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authorJohannes Ranke <jranke@uni-bremen.de>2019-10-26 22:52:53 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2019-10-26 22:52:53 +0200
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+ <h1>Confidence intervals for parameters of mkinfit objects</h1>
+
+ <div class="hidden name"><code>confint.mkinfit.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Confidence intervals for parameters of mkinfit objects</p>
+ </div>
+
+ <pre class="usage"><span class='co'># S3 method for mkinfit</span>
+<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>object</span>, <span class='no'>parm</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1</span> -
+ <span class='no'>level</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"profile"</span>, <span class='st'>"quadratic"</span>), <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>backtransform</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distribution</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"student_t"</span>, <span class='st'>"normal"</span>),
+ <span class='kw'>quiet</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>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>object</th>
+ <td><p>An <code><a href='mkinfit.html'>mkinfit</a></code> object</p></td>
+ </tr>
+ <tr>
+ <th>parm</th>
+ <td><p>A vector of names of the parameters which are to be given
+confidence intervals. If missing, all parameters are considered.</p></td>
+ </tr>
+ <tr>
+ <th>level</th>
+ <td><p>The confidence level required</p></td>
+ </tr>
+ <tr>
+ <th>alpha</th>
+ <td><p>The allowed error probability, overrides 'level' if specified.</p></td>
+ </tr>
+ <tr>
+ <th>method</th>
+ <td><p>The 'profile' method searches the parameter space for the
+cutoff of the confidence intervals by means of a likelihood ratio test.
+The 'quadratic' method approximates the likelihood function at the
+optimised parameters using the second term of the Taylor expansion, using
+a second derivative (hessian) contained in the object.</p></td>
+ </tr>
+ <tr>
+ <th>transformed</th>
+ <td><p>If the quadratic approximation is used, should it be
+applied to the likelihood based on the transformed parameters?</p></td>
+ </tr>
+ <tr>
+ <th>backtransform</th>
+ <td><p>If we approximate the likelihood in terms of the
+transformed parameters, should we backtransform the parameters with
+their confidence intervals?</p></td>
+ </tr>
+ <tr>
+ <th>distribution</th>
+ <td><p>For the quadratic approximation, should we use
+the student t distribution or assume normal distribution for
+the parameter estimate</p></td>
+ </tr>
+ <tr>
+ <th>quiet</th>
+ <td><p>Should we suppress messages?</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>Not used</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A matrix with columns giving lower and upper confidence limits for
+ each parameter.</p>
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Pawitan Y (2013) In all likelihood - Statistical modelling and
+ inference using likelihood. Clarendon Press, Oxford.</p>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</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'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 71.8242430 93.1600766
+#&gt; k_parent_sink 0.2109541 0.4440528
+#&gt; sigma 1.9778868 7.3681380</div><div class='input'><span class='co'># \dontrun{</span>
+ <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>)</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 71.3471007 93.9447024
+#&gt; k_parent_sink 0.2030765 0.4491067
+#&gt; sigma 2.9810656 8.8633278</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>
+
+ </div>
+</div>
+
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