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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'><-</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'>#> 2.5% 97.5% +#> parent_0 71.8242430 93.1600766 +#> k_parent_sink 0.2109541 0.4440528 +#> 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'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> 2.5% 97.5% +#> parent_0 71.3471007 93.9447024 +#> k_parent_sink 0.2030765 0.4491067 +#> 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> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 328f5aca..fa424060 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -185,12 +185,30 @@ more datasets</p></td> </tr><tr> <td> + <p><code><a href="parms.html">parms()</a></code> </p> + </td> + <td><p>Extract model parameters from mkinfit models</p></td> + </tr><tr> + + <td> + <p><code><a href="confint.mkinfit.html">confint(<i><mkinfit></i>)</a></code> </p> + </td> + <td><p>Confidence intervals for parameters of mkinfit objects</p></td> + </tr><tr> + + <td> <p><code><a href="summary.mkinfit.html">summary(<i><mkinfit></i>)</a></code> <code><a href="summary.mkinfit.html">print(<i><summary.mkinfit></i>)</a></code> </p> </td> <td><p>Summary method for class "mkinfit"</p></td> </tr><tr> <td> + <p><code><a href="logLik.mkinfit.html">logLik(<i><mkinfit></i>)</a></code> </p> + </td> + <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td> + </tr><tr> + + <td> <p><code><a href="mkinresplot.html">mkinresplot()</a></code> </p> </td> <td><p>Function to plot residuals stored in an mkin object</p></td> @@ -219,12 +237,6 @@ with mkinfit</p></td> <p><code><a href="mkinerrmin.html">mkinerrmin()</a></code> </p> </td> <td><p>Calculate the minimum error to assume in order to pass the variance test</p></td> - </tr><tr> - - <td> - <p><code><a href="logLik.mkinfit.html">logLik(<i><mkinfit></i>)</a></code> </p> - </td> - <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td> </tr> </tbody><tbody> <tr> diff --git a/docs/reference/parms.html b/docs/reference/parms.html new file mode 100644 index 00000000..8ab26240 --- /dev/null +++ b/docs/reference/parms.html @@ -0,0 +1,200 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html lang="en"> + <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>Extract model parameters from mkinfit models — parms • mkin</title> + + +<!-- jquery --> +<script 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evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + </ul> +</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>Extract model parameters from mkinfit models</h1> + + <div class="hidden name"><code>parms.Rd</code></div> + </div> + + <div class="ref-description"> + <p>This function always returns degradation model parameters as well as error +model parameters, in order to avoid working with a fitted model without +considering the error structure that was assumed for the fit.</p> + </div> + + <pre class="usage"><span class='fu'>parms</span>(<span class='no'>object</span>, <span class='no'>...</span>) + +<span class='co'># S3 method for mkinfit</span> +<span class='fu'>parms</span>(<span class='no'>object</span>, <span class='kw'>transformed</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>A fitted model object</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Not used</p></td> + </tr> + <tr> + <th>transformed</th> + <td><p>Should the parameters be returned +as used internally during the optimisation?</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>A numeric vector of fitted model parameters</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> + + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + |