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diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html deleted file mode 100644 index a3571fa5..00000000 --- a/docs/dev/reference/confint.mkinfit.html +++ /dev/null @@ -1,423 +0,0 @@ -<!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=1.0"><title>Confidence intervals for parameters of mkinfit objects — confint.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"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Confidence intervals for parameters of mkinfit objects — confint.mkinfit"><meta property="og: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. The speed of the method could likely be improved by using the -method of Venzon and Moolgavkar (1988)."><meta name="robots" content="noindex"><!-- 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 data-spy="scroll" data-target="#toc"> - - - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - 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<span class="fab fa-github fa-lg"></span> - - </a> -</li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <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="hidden name"><code>confint.mkinfit.Rd</code></div> - </div> - - <div class="ref-description"> - <p>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. The speed of the method could likely be improved by using the -method of Venzon and Moolgavkar (1988).</p> - </div> - - <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/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> -<span> level <span class="op">=</span> <span class="fl">0.95</span>,</span> -<span> alpha <span class="op">=</span> <span class="fl">1</span> <span class="op">-</span> <span class="va">level</span>,</span> -<span> <span class="va">cutoff</span>,</span> -<span> method <span class="op">=</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">"quadratic"</span>, <span class="st">"profile"</span><span class="op">)</span>,</span> -<span> transformed <span class="op">=</span> <span class="cn">TRUE</span>,</span> -<span> backtransform <span class="op">=</span> <span class="cn">TRUE</span>,</span> -<span> cores <span class="op">=</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span>,</span> -<span> rel_tol <span class="op">=</span> <span class="fl">0.01</span>,</span> -<span> quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span> -<span> <span class="va">...</span></span> -<span><span class="op">)</span></span></code></pre></div> - </div> - - <div id="arguments"> - <h2>Arguments</h2> - <dl><dt>object</dt> -<dd><p>An <code><a href="mkinfit.html">mkinfit</a></code> object</p></dd> - - -<dt>parm</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> -<dd><p>The confidence level required</p></dd> - - -<dt>alpha</dt> -<dd><p>The allowed error probability, overrides 'level' if specified.</p></dd> - - -<dt>cutoff</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> -<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. -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> -<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> -<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> -<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> -<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> -<dd><p>Should we suppress the message "Profiling the likelihood"</p></dd> - - -<dt>...</dt> -<dd><p>Not used</p></dd> - -</dl></div> - <div id="value"> - <h2>Value</h2> - - -<p>A matrix with columns giving lower and upper confidence limits for -each parameter.</p> - </div> - <div id="references"> - <h2>References</h2> - <p>Bates DM and Watts GW (1988) Nonlinear regression analysis & its applications</p> -<p>Pawitan Y (2013) In all likelihood - Statistical modelling and -inference using likelihood. Clarendon Press, Oxford.</p> -<p>Venzon DJ and Moolgavkar SH (1988) A Method for Computing -Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, -87–94.</p> - </div> - - <div id="ref-examples"> - <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_C</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/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</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 71.8242430 93.1600766</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.2109541 0.4440528</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 1.9778868 7.3681380</span> -<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="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f</span>, method <span class="op">=</span> <span class="st">"profile"</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> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 73.0641834 92.1392181</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.2170293 0.4235348</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 3.1307772 8.0628314</span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="co"># Set the number of cores for the profiling method for further examples</span></span></span> -<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"NOT_CRAN"</span><span class="op">)</span>, <span class="st">"true"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> -<span class="r-in"><span> <span class="va">n_cores</span> <span class="op"><-</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="fl">1</span></span></span> -<span class="r-in"><span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span></span> -<span class="r-in"><span> <span class="va">n_cores</span> <span class="op"><-</span> <span class="fl">1</span></span></span> -<span class="r-in"><span><span class="op">}</span></span></span> -<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"TRAVIS"</span><span class="op">)</span> <span class="op">!=</span> <span class="st">""</span><span class="op">)</span> <span class="va">n_cores</span> <span class="op">=</span> <span class="fl">1</span></span></span> -<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="va">n_cores</span> <span class="op">=</span> <span class="fl">1</span></span></span> -<span class="r-in"><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>parent <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="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></span> -<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"min"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">SFO_SFO.ff</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>, <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></span> -<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<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> 1.183 0.000 1.182 </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> -<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_no_parent_0</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>,</span></span> -<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> 0.418 0.116 0.294 </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> -<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.040762501 5.549764e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.046786482 5.500879e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.003892605 6.702778e-03</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 2.535612399 3.985263e+00</span> -<span class="r-in"><span><span class="va">ci_quadratic_transformed</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">"quadratic"</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">ci_quadratic_transformed</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 96.403841640 1.027931e+02</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.041033378 5.596269e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.046777902 5.511931e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.004012217 6.897547e-03</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.854918e+00</span> -<span class="r-in"><span><span class="va">ci_quadratic_untransformed</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">"quadratic"</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">ci_quadratic_untransformed</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 96.403841645 102.79312449</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.040485331 0.05535491</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.046611582 0.05494364</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.003835483 0.00668582</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.85491806</span> -<span class="r-in"><span><span class="co"># Against the expectation based on Bates and Watts (1988), the confidence</span></span></span> -<span class="r-in"><span><span class="co"># intervals based on the internal parameter transformation are less</span></span></span> -<span class="r-in"><span><span class="co"># congruent with the likelihood based intervals. Note the superiority of the</span></span></span> -<span class="r-in"><span><span class="co"># interval based on the untransformed fit for k_m1_sink</span></span></span> -<span class="r-in"><span><span class="va">rel_diffs_transformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_transformed</span> <span class="op">-</span> <span class="va">ci_profile</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">rel_diffs_untransformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_untransformed</span> <span class="op">-</span> <span class="va">ci_profile</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">rel_diffs_transformed</span> <span class="op"><</span> <span class="va">rel_diffs_untransformed</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 FALSE FALSE</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_sink TRUE FALSE</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 TRUE FALSE</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1_sink FALSE FALSE</span> -<span class="r-out co"><span class="r-pr">#></span> sigma FALSE FALSE</span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">signif</a></span><span class="op">(</span><span class="va">rel_diffs_transformed</span>, <span class="fl">3</span><span class="op">)</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 0.000541 0.000222</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.006650 0.008380</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.000183 0.002010</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.030700 0.029100</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 0.055000 0.032700</span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">signif</a></span><span class="op">(</span><span class="va">rel_diffs_untransformed</span>, <span class="fl">3</span><span class="op">)</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 0.000541 0.000222</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.006800 0.002570</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.003740 0.001180</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.014700 0.002530</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 0.055000 0.032700</span> -<span class="r-in"><span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="co"># Investigate a case with formation fractions</span></span></span> -<span class="r-in"><span><span class="va">f_d_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff</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="va">ci_profile_ff</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_2</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> -<span class="r-in"><span><span class="va">ci_profile_ff</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> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.090911032 1.071578e-01</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.003892606 6.702775e-03</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.471328495 5.611550e-01</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 2.535612399 3.985263e+00</span> -<span class="r-in"><span><span class="va">ci_quadratic_transformed_ff</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_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">ci_quadratic_transformed_ff</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 96.403833578 102.79311649</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.090823771 0.10725430</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.004012219 0.00689755</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469118824 0.55959615</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.85491806</span> -<span class="r-in"><span><span class="va">ci_quadratic_untransformed_ff</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_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">ci_quadratic_untransformed_ff</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 96.403833583 1.027931e+02</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.090491913 1.069035e-01</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.003835485 6.685823e-03</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469113477 5.598387e-01</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.854918e+00</span> -<span class="r-in"><span><span class="va">rel_diffs_transformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_transformed_ff</span> <span class="op">-</span> <span class="va">ci_profile_ff</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile_ff</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">rel_diffs_untransformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_untransformed_ff</span> <span class="op">-</span> <span class="va">ci_profile_ff</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile_ff</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="co"># While the confidence interval for the parent rate constant is closer to</span></span></span> -<span class="r-in"><span><span class="co"># the profile based interval when using the internal parameter</span></span></span> -<span class="r-in"><span><span class="co"># transformation, the interval for the metabolite rate constant is 'better</span></span></span> -<span class="r-in"><span><span class="co"># without internal parameter transformation.</span></span></span> -<span class="r-in"><span><span class="va">rel_diffs_transformed_ff</span> <span class="op"><</span> <span class="va">rel_diffs_untransformed_ff</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 FALSE FALSE</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent TRUE TRUE</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 FALSE FALSE</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 TRUE FALSE</span> -<span class="r-out co"><span class="r-pr">#></span> sigma TRUE FALSE</span> -<span class="r-in"><span><span class="va">rel_diffs_transformed_ff</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 0.0005408690 0.0002217233</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0009598532 0.0009001864</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0307283041 0.0290588361</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046881769 0.0027780063</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> -<span class="r-in"><span><span class="va">rel_diffs_untransformed_ff</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 0.0005408689 0.0002217232</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0046102156 0.0023732281</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0146740690 0.0025291820</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046995211 0.0023457712</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="co"># The profiling for the following fit does not finish in a reasonable time,</span></span></span> -<span class="r-in"><span><span class="co"># therefore we use the quadratic approximation</span></span></span> -<span class="r-in"><span><span class="va">m_synth_DFOP_par</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">"DFOP"</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">"M1"</span>, <span class="st">"M2"</span><span class="op">)</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> M2 <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> use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">DFOP_par_c</span> <span class="op"><-</span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span></span> -<span class="r-in"><span><span class="va">f_tc_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>, <span class="va">DFOP_par_c</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span></span> -<span class="r-in"><span> error_model_algorithm <span class="op">=</span> <span class="st">"direct"</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/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_tc_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</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 94.596039609 106.19954892</span> -<span class="r-out co"><span class="r-pr">#></span> k_M1 0.037605368 0.04490762</span> -<span class="r-out co"><span class="r-pr">#></span> k_M2 0.008568731 0.01087676</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.021462489 0.62023882</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.015165617 0.37975348</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.273897348 0.33388101</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.018614554 0.02250378</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.671943411 0.73583305</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.251283495 0.83992077</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.040411024 0.07662008</span> -<span class="r-in"><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_tc_2</span>, <span class="st">"parent_0"</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</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 94.59604 106.1995</span> -<span class="r-in"><span><span class="co"># }</span></span></span> -</code></pre></div> - </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> - - - <footer><div class="copyright"> - <p></p><p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> -</div> - - </footer></div> - - - - - - - </body></html> - |