co'># summary(f.w.value)</span>
+<span class='co'>## ---------------------------------------------</span>
+
+<span class='co'>## Not run: ------------------------------------</span>
+<span class='co'># # Manual weighting</span>
+<span class='co'># dw &lt;- FOCUS_2006_D</span>
+<span class='co'># errors &lt;- c(parent = 2, m1 = 1)</span>
+<span class='co'># dw$err.man &lt;- errors[FOCUS_2006_D$name]</span>
+<span class='co'># f.w.man &lt;- mkinfit(SFO_SFO.ff, dw, err = "err.man")</span>
+<span class='co'># summary(f.w.man)</span>
+<span class='co'># f.w.man.irls &lt;- mkinfit(SFO_SFO.ff, dw, err = "err.man",</span>
+<span class='co'># reweight.method = "obs")</span>
+<span class='co'># summary(f.w.man.irls)</span>
+<span class='co'>## ---------------------------------------------</span></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="#see-also">See also</a></li>
+
+ <li><a href="#note">Note</a></li>
+
+ <li><a href="#note">Note</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, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
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+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>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.</p>
+
+ <p>For the definition of model types and their parameters, the equations given
+ in the FOCUS and NAFTA guidance documents are used.</p>
+
+
+ <pre><span class='fu'>mkinmod</span>(<span class='no'>...</span>, <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>, <span class='kw'>speclist</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>...</dt>
+ <dd>
+ For each observed variable, a list has to be specified as an argument, containing
+ at least a component <code>type</code>, specifying the type of kinetics to use
+ for the variable. Currently, single first order kinetics &quot;SFO&quot;,
+ indeterminate order rate equation kinetics &quot;IORE&quot;, or
+ single first order with reversible binding &quot;SFORB&quot; are implemented for all
+ variables, while
+ &quot;FOMC&quot;, &quot;DFOP&quot; and &quot;HS&quot; can additionally be chosen for the first
+ variable which is assumed to be the source compartment.
+ Additionally, each component of the list can include a character vector <code>to</code>,
+ specifying names of variables to which a transfer is to be assumed in the
+ model.
+ If the argument <code>use_of_ff</code> is set to &quot;min&quot; (default) and the model for
+ the compartment is &quot;SFO&quot; or &quot;SFORB&quot;, an additional component of the list
+ can be &quot;sink=FALSE&quot; effectively fixing the flux to sink to zero.
+ </dd>
+ <dt>use_of_ff</dt>
+ <dd>
+ Specification of the use of formation fractions in the model equations and, if
+ applicable, the coefficient matrix. If &quot;min&quot;, a minimum use of formation
+ fractions is made in order to avoid fitting the product of formation fractions
+ and rate constants. If &quot;max&quot;, formation fractions are always used.
+ </dd>
+ <dt>speclist</dt>
+ <dd>
+ The specification of the observed variables and their submodel types and
+ pathways can be given as a single list using this argument. Default is NULL.
+ </dd>
+ <dt>quiet</dt>
+ <dd>
+ Should messages be suppressed?
+ </dd>
+ <dt>verbose</dt>
+ <dd>
+ If <code>TRUE</code>, passed to <code>cfunction</code> if applicable to give
+ detailed information about the C function being built.
+ </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A list of class <code>mkinmod</code> for use with <code><a href='mkinfit.html'>mkinfit</a></code>, containing</p>
+
+ <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+ <p>The IORE submodel is not well tested (yet). When using this model for metabolites,
+ you may want to read the second note in the help page to
+ <code><a href='mkinfit.html'>mkinfit</a></code>.</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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
+ <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for
+ Evaluating and Calculating Degradation Kinetics in Environmental
+ Media</p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='co'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span>
+<span class='no'>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='co'># One parent compound, one metabolite, both single first order</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>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'>
+<span class='co'>## Not run: ------------------------------------</span>
+<span class='co'># # The above model used to be specified like this, before the advent of mkinsub()</span>
+<span class='co'># SFO_SFO &lt;- mkinmod(</span>
+<span class='co'># parent = list(type = "SFO", to = "m1"),</span>
+<span class='co'># m1 = list(type = "SFO"))</span>
+<span class='co'># </span>
+<span class='co'># # Show details of creating the C function</span>
+<span class='co'># SFO_SFO &lt;- mkinmod(</span>
+<span class='co'># parent = mkinsub("SFO", "m1"),</span>
+<span class='co'># m1 = mkinsub("SFO"), verbose = TRUE)</span>
+<span class='co'># </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='co'># m_synth_DFOP_par &lt;- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),</span>
+<span class='co'># M1 = mkinsub("SFO"),</span>
+<span class='co'># M2 = mkinsub("SFO"),</span>
+<span class='co'># use_of_ff = "max", quiet = TRUE)</span>
+<span class='co'># </span>
+<span class='co'># fit_DFOP_par_c &lt;- mkinfit(m_synth_DFOP_par, </span>
+<span class='co'># synthetic_data_for_UBA_2014[[12]]$data,</span>
+<span class='co'># quiet = TRUE)</span>
+<span class='co'>## ---------------------------------------------</span></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="#note">Note</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, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/mkinparplot-4.png b/docs/reference/mkinparplot-4.png
new file mode 100644
index 00000000..77eafd95
--- /dev/null
+++ b/docs/reference/mkinparplot-4.png
Binary files differ
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
new file mode 100644
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--- /dev/null
+++ b/docs/reference/mkinparplot.html
@@ -0,0 +1,140 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>
+ — mkinparplot • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- 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">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
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+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>This function plots the confidence intervals for the parameters
+ fitted using <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
+
+
+ <pre><span class='fu'>mkinparplot</span>(<span class='no'>object</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>object</dt>
+ <dd>
+ A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object.
+ </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p>
+
+
+ <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'>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='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'>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='fu'>c</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>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='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>
+ </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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
new file mode 100644
index 00000000..d3f0c1f6
--- /dev/null
+++ b/docs/reference/mkinplot.html
@@ -0,0 +1,132 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>
+ — mkinplot • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- 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">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>Deprecated function. It now only calls the plot method <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p>
+
+
+ <pre><span class='fu'>mkinplot</span>(<span class='no'>fit</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>fit</dt>
+ <dd>
+ an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.
+ </dd>
+ <dt>&amp;#8230;</dt>
+ <dd>
+ further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.
+</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The function is called for its side effect.</p>
+
+
+ </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>
+ </ul>
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
new file mode 100644
index 00000000..31556527
--- /dev/null
+++ b/docs/reference/mkinpredict.html
@@ -0,0 +1,336 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>
+ — mkinpredict • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+
+<!-- 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">
+
+
+<!-- pkgdown -->
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+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
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+
+<!--[if lt IE 9]>
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </head>
+
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+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
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+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>This function produces a time series for all the observed variables in a
+ kinetic model as specified by <code><a href='mkinmod.html'>mkinmod</a></code>, using a specific set of
+ kinetic parameters and initial values for the state variables.</p>
+
+
+ <pre><span class='fu'>mkinpredict</span>(<span class='no'>mkinmod</span>, <span class='no'>odeparms</span>, <span class='no'>odeini</span>, <span class='no'>outtimes</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='st'>"auto"</span>, <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
+ <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>mkinmod</dt>
+ <dd>
+ A kinetic model as produced by <code><a href='mkinmod.html'>mkinmod</a></code>.
+ </dd>
+ <dt>odeparms</dt>
+ <dd>
+ A numeric vector specifying the parameters used in the kinetic model, which
+ is generally defined as a set of ordinary differential equations.
+ </dd>
+ <dt>odeini</dt>
+ <dd>
+ A numeric vectory containing the initial values of the state variables of
+ the model. Note that the state variables can differ from the observed
+ variables, for example in the case of the SFORB model.
+ </dd>
+ <dt>outtimes</dt>
+ <dd>
+ A numeric vector specifying the time points for which model predictions
+ should be generated.
+ </dd>
+ <dt>solution_type</dt>
+ <dd>
+ The method that should be used for producing the predictions. This should
+ generally be &quot;analytical&quot; if there is only one observed variable, and
+ usually &quot;deSolve&quot; in the case of several observed variables. The third
+ possibility &quot;eigen&quot; is faster but not applicable to some models e.g.
+ using FOMC for the parent compound.
+ </dd>
+ <dt>method.ode</dt>
+ <dd>
+ The solution method passed via <code>mkinpredict</code> to
+ <code>ode</code> in case the solution type is &quot;deSolve&quot;. The default
+ &quot;lsoda&quot; is performant, but sometimes fails to converge.
+ </dd>
+ <dt>use_compiled</dt>
+ <dd>
+ If set to <code>FALSE</code>, no compiled version of the <code><a href='mkinmod.html'>mkinmod</a></code>
+ model is used, even if is present.
+ </dd>
+ <dt>atol</dt>
+ <dd>
+ Absolute error tolerance, passed to <code>ode</code>. Default is 1e-8,
+ lower than in <code>lsoda</code>.
+ </dd>
+ <dt>rtol</dt>
+ <dd>
+ Absolute error tolerance, passed to <code>ode</code>. Default is 1e-10,
+ much lower than in <code>lsoda</code>.
+ </dd>
+ <dt>map_output</dt>
+ <dd>
+ Boolean to specify if the output should list values for the observed
+ variables (default) or for all state variables (if set to FALSE).
+ </dd>
+ <dt>&amp;#8230;</dt>
+ <dd>
+ Further arguments passed to the ode solver in case such a solver is used.
+ </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A matrix in the same format as the output of <code>ode</code>.</p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'> <span class='no'>SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</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'># Compare solution types</span>
+ <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)</div><div class='output co'>#&gt; time degradinol
+#&gt; 1 0 100.0000000
+#&gt; 2 1 74.0818221
+#&gt; 3 2 54.8811636
+#&gt; 4 3 40.6569660
+#&gt; 5 4 30.1194212
+#&gt; 6 5 22.3130160
+#&gt; 7 6 16.5298888
+#&gt; 8 7 12.2456428
+#&gt; 9 8 9.0717953
+#&gt; 10 9 6.7205513
+#&gt; 11 10 4.9787068
+#&gt; 12 11 3.6883167
+#&gt; 13 12 2.7323722
+#&gt; 14 13 2.0241911
+#&gt; 15 14 1.4995577
+#&gt; 16 15 1.1108997
+#&gt; 17 16 0.8229747
+#&gt; 18 17 0.6096747
+#&gt; 19 18 0.4516581
+#&gt; 20 19 0.3345965
+#&gt; 21 20 0.2478752
+#&gt; </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)</div><div class='output co'>#&gt; time degradinol
+#&gt; 1 0 100.0000000
+#&gt; 2 1 74.0818221
+#&gt; 3 2 54.8811636
+#&gt; 4 3 40.6569660
+#&gt; 5 4 30.1194212
+#&gt; 6 5 22.3130160
+#&gt; 7 6 16.5298888
+#&gt; 8 7 12.2456428
+#&gt; 9 8 9.0717953
+#&gt; 10 9 6.7205513
+#&gt; 11 10 4.9787068
+#&gt; 12 11 3.6883167
+#&gt; 13 12 2.7323722
+#&gt; 14 13 2.0241911
+#&gt; 15 14 1.4995577
+#&gt; 16 15 1.1108996
+#&gt; 17 16 0.8229747
+#&gt; 18 17 0.6096747
+#&gt; 19 18 0.4516581
+#&gt; 20 19 0.3345965
+#&gt; 21 20 0.2478752
+#&gt; </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</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>)</div><div class='output co'>#&gt; time degradinol
+#&gt; 1 0 100.0000000
+#&gt; 2 1 74.0818221
+#&gt; 3 2 54.8811636
+#&gt; 4 3 40.6569660
+#&gt; 5 4 30.1194212
+#&gt; 6 5 22.3130160
+#&gt; 7 6 16.5298888
+#&gt; 8 7 12.2456428
+#&gt; 9 8 9.0717953
+#&gt; 10 9 6.7205513
+#&gt; 11 10 4.9787068
+#&gt; 12 11 3.6883167
+#&gt; 13 12 2.7323722
+#&gt; 14 13 2.0241911
+#&gt; 15 14 1.4995577
+#&gt; 16 15 1.1108996
+#&gt; 17 16 0.8229747
+#&gt; 18 17 0.6096747
+#&gt; 19 18 0.4516581
+#&gt; 20 19 0.3345965
+#&gt; 21 20 0.2478752
+#&gt; </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)</div><div class='output co'>#&gt; time degradinol
+#&gt; 1 0 100.0000000
+#&gt; 2 1 74.0818221
+#&gt; 3 2 54.8811636
+#&gt; 4 3 40.6569660
+#&gt; 5 4 30.1194212
+#&gt; 6 5 22.3130160
+#&gt; 7 6 16.5298888
+#&gt; 8 7 12.2456428
+#&gt; 9 8 9.0717953
+#&gt; 10 9 6.7205513
+#&gt; 11 10 4.9787068
+#&gt; 12 11 3.6883167
+#&gt; 13 12 2.7323722
+#&gt; 14 13 2.0241911
+#&gt; 15 14 1.4995577
+#&gt; 16 15 1.1108997
+#&gt; 17 16 0.8229747
+#&gt; 18 17 0.6096747
+#&gt; 19 18 0.4516581
+#&gt; 20 19 0.3345965
+#&gt; 21 20 0.2478752
+#&gt; </div><div class='input'>
+
+ <span class='co'># Compare integration methods to analytical solution</span>
+ <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 21 20 0.2478752
+#&gt; </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 21 20 0.2478752
+#&gt; </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"ode45"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 21 20 0.2478752
+#&gt; </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"rk4"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 21 20 0.2480043
+#&gt; </div><div class='input'> <span class='co'># rk4 is not as precise here</span>
+
+ <span class='co'># The number of output times used to make a lot of difference until the</span>
+ <span class='co'># default for atol was adjusted</span>
+ <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</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='fl'>201</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 201 20 0.2478752
+#&gt; </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</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'>0.01</span>))[<span class='fl'>2001</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 2001 20 0.2478752
+#&gt; </div><div class='input'>
+ <span class='co'># Check compiled model versions - they are faster than the eigenvalue based solutions!</span>
+ <span class='no'>SFO_SFO</span> <span class='kw'>=</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'>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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
+#&gt; 201 20 4.978707 27.46227
+#&gt; </div><div class='output co'>#&gt; user system elapsed
+#&gt; 0.028 0.004 0.004
+#&gt; </div><div class='input'> <span class='fu'>system.time</span>(
+ <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
+ <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
+#&gt; 201 20 4.978707 27.46227
+#&gt; </div><div class='output co'>#&gt; user system elapsed
+#&gt; 0.016 0.004 0.002
+#&gt; </div><div class='input'> <span class='fu'>system.time</span>(
+ <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
+ <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
+#&gt; 201 20 4.978707 27.46227
+#&gt; </div><div class='output co'>#&gt; user system elapsed
+#&gt; 0.052 0.000 0.052
+#&gt; </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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
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+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>This function plots the residuals for the specified subset of the
+ observed variables from an mkinfit object. A combined plot of the fitted
+ model and the residuals can be obtained using <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>
+ using the argument <code>show_residuals = TRUE</code>.</p>
+
+
+ <pre><span class='fu'>mkinresplot</span>(<span class='no'>object</span>,
+ <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'>names</span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>),
+ <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>1.1</span> * <span class='fu'>max</span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>time</span>)),
+ <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residual"</span>,
+ <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>object</dt>
+ <dd>
+ A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object.
+</dd>
+ <dt>obs_vars</dt>
+ <dd>
+ A character vector of names of the observed variables for which residuals
+ should be plotted. Defaults to all observed variables in the model
+</dd>
+ <dt>xlim</dt>
+ <dd>
+ plot range in x direction.
+ </dd>
+ <dt>xlab</dt>
+ <dd>
+ Label for the x axis. Defaults to &quot;Time [days]&quot;.
+</dd>
+ <dt>ylab</dt>
+ <dd>
+ Label for the y axis. Defaults to &quot;Residual [% of applied radioactivity]&quot;.
+</dd>
+ <dt>maxabs</dt>
+ <dd>
+ Maximum absolute value of the residuals. This is used for the scaling of
+ the y axis and defaults to &quot;auto&quot;.
+</dd>
+ <dt>legend</dt>
+ <dd>
+ Should a legend be plotted? Defaults to &quot;TRUE&quot;.
+</dd>
+ <dt>lpos</dt>
+ <dd>
+ Where should the legend be placed? Default is &quot;topright&quot;. Will be passed on to
+ <code>legend</code>. </dd>
+ <dt>&amp;#8230;</dt>
+ <dd>
+ further arguments passed to <code>plot</code>.
+</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p>
+
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted lines of the
+ mkinfit object.</p>
+
+
+ <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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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>
+ </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="#see-also">See also</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, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
new file mode 100644
index 00000000..89387468
--- /dev/null
+++ b/docs/reference/mkinsub.html
@@ -0,0 +1,165 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>
+ — mkinsub • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- 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">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>This is a convenience function to set up the lists used as arguments for
+ <code><a href='mkinmod.html'>mkinmod</a></code>.</p>
+
+
+ <pre><span class='fu'>mkinsub</span>(<span class='no'>submodel</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>submodel</dt>
+ <dd>
+ Character vector of length one to specify the submodel type. See
+ <code><a href='mkinmod.html'>mkinmod</a></code> for the list of allowed submodel names.
+ </dd>
+ <dt>to</dt>
+ <dd>
+ Vector of the names of the state variable to which a transformation
+ shall be included in the model.
+ </dd>
+ <dt>sink</dt>
+ <dd>
+ Should a pathway to sink be included in the model in addition to the
+ pathways to other state variables?
+ </dd>
+ <dt>full_name</dt>
+ <dd>
+ An optional name to be used e.g. for plotting fits performed with the model.
+ You can use non-ASCII characters here, but then your R code will not be
+ portable, <em>i.e.</em> may produce unintended plot results on other
+ operating systems or system configurations.
+ </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A list for use with <code><a href='mkinmod.html'>mkinmod</a></code>.</p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order.</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'>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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'>
+<span class='co'># The same model using mkinsub</span>
+<span class='no'>SFO_SFO.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'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'>
+<span class='co'># Now supplying full names</span>
+<span class='no'>SFO_SFO.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'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Test compound"</span>),
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
new file mode 100644
index 00000000..a6e74b8a
--- /dev/null
+++ b/docs/reference/mmkin.html
@@ -0,0 +1,196 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>
+ — mmkin • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- 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">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>This function calls <code><a href='mkinfit.html'>mkinfit</a></code> on all combinations of models and datasets
+ specified in its first two arguments.</p>
+
+
+ <pre><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='fu'>round</span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>models</dt>
+ <dd>
+ Either a character vector of shorthand names (&quot;SFO&quot;, &quot;FOMC&quot;, &quot;DFOP&quot;,
+ &quot;HS&quot;, &quot;SFORB&quot;), or an optionally named list of <code><a href='mkinmod.html'>mkinmod</a></code>
+ objects.
+ </dd>
+ <dt>datasets</dt>
+ <dd>
+ An optionally named list of datasets suitable as observed data for
+ <code><a href='mkinfit.html'>mkinfit</a></code>.
+ </dd>
+ <dt>cores</dt>
+ <dd>
+ The number of cores to be used for multicore processing. This is only
+ used when the <code>cluster</code> argument is <code>NULL</code>.
+ </dd>
+ <dt>cluster</dt>
+ <dd>
+ A cluster as returned by <code>makeCluster</code> to be used for parallel
+ execution.
+ </dd>
+ <dt>&amp;#8230;</dt>
+ <dd>
+ Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>.
+ </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A matrix of <code><a href='mkinfit.html'>mkinfit</a></code> objects that can be indexed using the model
+ and dataset names as row and column indices.</p>
+
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <p><code><a href='[.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for plotting.</p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span>
+<span class='co'># m_synth_SFO_lin &lt;- mkinmod(parent = mkinsub("SFO", "M1"),</span>
+<span class='co'># M1 = mkinsub("SFO", "M2"),</span>
+<span class='co'># M2 = mkinsub("SFO"), use_of_ff = "max")</span>
+<span class='co'># </span>
+<span class='co'># m_synth_FOMC_lin &lt;- mkinmod(parent = mkinsub("FOMC", "M1"),</span>
+<span class='co'># M1 = mkinsub("SFO", "M2"),</span>
+<span class='co'># M2 = mkinsub("SFO"), use_of_ff = "max")</span>
+<span class='co'># </span>
+<span class='co'># models &lt;- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)</span>
+<span class='co'># datasets &lt;- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)</span>
+<span class='co'># names(datasets) &lt;- paste("Dataset", 1:3)</span>
+<span class='co'># </span>
+<span class='co'># time_default &lt;- system.time(fits.0 &lt;- mmkin(models, datasets))</span>
+<span class='co'># time_1 &lt;- system.time(fits.1 &lt;- mmkin(models, datasets, cores = 1))</span>
+<span class='co'># </span>
+<span class='co'># time_default</span>
+<span class='co'># time_1</span>
+<span class='co'># </span>
+<span class='co'># endpoints(fits[["SFO_lin", 2]])</span>
+<span class='co'># </span>
+<span class='co'># # Plot.mkinfit handles rows or columns of mmkin result objects</span>
+<span class='co'># plot(fits.0[1, ])</span>
+<span class='co'># plot(fits.0[1, ], obs_var = c("M1", "M2"))</span>
+<span class='co'># plot(fits.0[, 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</span>
+<span class='co'># plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)</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='co'># plot(fits.0[1, 1])</span>
+<span class='co'>## ---------------------------------------------</span></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="#see-also">See also</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, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
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+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>
+ — plot.mkinfit • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- 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">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>Solves the differential equations with the optimised and fixed parameters
+ from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots
+ the observed data together with the solution of the fitted model.</p>
+
+
+ <pre># S3 method for mkinfit
+plot(x, fit = x,
+ obs_vars = names(fit$mkinmod$map),
+ xlab = "Time", ylab = "Observed",
+ xlim = range(fit$data$time),
+ ylim = "default",
+ col_obs = 1:length(obs_vars), pch_obs = col_obs,
+ lty_obs = rep(1, length(obs_vars)),
+ add = FALSE, legend = !add,
+ show_residuals = FALSE, maxabs = "auto",
+ sep_obs = FALSE, rel.height.middle = 0.9,
+ lpos = "topright", inset = c(0.05, 0.05),
+ show_errmin = FALSE, errmin_digits = 3, &#8230;)
+plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, &#8230;)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>x</dt>
+ <dd>
+ Alias for fit introduced for compatibility with the generic S3 method.
+ </dd>
+ <dt>fit</dt>
+ <dd>
+ An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.
+ </dd>
+ <dt>obs_vars</dt>
+ <dd>
+ A character vector of names of the observed variables for which the
+ data and the model should be plotted. Defauls to all observed variables
+ in the model.
+ </dd>
+ <dt>xlab</dt>
+ <dd>
+ Label for the x axis.
+ </dd>
+ <dt>ylab</dt>
+ <dd>
+ Label for the y axis.
+ </dd>
+ <dt>xlim</dt>
+ <dd>
+ Plot range in x direction.
+ </dd>
+ <dt>ylim</dt>
+ <dd>
+ Plot range in y direction.
+ </dd>
+ <dt>col_obs</dt>
+ <dd>
+ Colors used for plotting the observed data and the corresponding model prediction lines.
+ </dd>
+ <dt>pch_obs</dt>
+ <dd>
+ Symbols to be used for plotting the data.
+ </dd>
+ <dt>lty_obs</dt>
+ <dd>
+ Line types to be used for the model predictions.
+ </dd>
+ <dt>add</dt>
+ <dd>
+ Should the plot be added to an existing plot?
+ </dd>
+ <dt>legend</dt>
+ <dd>
+ Should a legend be added to the plot?
+ </dd>
+ <dt>show_residuals</dt>
+ <dd>
+ Should residuals be shown? If only one plot of the fits is shown, the
+ residual plot is in the lower third of the plot? Otherwise, i.e. if
+ &quot;sep_obs&quot; is given, the residual plots will be located to the right of
+ the plots of the fitted curves.
+ </dd>
+ <dt>maxabs</dt>
+ <dd>
+ Maximum absolute value of the residuals. This is used for the scaling of
+ the y axis and defaults to &quot;auto&quot;.
+ </dd>
+ <dt>sep_obs</dt>
+ <dd>
+ Should the observed variables be shown in separate subplots? If yes, residual plots
+ requested by &quot;show_residuals&quot; will be shown next to, not below the plot of the fits.
+ </dd>
+ <dt>rel.height.middle</dt>
+ <dd>
+ The relative height of the middle plot, if more than two rows of plots are shown.
+ </dd>
+ <dt>lpos</dt>
+ <dd>
+ Position(s) of the legend(s). Passed to <code>legend</code> as the first argument.
+ If not length one, this should be of the same length as the obs_var argument.
+ </dd>
+ <dt>inset</dt>
+ <dd>
+ Passed to <code>legend</code> if applicable.
+ </dd>
+ <dt>show_errmin</dt>
+ <dd>
+ Should the FOCUS chi2 error value be shown in the upper margin of the plot?
+ </dd>
+ <dt>errmin_digits</dt>
+ <dd>
+ The number of significant digits for rounding the FOCUS chi2 error percentage.
+ </dd>
+ <dt>&amp;#8230;</dt>
+ <dd>
+ Further arguments passed to <code>plot</code>.
+ </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The function is called for its side effect.</p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order, path from</span>
+<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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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='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='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='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>
+ <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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png
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diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
new file mode 100644
index 00000000..e0a20f3d
--- /dev/null
+++ b/docs/reference/plot.mmkin.html
@@ -0,0 +1,174 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>
+ — plot.mmkin • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- 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">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>When x is a row selected from an mmkin object (<code><a href='[.mmkin.html'>[.mmkin</a></code>), 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.</p>
+
+
+ <pre><span class='co'># S3 method for mmkin</span>
+<span class='fu'>plot</span>(<span class='no'>x</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>errmin_var</span> <span class='kw'>=</span> <span class='st'>"All data"</span>, <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>,
+ <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>x</dt>
+ <dd>
+ An object of class <code><a href='mmkin.html'>mmkin</a></code>, with either one row or one column.
+</dd>
+ <dt>main</dt>
+ <dd>
+ The main title placed on the outer margin of the plot.
+</dd>
+ <dt>legends</dt>
+ <dd>
+ An index for the fits for which legends should be shown.
+</dd>
+ <dt>errmin_var</dt>
+ <dd>
+ The variable for which the FOCUS chi2 error value should be shown.
+</dd>
+ <dt>errmin_digits</dt>
+ <dd>
+ The number of significant digits for rounding the FOCUS chi2 error percentage.
+</dd>
+ <dt>cex</dt>
+ <dd>
+ Passed to the plot functions and <code>mtext</code>.
+</dd>
+ <dt>rel.height.middle</dt>
+ <dd>
+ The relative height of the middle plot, if more than two rows of plots are shown.
+</dd>
+ <dt>&amp;#8230;</dt>
+ <dd>
+ Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinresplot.html'>mkinresplot</a></code>.
+</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The function is called for its side effect.</p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'> <span class='co'># Only use one core not to offend CRAN checks, use Levenberg-Marquardt for speed</span>
+ <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='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='co'># We can also plot a single fit, if we like the way 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 staticdocs, 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>
+ </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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
new file mode 100644
index 00000000..a586a103
--- /dev/null
+++ b/docs/reference/print.mkinds.html
@@ -0,0 +1,123 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>
+ — print.mkinds • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
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+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- 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">
+
+
+<!-- pkgdown -->
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+<script src="../pkgdown.js"></script>
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+
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+ <div class="container">
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+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
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+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
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+
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+
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+</div><!--/.navbar -->
+
+
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+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>Print mkinds objects.</p>
+
+
+ <pre><span class='co'># S3 method for mkinds</span>
+<span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>x</dt>
+ <dd>
+ An <code><a href='mkinds.html'>mkinds</a></code> object.
+ </dd>
+ <dt>&amp;#8230;</dt>
+ <dd>
+ Not used.
+ </dd>
+ </dl>
+
+
+ </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>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
new file mode 100644
index 00000000..73bfd60e
--- /dev/null
+++ b/docs/reference/print.mkinmod.html
@@ -0,0 +1,123 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>
+ — print.mkinmod • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
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+
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+
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+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>Print mkinmod objects in a way that the user finds his way to get to its components.</p>
+
+
+ <pre><span class='co'># S3 method for mkinmod</span>
+<span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>x</dt>
+ <dd>
+ An <code><a href='mkinmod.html'>mkinmod</a></code> object.
+ </dd>
+ <dt>&amp;#8230;</dt>
+ <dd>
+ Not used.
+ </dd>
+ </dl>
+
+
+ </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>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
new file mode 100644
index 00000000..4714747a
--- /dev/null
+++ b/docs/reference/schaefer07_complex_case.html
@@ -0,0 +1,148 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
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+ — schaefer07_complex_case • mkin</title>
+
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+<!-- Bootstrap -->
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+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
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+
+
+<!-- pkgdown -->
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+<script src="../pkgdown.js"></script>
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+
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
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+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
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+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>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.</p>
+
+
+ <pre><span class='fu'>data</span>(<span class='no'>schaefer07_complex_case</span>)</pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>The data set is a data frame with 8 observations on the following 6 variables.
+ <dl class='dl-horizontal'>
+ <dt><code>time</code></dt><dd>a numeric vector</dd>
+ <dt><code>parent</code></dt><dd>a numeric vector</dd>
+ <dt><code>A1</code></dt><dd>a numeric vector</dd>
+ <dt><code>B1</code></dt><dd>a numeric vector</dd>
+ <dt><code>C1</code></dt><dd>a numeric vector</dd>
+ <dt><code>A2</code></dt><dd>a numeric vector</dd>
+ </dl></p>
+ <p>The results are a data frame with 14 results for different parameter values</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Schäfer D, Mikolasch B, Rainbird P and Harvey B (2007). KinGUI: a new kinetic
+ software tool for evaluations according to FOCUS degradation kinetics. In: Del
+ Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII
+ Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.</p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='no'>data</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>schaefer07_complex_case</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>)
+<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'>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='fu'>c</span>(<span class='st'>"A1"</span>, <span class='st'>"B1"</span>, <span class='st'>"C1"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
+ <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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'>## Not run: mkinfit(model, data, plot=TRUE)</span></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="#format">Format</a></li>
+
+ <li><a href="#references">References</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
new file mode 100644
index 00000000..b88a5469
--- /dev/null
+++ b/docs/reference/summary.mkinfit.html
@@ -0,0 +1,247 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>
+ — summary.mkinfit • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- 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">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">mkin</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>Lists model equations, the summary as returned by <code>summary.modFit</code>,
+ 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.</p>
+
+
+ <pre><span class='co'># S3 method for mkinfit</span>
+<span class='fu'>summary</span>(<span class='no'>object</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distimes</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='no'>...</span>)
+<span class='co'># S3 method for summary.mkinfit</span>
+<span class='fu'>print</span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'>max</span>(<span class='fl'>3</span>, <span class='fu'>getOption</span>(<span class='st'>"digits"</span>) - <span class='fl'>3</span>), <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>object</dt>
+ <dd>
+ an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.
+</dd>
+ <dt>x</dt>
+ <dd>
+ an object of class <code>summary.mkinfit</code>.
+</dd>
+ <dt>data</dt>
+ <dd>
+ logical, indicating whether the data should be included in the summary.
+</dd>
+ <dt>distimes</dt>
+ <dd>
+ logical, indicating whether DT50 and DT90 values should be included.
+</dd>
+ <dt>alpha</dt>
+ <dd>
+ error level for confidence interval estimation from t distribution
+</dd>
+ <dt>digits</dt>
+ <dd>
+ Number of digits to use for printing
+</dd>
+ <dt>&amp;#8230;</dt>
+ <dd>
+ optional arguments passed to methods like <code>print</code>.
+</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The summary function returns a list derived from
+ <code>summary.modFit</code>, with components, among others</p>
+ <p>The print method is called for its side effect, i.e. printing the summary.</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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; R version: 3.3.1
+#&gt; Date of fit: Wed Oct 26 23:50:50 2016
+#&gt; Date of summary: Wed Oct 26 23:50:50 2016
+#&gt;
+#&gt; Equations:
+#&gt; d_parent = - k_parent_sink * parent
+#&gt;
+#&gt; Model predictions using solution type analytical
+#&gt;
+#&gt; Fitted with method Port using 35 model solutions performed in 0.083 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 101.24 state
+#&gt; k_parent_sink 0.10 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 101.240000 -Inf Inf
+#&gt; log_k_parent_sink -2.302585 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; None
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 109.200 4.3910 98.410 119.900
+#&gt; log_k_parent_sink -3.291 0.1152 -3.573 -3.009
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent_sink
+#&gt; parent_0 1.000 0.575
+#&gt; log_k_parent_sink 0.575 1.000
+#&gt;
+#&gt; Residual standard error: 6.08 on 6 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_0 109.20000 24.860 1.394e-07 98.41000 119.90000
+#&gt; k_parent_sink 0.03722 8.679 6.457e-05 0.02807 0.04934
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 8.385 2 6
+#&gt; parent 8.385 2 6
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_sink 1
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 18.62 61.87
+#&gt;
+#&gt; Data:
+#&gt; time variable observed predicted residual
+#&gt; 0 parent 101.24 109.153 -7.9132
+#&gt; 3 parent 99.27 97.622 1.6484
+#&gt; 7 parent 90.11 84.119 5.9913
+#&gt; 14 parent 72.19 64.826 7.3641
+#&gt; 30 parent 29.71 35.738 -6.0283
+#&gt; 62 parent 5.98 10.862 -4.8818
+#&gt; 90 parent 1.54 3.831 -2.2911
+#&gt; 118 parent 0.39 1.351 -0.9613
+#&gt; </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, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
new file mode 100644
index 00000000..45d5f53a
--- /dev/null
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -0,0 +1,174 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
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+ — synthetic_data_for_UBA_2014 • mkin</title>
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+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
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+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
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+
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+
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+ </div><!--/.nav-collapse -->
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+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>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.</p>
+
+ <p>Variance component &#39;a&#39; is based on a normal distribution with standard deviation of 3,
+ Variance component &#39;b&#39; is also based on a normal distribution, but with a standard deviation of 7.
+ Variance component &#39;c&#39; 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.</p>
+
+ <p>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 <code>NA</code>.</p>
+
+ <p>As an example, the first dataset has the title <code>SFO_lin_a</code> and is based on the SFO model
+ with two sequential metabolites (linear pathway), with added variance component &#39;a&#39;.</p>
+
+ <p>Compare also the code in the example section to see the degradation models.</p>
+
+
+ <pre><span class='no'>synthetic_data_for_UBA_2014</span></pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>A list containing datasets in the form internally used by the &#39;gmkin&#39; package.
+ The list has twelfe components. Each of the components is one dataset that has,
+ among others, the following components
+ <dl class='dl-horizontal'>
+ <dt><code>title</code></dt><dd>The name of the dataset, e.g. <code>SFO_lin_a</code></dd>
+ <dt><code>data</code></dt><dd>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></dd>
+ </dl></p>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+ <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative
+ zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p>
+ <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for
+ measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p>
+
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span>
+<span class='co'># m_synth_SFO_lin &lt;- mkinmod(parent = list(type = "SFO", to = "M1"),</span>
+<span class='co'># M1 = list(type = "SFO", to = "M2"),</span>
+<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span>
+<span class='co'># </span>
+<span class='co'># </span>
+<span class='co'># m_synth_SFO_par &lt;- mkinmod(parent = list(type = "SFO", to = c("M1", "M2"),</span>
+<span class='co'># sink = FALSE),</span>
+<span class='co'># M1 = list(type = "SFO"),</span>
+<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span>
+<span class='co'># </span>
+<span class='co'># m_synth_DFOP_lin &lt;- mkinmod(parent = list(type = "DFOP", to = "M1"),</span>
+<span class='co'># M1 = list(type = "SFO", to = "M2"),</span>
+<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span>
+<span class='co'># </span>
+<span class='co'># m_synth_DFOP_par &lt;- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"),</span>
+<span class='co'># sink = FALSE),</span>
+<span class='co'># M1 = list(type = "SFO"),</span>
+<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span>
+<span class='co'># </span>
+<span class='co'># mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data)</span>
+<span class='co'>## ---------------------------------------------</span></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="#format">Format</a></li>
+
+ <li><a href="#source">Source</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
new file mode 100644
index 00000000..ab5ce062
--- /dev/null
+++ b/docs/reference/transform_odeparms.html
@@ -0,0 +1,294 @@
+<!-- Generated by pkgdown: do not edit by hand -->
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+ <a href="../reference/index.html">Reference</a>
+</li>
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+<li>
+ <a href="../news/index.html">News</a>
+</li>
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+
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+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
+</h1>
+ </div>
+
+
+ <p>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 <code><a href='ilr.html'>ilr</a></code> transformation is used.</p>
+
+ <p>The transformation of sets of formation fractions is fragile, as it supposes
+ the same ordering of the components in forward and backward transformation.
+ This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
+
+
+ <pre><span class='fu'>transform_odeparms</span>(<span class='no'>parms</span>, <span class='no'>mkinmod</span>,
+ <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>backtransform_odeparms</span>(<span class='no'>transparms</span>, <span class='no'>mkinmod</span>,
+ <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>parms</dt>
+ <dd>
+ Parameters of kinetic models as used in the differential equations.
+ </dd>
+ <dt>transparms</dt>
+ <dd>
+ Transformed parameters of kinetic models as used in the fitting procedure.
+ </dd>
+ <dt>mkinmod</dt>
+ <dd>
+ The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the names of
+ the model variables that are needed for grouping the formation fractions
+ before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter names and
+ the information if the pathway to sink is included in the model.
+ </dd>
+ <dt>transform_rates</dt>
+ <dd>
+ Boolean specifying if kinetic rate constants should be transformed in the
+ model specification used in the fitting for better compliance with the
+ assumption of normal distribution of the estimator. If TRUE, also
+ alpha and beta parameters of the FOMC model are log-transformed, as well
+ as k1 and k2 rate constants for the DFOP and HS models and the break point tb
+ of the HS model.
+ </dd>
+ <dt>transform_fractions</dt>
+ <dd>
+ Boolean specifying if formation fractions constants should be transformed in the
+ model specification used in the fitting for better compliance with the
+ assumption of normal distribution of the estimator. The default (TRUE) is
+ to do transformations. The g parameter of the DFOP and HS models are also
+ transformed, as they can also be seen as compositional data. The
+ transformation used for these transformations is the <code><a href='ilr.html'>ilr</a></code>
+ transformation.
+ </dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A vector of transformed or backtransformed parameters with the same names
+ as the original parameters.</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</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>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
+<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; R version: 3.3.1
+#&gt; Date of fit: Wed Oct 26 23:50:51 2016
+#&gt; Date of summary: Wed Oct 26 23:50:51 2016
+#&gt;
+#&gt; Equations:
+#&gt; d_parent = - k_parent_sink * parent - k_parent_m1 * parent
+#&gt; d_m1 = + k_parent_m1 * parent - k_m1_sink * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 153 model solutions performed in 0.629 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_0 100.750000 -Inf Inf
+#&gt; log_k_parent_sink -2.302585 -Inf Inf
+#&gt; log_k_parent_m1 -2.301586 -Inf Inf
+#&gt; log_k_m1_sink -2.300587 -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 99.600 1.61400 96.330 102.900
+#&gt; log_k_parent_sink -3.038 0.07826 -3.197 -2.879
+#&gt; log_k_parent_m1 -2.980 0.04124 -3.064 -2.897
+#&gt; log_k_m1_sink -5.248 0.13610 -5.523 -4.972
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; parent_0 1.00000 0.6075 -0.06625 -0.1701
+#&gt; log_k_parent_sink 0.60752 1.0000 -0.08740 -0.6253
+#&gt; log_k_parent_m1 -0.06625 -0.0874 1.00000 0.4716
+#&gt; log_k_m1_sink -0.17006 -0.6253 0.47163 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 0.040890 5.616e-02
+#&gt; k_parent_m1 0.050780 24.250 3.407e-24 0.046700 5.521e-02
+#&gt; k_m1_sink 0.005261 7.349 5.758e-09 0.003992 6.933e-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
+#&gt; </div><div class='input'>
+<span class='co'>## Not run: ------------------------------------</span>
+<span class='co'># fit.2 &lt;- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)</span>
+<span class='co'># summary(fit.2, data=FALSE) </span>
+<span class='co'>## ---------------------------------------------</span>
+
+<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>$<span class='no'>value</span>
+<span class='fu'>names</span>(<span class='no'>transformed</span>) <span class='kw'>&lt;-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start_transformed</span>)
+<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
+#&gt; </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
+#&gt; </div><div class='input'>
+<span class='co'>## Not run: ------------------------------------</span>
+<span class='co'># # The case of formation fractions</span>
+<span class='co'># SFO_SFO.ff &lt;- mkinmod(</span>
+<span class='co'># parent = list(type = "SFO", to = "m1", sink = TRUE),</span>
+<span class='co'># m1 = list(type = "SFO"),</span>
+<span class='co'># use_of_ff = "max")</span>
+<span class='co'># </span>
+<span class='co'># fit.ff &lt;- mkinfit(SFO_SFO.ff, FOCUS_2006_D)</span>
+<span class='co'># summary(fit.ff, data = FALSE)</span>
+<span class='co'># initials &lt;- c("f_parent_to_m1" = 0.5)</span>
+<span class='co'># transformed &lt;- transform_odeparms(initials, SFO_SFO.ff)</span>
+<span class='co'># backtransform_odeparms(transformed, SFO_SFO.ff)</span>
+<span class='co'># </span>
+<span class='co'># # And without sink</span>
+<span class='co'># SFO_SFO.ff.2 &lt;- mkinmod(</span>
+<span class='co'># parent = list(type = "SFO", to = "m1", sink = FALSE),</span>
+<span class='co'># m1 = list(type = "SFO"),</span>
+<span class='co'># use_of_ff = "max")</span>
+<span class='co'># </span>
+<span class='co'># </span>
+<span class='co'># fit.ff.2 &lt;- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D)</span>
+<span class='co'># summary(fit.ff.2, data = FALSE)</span>
+<span class='co'>## ---------------------------------------------</span></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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
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