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diff --git a/docs/dev/reference/logLik.mkinfit.html b/docs/dev/reference/logLik.mkinfit.html index 3e9452c6..e77121d1 100644 --- a/docs/dev/reference/logLik.mkinfit.html +++ b/docs/dev/reference/logLik.mkinfit.html @@ -1,71 +1,16 @@ -<!-- 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>Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - 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<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,136 +45,143 @@ the error model." /> <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> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</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> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculated the log-likelihood of a fitted mkinfit object</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/logLik.mkinfit.R'><code>R/logLik.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/logLik.mkinfit.R" class="external-link"><code>R/logLik.mkinfit.R</code></a></small> <div class="hidden name"><code>logLik.mkinfit.Rd</code></div> </div> <div class="ref-description"> <p>This function returns the product of the likelihood densities of each observed value, as calculated as part of the fitting procedure using -<code><a href='https://rdrr.io/r/stats/Normal.html'>dnorm</a></code>, i.e. assuming normal distribution, and with the means +<code><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">dnorm</a></code>, i.e. assuming normal distribution, and with the means predicted by the degradation model, and the standard deviations predicted by the error model.</p> </div> - <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</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 object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>For compatibility with the generic method</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>An object of class <code><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></code> with the number of estimated + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> + + +<dt>...</dt> +<dd><p>For compatibility with the generic method</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>An object of class <code><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></code> with the number of estimated parameters (degradation model parameters plus variance model parameters) as attribute.</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - + </div> + <div id="details"> + <h2>Details</h2> <p>The total number of estimated parameters returned with the value of the likelihood is calculated as the sum of fitted degradation model parameters and the fitted error model parameters.</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p>Compare the AIC of columns of <code><a href='mmkin.html'>mmkin</a></code> objects using -<code><a href='AIC.mmkin.html'>AIC.mmkin</a></code>.</p></div> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p>Compare the AIC of columns of <code><a href="mmkin.html">mmkin</a></code> objects using +<code><a href="AIC.mmkin.html">AIC.mmkin</a></code>.</p></div> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> - <span class='co'># \dontrun{</span> - <span class='va'>sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span> - <span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>d_t</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span> - <span class='va'>f_nw</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>sfo_sfo</span>, <span class='va'>d_t</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># no weighting (weights are unity)</span> - <span class='va'>f_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nw</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span> - <span class='va'>f_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nw</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nw</span>, <span class='va'>f_obs</span>, <span class='va'>f_tc</span><span class='op'>)</span> -</div><div class='output co'>#> df AIC -#> f_nw 5 204.4486 -#> f_obs 6 205.8727 -#> f_tc 6 141.9656</div><div class='input'> <span class='co'># }</span> - -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span> <span class="va">d_t</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_nw</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">sfo_sfo</span>, <span class="va">d_t</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># no weighting (weights are unity)</span></span></span> +<span class="r-in"><span> <span class="va">f_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_nw</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_nw</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_nw</span>, <span class="va">f_obs</span>, <span class="va">f_tc</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df AIC</span> +<span class="r-out co"><span class="r-pr">#></span> f_nw 5 204.4486</span> +<span class="r-out co"><span class="r-pr">#></span> f_obs 6 205.8727</span> +<span class="r-out co"><span class="r-pr">#></span> f_tc 6 141.9656</span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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