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-rw-r--r--docs/reference/summary.mkinfit.html124
1 files changed, 65 insertions, 59 deletions
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 73410181..65bc6326 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -8,11 +8,13 @@
<title>Summary method for class "mkinfit" — summary.mkinfit • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,16 +34,18 @@
-<meta property="og:title" content="Summary method for class "mkinfit" — summary.mkinfit" />
-<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters with some
- uncertainty statistics, the chi2 error levels calculated according to FOCUS
- guidance (2006) as defined therein, formation fractions, DT50 values and
- optionally the data, consisting of observed, predicted and residual values." />
+<meta property="og:title" content="Summary method for class "mkinfit" — summary.mkinfit" />
+<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters with
+some uncertainty statistics, the chi2 error levels calculated according to
+FOCUS guidance (2006) as defined therein, formation fractions, DT50 values
+and optionally the data, consisting of observed, predicted and residual
+values." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -112,7 +116,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -134,19 +137,21 @@
</div>
<div class="ref-description">
-
- <p>Lists model equations, initial parameter values, optimised parameters with some
- uncertainty statistics, the chi2 error levels calculated according to FOCUS
- guidance (2006) as defined therein, formation fractions, DT50 values and
- optionally the data, consisting of observed, predicted and residual values.</p>
-
+ <p>Lists model equations, initial parameter values, optimised parameters with
+some uncertainty statistics, the chi2 error levels calculated according to
+FOCUS guidance (2006) as defined therein, formation fractions, DT50 values
+and optionally the data, consisting of observed, predicted and residual
+values.</p>
</div>
<pre class="usage"><span class='co'># S3 method for mkinfit</span>
-<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></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='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></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'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"digits"</span>) - <span class='fl'>3</span>), <span class='no'>...</span>)</pre>
-
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></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>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -155,91 +160,94 @@
<td><p>an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
</tr>
<tr>
- <th>x</th>
- <td><p>an object of class <code>summary.mkinfit</code>.</p></td>
- </tr>
- <tr>
<th>data</th>
- <td><p>logical, indicating whether the data should be included in the summary.</p></td>
+ <td><p>logical, indicating whether the data should be included in the
+summary.</p></td>
</tr>
<tr>
<th>distimes</th>
- <td><p>logical, indicating whether DT50 and DT90 values should be included.</p></td>
+ <td><p>logical, indicating whether DT50 and DT90 values should be
+included.</p></td>
</tr>
<tr>
<th>alpha</th>
- <td><p>error level for confidence interval estimation from t distribution</p></td>
- </tr>
- <tr>
- <th>digits</th>
- <td><p>Number of digits to use for printing</p></td>
+ <td><p>error level for confidence interval estimation from t
+distribution</p></td>
</tr>
<tr>
<th>...</th>
<td><p>optional arguments passed to methods like <code>print</code>.</p></td>
</tr>
+ <tr>
+ <th>x</th>
+ <td><p>an object of class <code>summary.mkinfit</code>.</p></td>
+ </tr>
+ <tr>
+ <th>digits</th>
+ <td><p>Number of digits to use for printing</p></td>
+ </tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The summary function returns a list with components, among others</p>
<dt>version, Rversion</dt><dd><p>The mkin and R versions used</p></dd>
- <dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were produced</p></dd>
+ <dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were
+ produced</p></dd>
+ <dt>diffs</dt><dd><p>The differential equations used in the model</p></dd>
<dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd>
- <dt>residuals, residualVariance, sigma, modVariance, df</dt><dd><p>As in summary.modFit</p></dd>
- <dt>cov.unscaled, cov.scaled, info, niter, stopmess, par</dt><dd><p>As in summary.modFit</p></dd>
- <dt>bpar</dt><dd><p>Optimised and backtransformed parameters</p></dd>
- <dt>diffs </dt><dd><p>The differential equations used in the model</p></dd>
- <dt>data </dt><dd><p>The data (see Description above).</p></dd>
- <dt>start </dt><dd><p>The starting values and bounds, if applicable, for optimised parameters.</p></dd>
- <dt>fixed </dt><dd><p>The values of fixed parameters.</p></dd>
- <dt>errmin </dt><dd><p>The chi2 error levels for each observed variable.</p></dd>
- <dt>bparms.ode </dt><dd><p>All backtransformed ODE parameters, for use as starting parameters for
- related models.</p></dd>
- <dt>errparms </dt><dd><p>Error model parameters.</p></dd>
- <dt>ff </dt><dd><p>The estimated formation fractions derived from the fitted model.</p></dd>
- <dt>distimes </dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd>
+ <dt>bpar</dt><dd><p>Optimised and backtransformed
+ parameters</p></dd>
+ <dt>data</dt><dd><p>The data (see Description above).</p></dd>
+ <dt>start</dt><dd><p>The starting values and bounds, if applicable, for optimised
+ parameters.</p></dd>
+ <dt>fixed</dt><dd><p>The values of fixed parameters.</p></dd>
+ <dt>errmin </dt><dd><p>The chi2 error levels for
+ each observed variable.</p></dd>
+ <dt>bparms.ode</dt><dd><p>All backtransformed ODE
+ parameters, for use as starting parameters for related models.</p></dd>
+ <dt>errparms</dt><dd><p>Error model parameters.</p></dd>
+ <dt>ff</dt><dd><p>The estimated formation fractions derived from the fitted
+ model.</p></dd>
+ <dt>distimes</dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd>
<dt>SFORB</dt><dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd>
The print method is called for its side effect, i.e. printing the summary.
-
<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,
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
+ <pre class="examples"><div class='input'>
+ <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
#&gt; R version used for fitting: 3.6.1
-#&gt; Date of fit: Thu Sep 19 09:52:40 2019
-#&gt; Date of summary: Thu Sep 19 09:52:40 2019
+#&gt; Date of fit: Fri Oct 25 02:09:45 2019
+#&gt; Date of summary: Fri Oct 25 02:09:45 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted using 131 model solutions performed in 0.27 s
+#&gt; Fitted using 131 model solutions performed in 0.274 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
#&gt; Error model algorithm: OLS
#&gt;
#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; parent_0 101.240000 state
-#&gt; k_parent_sink 0.100000 deparm
-#&gt; sigma 5.265546 error
+#&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; sigma 5.265546 0 Inf
#&gt;
#&gt; Fixed parameter values:
#&gt; None
@@ -287,17 +295,15 @@
#&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</div></pre>
+#&gt; 118 parent 0.39 1.351 -0.9613</div><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>

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