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diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html new file mode 100644 index 00000000..a0051a85 --- /dev/null +++ b/docs/dev/reference/confint.mkinfit.html @@ -0,0 +1,382 @@ +<!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"><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. The speed of the method could likely be improved by using the +method of Venzon and Moolgavkar (1988)."><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"></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + + <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> + + <small class="nav-text text-info me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">1.2.10</small> + + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> 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class="external-link"><code>R/confint.mkinfit.R</code></a></small> + <div class="d-none name"><code>confint.mkinfit.Rd</code></div> + </div> + + <div class="ref-description section level2"> + <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 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 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> +<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 class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + + +<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 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 id="arg-level">level<a class="anchor" aria-label="anchor" href="#arg-level"></a></dt> +<dd><p>The confidence level required</p></dd> + + +<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 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 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. +The 'profile' method searches the parameter space for the +cutoff of the confidence intervals by means of a likelihood ratio test.</p></dd> + + +<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 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 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 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 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 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 +each parameter.</p> + </div> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></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 class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></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> 1.182 0.004 1.186 </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> 0.429 0.171 0.324 </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 96.403833581 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 96.403833586 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 0.0307283045 0.0290588367</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046881768 0.0027780062</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 0.0002217233</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0046102155 0.0023732280</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0146740687 0.0025291815</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046995210 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 94.596181875 106.19936592</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.037605432 0.04490757</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.008568745 0.01087675</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.021464676 0.62023880</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.015167158 0.37975350</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.273897535 0.33388072</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.018614555 0.02250379</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.671943738 0.73583261</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.251283679 0.83992102</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.040411022 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 94.59618 106.1994</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> + </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>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown-footer-right"> + <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> + |