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diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 4d4fa012..195ad75b 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -1,88 +1,75 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="The default method 'quadratic' is based on the quadratic approximation of +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Confidence intervals for parameters of mkinfit objects — confint.mkinfit • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Confidence intervals for parameters of mkinfit objects — confint.mkinfit"><meta name="description" content="The default method 'quadratic' is based on the quadratic approximation of the curvature of the likelihood function at the maximum likelihood parameter estimates. The alternative method 'profile' is based on the profile likelihood for each parameter. The 'profile' method uses two nested optimisations and can take a very long time, even if parallelized by specifying 'cores' on unixoid platforms. 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The alternative method 'profile' is based on the profile likelihood for each parameter. The 'profile' method uses two nested optimisations and can take a very long time, even if parallelized by specifying 'cores' on unixoid platforms. The speed of the method could likely be improved by using the -method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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> +method of Venzon and Moolgavkar (1988)."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-default navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">mkin</a> - 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+ </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Confidence intervals for parameters of mkinfit objects</h1> + + <h1>Confidence intervals for parameters of mkinfit objects</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/confint.mkinfit.R" class="external-link"><code>R/confint.mkinfit.R</code></a></small> <div class="d-none name"><code>confint.mkinfit.Rd</code></div> </div> @@ -100,7 +87,7 @@ method of Venzon and Moolgavkar (1988).</p> <div class="section level2"> <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for class 'mkinfit'</span></span> <span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span></span> <span> <span class="va">object</span>,</span> <span> <span class="va">parm</span>,</span> @@ -119,30 +106,32 @@ method of Venzon and Moolgavkar (1988).</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>object</dt> + + +<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt> <dd><p>An <code><a href="mkinfit.html">mkinfit</a></code> object</p></dd> -<dt>parm</dt> +<dt id="arg-parm">parm<a class="anchor" aria-label="anchor" href="#arg-parm"></a></dt> <dd><p>A vector of names of the parameters which are to be given confidence intervals. If missing, all parameters are considered.</p></dd> -<dt>level</dt> +<dt id="arg-level">level<a class="anchor" aria-label="anchor" href="#arg-level"></a></dt> <dd><p>The confidence level required</p></dd> -<dt>alpha</dt> +<dt id="arg-alpha">alpha<a class="anchor" aria-label="anchor" href="#arg-alpha"></a></dt> <dd><p>The allowed error probability, overrides 'level' if specified.</p></dd> -<dt>cutoff</dt> +<dt id="arg-cutoff">cutoff<a class="anchor" aria-label="anchor" href="#arg-cutoff"></a></dt> <dd><p>Possibility to specify an alternative cutoff for the difference in the log-likelihoods at the confidence boundary. Specifying an explicit cutoff value overrides arguments 'level' and 'alpha'</p></dd> -<dt>method</dt> +<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt> <dd><p>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. @@ -150,41 +139,39 @@ The 'profile' method searches the parameter space for the cutoff of the confidence intervals by means of a likelihood ratio test.</p></dd> -<dt>transformed</dt> +<dt id="arg-transformed">transformed<a class="anchor" aria-label="anchor" href="#arg-transformed"></a></dt> <dd><p>If the quadratic approximation is used, should it be applied to the likelihood based on the transformed parameters?</p></dd> -<dt>backtransform</dt> +<dt id="arg-backtransform">backtransform<a class="anchor" aria-label="anchor" href="#arg-backtransform"></a></dt> <dd><p>If we approximate the likelihood in terms of the transformed parameters, should we backtransform the parameters with their confidence intervals?</p></dd> -<dt>cores</dt> +<dt id="arg-cores">cores<a class="anchor" aria-label="anchor" href="#arg-cores"></a></dt> <dd><p>The number of cores to be used for multicore processing. On Windows machines, cores > 1 is currently not supported.</p></dd> -<dt>rel_tol</dt> +<dt id="arg-rel-tol">rel_tol<a class="anchor" aria-label="anchor" href="#arg-rel-tol"></a></dt> <dd><p>If the method is 'profile', what should be the accuracy of the lower and upper bounds, relative to the estimate obtained from the quadratic method?</p></dd> -<dt>quiet</dt> +<dt id="arg-quiet">quiet<a class="anchor" aria-label="anchor" href="#arg-quiet"></a></dt> <dd><p>Should we suppress the message "Profiling the likelihood"</p></dd> -<dt>...</dt> +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dd><p>Not used</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>A matrix with columns giving lower and upper confidence limits for + <p>A matrix with columns giving lower and upper confidence limits for each parameter.</p> </div> <div class="section level2"> @@ -230,7 +217,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span><span class="va">f_d_1</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="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>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.203 0.000 1.203 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.206 0.000 1.206 </span> <span class="r-in"><span><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span></span> <span class="r-in"><span><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span></span> <span class="r-in"><span><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span></span> @@ -238,7 +225,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"k_parent_sink"</span>, <span class="st">"k_parent_m1"</span>, <span class="st">"k_m1_sink"</span>, <span class="st">"sigma"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 0.438 0.097 0.301 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.406 0.172 0.317 </span> <span class="r-in"><span><span class="va">ci_profile</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> @@ -373,23 +360,23 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> </footer></div> - - + + </body></html> |