aboutsummaryrefslogtreecommitdiff
path: root/docs/reference/confint.mkinfit.html
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
commit8d1a84ac2190538ed3bac53a303064e281595868 (patch)
treeacb894d85ab7ec87c4911c355a5264a77e08e34b /docs/reference/confint.mkinfit.html
parent51d63256a7b3020ee11931d61b4db97b9ded02c0 (diff)
parent4200e566ad2600f56bc3987669aeab88582139eb (diff)
Merge branch 'main' into custom_lsoda_call
Diffstat (limited to 'docs/reference/confint.mkinfit.html')
-rw-r--r--docs/reference/confint.mkinfit.html261
1 files changed, 146 insertions, 115 deletions
diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html
index 5469f8f8..8d7c272f 100644
--- a/docs/reference/confint.mkinfit.html
+++ b/docs/reference/confint.mkinfit.html
@@ -24,7 +24,7 @@ method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cd
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
</span>
</div>
@@ -51,19 +51,25 @@ method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cd
<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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ <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>
+ <li>
+ <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
</li>
</ul></li>
<li>
@@ -101,66 +107,91 @@ method of Venzon and Moolgavkar (1988).</p>
</div>
<div id="ref-usage">
- <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mkinfit</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">object</span>,
- <span class="va">parm</span>,
- level <span class="op">=</span> <span class="fl">0.95</span>,
- alpha <span class="op">=</span> <span class="fl">1</span> <span class="op">-</span> <span class="va">level</span>,
- <span class="va">cutoff</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>,
- transformed <span class="op">=</span> <span class="cn">TRUE</span>,
- backtransform <span class="op">=</span> <span class="cn">TRUE</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>,
- rel_tol <span class="op">=</span> <span class="fl">0.01</span>,
- quiet <span class="op">=</span> <span class="cn">FALSE</span>,
- <span class="va">...</span>
-<span class="op">)</span></code></pre></div>
+ <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 &gt; 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
+
+
+<p>A matrix with columns giving lower and upper confidence limits for
each parameter.</p>
</div>
<div id="references">
@@ -175,178 +206,178 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
<div id="ref-examples">
<h2>Examples</h2>
- <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">f</span> <span class="op">&lt;-</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 class="r-in"><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>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">f</span> <span class="op">&lt;-</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">#&gt;</span> 2.5% 97.5%</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 71.8242430 93.1600766</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent 0.2109541 0.4440528</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 1.9778868 7.3681380</span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># \dontrun{</span></span>
-<span class="r-in"><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 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">#&gt;</span> Profiling the likelihood</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2.5% 97.5%</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 73.0641834 92.1392181</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent 0.2170293 0.4235348</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 3.1307772 8.0628314</span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># Set the number of cores for the profiling method for further examples</span></span>
-<span class="r-in"><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 class="r-in"> <span class="va">n_cores</span> <span class="op">&lt;-</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 class="r-in"><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span>
-<span class="r-in"> <span class="va">n_cores</span> <span class="op">&lt;-</span> <span class="fl">1</span></span>
-<span class="r-in"><span class="op">}</span></span>
-<span class="r-in"><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 class="r-in"><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 class="r-in"></span>
-<span class="r-in"><span class="va">SFO_SFO</span> <span class="op">&lt;-</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 class="r-in"> 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 class="r-in"><span class="va">SFO_SFO.ff</span> <span class="op">&lt;-</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 class="r-in"> 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 class="r-in"><span class="va">f_d_1</span> <span class="op">&lt;-</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 class="r-in"><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">&lt;-</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 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">&lt;-</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">&lt;-</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">&lt;-</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">&lt;-</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">&lt;-</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">&lt;-</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">#&gt;</span> user system elapsed </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3.409 0.000 3.411 </span>
-<span class="r-in"><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span>
-<span class="r-in"><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span>
-<span class="r-in"><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span>
-<span class="r-in"><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">&lt;-</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 class="r-in"> <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 class="r-out co"><span class="r-pr">#&gt;</span> 3.931 0.000 3.932 </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">&lt;-</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">#&gt;</span> Profiling the likelihood</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> user system elapsed </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1.317 0.152 0.847 </span>
-<span class="r-in"><span class="va">ci_profile</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2.219 0.000 2.219 </span>
+<span class="r-in"><span><span class="va">ci_profile</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2.5% 97.5%</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 96.456003640 1.027703e+02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_sink 0.040762501 5.549764e-02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_m1 0.046786482 5.500879e-02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1_sink 0.003892605 6.702778e-03</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 2.535612399 3.985263e+00</span>
-<span class="r-in"><span class="va">ci_quadratic_transformed</span> <span class="op">&lt;-</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 class="r-in"><span class="va">ci_quadratic_transformed</span></span>
+<span class="r-in"><span><span class="va">ci_quadratic_transformed</span> <span class="op">&lt;-</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">#&gt;</span> 2.5% 97.5%</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 96.403841640 1.027931e+02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_sink 0.041033378 5.596269e-02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_m1 0.046777902 5.511931e-02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1_sink 0.004012217 6.897547e-03</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 2.396089689 3.854918e+00</span>
-<span class="r-in"><span class="va">ci_quadratic_untransformed</span> <span class="op">&lt;-</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 class="r-in"><span class="va">ci_quadratic_untransformed</span></span>
+<span class="r-in"><span><span class="va">ci_quadratic_untransformed</span> <span class="op">&lt;-</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">#&gt;</span> 2.5% 97.5%</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 96.403841645 102.79312449</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_sink 0.040485331 0.05535491</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_m1 0.046611582 0.05494364</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1_sink 0.003835483 0.00668582</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 2.396089689 3.85491806</span>
-<span class="r-in"><span class="co"># Against the expectation based on Bates and Watts (1988), the confidence</span></span>
-<span class="r-in"><span class="co"># intervals based on the internal parameter transformation are less</span></span>
-<span class="r-in"><span class="co"># congruent with the likelihood based intervals. Note the superiority of the</span></span>
-<span class="r-in"><span class="co"># interval based on the untransformed fit for k_m1_sink</span></span>
-<span class="r-in"><span class="va">rel_diffs_transformed</span> <span class="op">&lt;-</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 class="r-in"><span class="va">rel_diffs_untransformed</span> <span class="op">&lt;-</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 class="r-in"><span class="va">rel_diffs_transformed</span> <span class="op">&lt;</span> <span class="va">rel_diffs_untransformed</span></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">&lt;-</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">&lt;-</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">&lt;</span> <span class="va">rel_diffs_untransformed</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2.5% 97.5%</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_sink TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_m1 TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1_sink FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma FALSE FALSE</span>
-<span class="r-in"><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 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">#&gt;</span> 2.5% 97.5%</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 0.000541 0.000222</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_sink 0.006650 0.008380</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_m1 0.000183 0.002010</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1_sink 0.030700 0.029100</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 0.055000 0.032700</span>
-<span class="r-in"><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 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">#&gt;</span> 2.5% 97.5%</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 0.000541 0.000222</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_sink 0.006800 0.002570</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_m1 0.003740 0.001180</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1_sink 0.014700 0.002530</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 0.055000 0.032700</span>
-<span class="r-in"></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># Investigate a case with formation fractions</span></span>
-<span class="r-in"><span class="va">f_d_2</span> <span class="op">&lt;-</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 class="r-in"><span class="va">ci_profile_ff</span> <span class="op">&lt;-</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 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">&lt;-</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">&lt;-</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">#&gt;</span> Profiling the likelihood</span>
-<span class="r-in"><span class="va">ci_profile_ff</span></span>
+<span class="r-in"><span><span class="va">ci_profile_ff</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2.5% 97.5%</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 96.456003640 1.027703e+02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent 0.090911032 1.071578e-01</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1 0.003892606 6.702775e-03</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1 0.471328495 5.611550e-01</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 2.535612399 3.985263e+00</span>
-<span class="r-in"><span class="va">ci_quadratic_transformed_ff</span> <span class="op">&lt;-</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 class="r-in"><span class="va">ci_quadratic_transformed_ff</span></span>
+<span class="r-in"><span><span class="va">ci_quadratic_transformed_ff</span> <span class="op">&lt;-</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">#&gt;</span> 2.5% 97.5%</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 96.403833565 102.79311648</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 96.403833578 102.79311649</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent 0.090823771 0.10725430</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1 0.004012219 0.00689755</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1 0.469118824 0.55959615</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 2.396089689 3.85491806</span>
-<span class="r-in"><span class="va">ci_quadratic_untransformed_ff</span> <span class="op">&lt;-</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 class="r-in"><span class="va">ci_quadratic_untransformed_ff</span></span>
+<span class="r-in"><span><span class="va">ci_quadratic_untransformed_ff</span> <span class="op">&lt;-</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">#&gt;</span> 2.5% 97.5%</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 96.403833570 1.027931e+02</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 96.403833583 1.027931e+02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent 0.090491913 1.069035e-01</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1 0.003835485 6.685823e-03</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1 0.469113477 5.598387e-01</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 2.396089689 3.854918e+00</span>
-<span class="r-in"><span class="va">rel_diffs_transformed_ff</span> <span class="op">&lt;-</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 class="r-in"><span class="va">rel_diffs_untransformed_ff</span> <span class="op">&lt;-</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 class="r-in"><span class="co"># While the confidence interval for the parent rate constant is closer to</span></span>
-<span class="r-in"><span class="co"># the profile based interval when using the internal parameter</span></span>
-<span class="r-in"><span class="co"># transformation, the interval for the metabolite rate constant is 'better</span></span>
-<span class="r-in"><span class="co"># without internal parameter transformation.</span></span>
-<span class="r-in"><span class="va">rel_diffs_transformed_ff</span> <span class="op">&lt;</span> <span class="va">rel_diffs_untransformed_ff</span></span>
+<span class="r-in"><span><span class="va">rel_diffs_transformed_ff</span> <span class="op">&lt;-</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">&lt;-</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">&lt;</span> <span class="va">rel_diffs_untransformed_ff</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2.5% 97.5%</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1 FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1 TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma TRUE FALSE</span>
-<span class="r-in"><span class="va">rel_diffs_transformed_ff</span></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">#&gt;</span> 2.5% 97.5%</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 0.0005408691 0.0002217232</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent 0.0009598534 0.0009001862</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1 0.0307283050 0.0290588375</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1 0.0046881765 0.0027780058</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 0.0005408690 0.0002217233</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent 0.0009598532 0.0009001864</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1 0.0307283041 0.0290588361</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1 0.0046881769 0.0027780063</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 0.0550252516 0.0327066836</span>
-<span class="r-in"><span class="va">rel_diffs_untransformed_ff</span></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">#&gt;</span> 2.5% 97.5%</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 0.0005408691 0.0002217231</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent 0.0046102157 0.0023732283</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1 0.0146740682 0.0025291807</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1 0.0046995207 0.0023457708</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 0.0005408689 0.0002217232</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent 0.0046102156 0.0023732281</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1 0.0146740690 0.0025291820</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1 0.0046995211 0.0023457712</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 0.0550252516 0.0327066836</span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># The profiling for the following fit does not finish in a reasonable time,</span></span>
-<span class="r-in"><span class="co"># therefore we use the quadratic approximation</span></span>
-<span class="r-in"><span class="va">m_synth_DFOP_par</span> <span class="op">&lt;-</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 class="r-in"> 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 class="r-in"> 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 class="r-in"> 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 class="r-in"><span class="va">DFOP_par_c</span> <span class="op">&lt;-</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 class="r-in"><span class="va">f_tc_2</span> <span class="op">&lt;-</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 class="r-in"> 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 class="r-in"><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 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">&lt;-</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">&lt;-</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">&lt;-</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">#&gt;</span> 2.5% 97.5%</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 94.596210088 106.19935874</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> k_M1 0.037605436 0.04490756</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> k_M2 0.008568746 0.01087674</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_M1 0.021466645 0.62023879</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_M2 0.015168549 0.37975352</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> k1 0.273897574 0.33388069</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> k2 0.018614555 0.02250379</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> g 0.671943815 0.73583258</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> sigma_low 0.251283808 0.83992121</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> rsd_high 0.040411010 0.07662004</span>
-<span class="r-in"><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 class="r-out co"><span class="r-pr">#&gt;</span> parent_0 94.596039609 106.19954892</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_M1 0.037605368 0.04490762</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_M2 0.008568731 0.01087676</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_M1 0.021462489 0.62023882</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_M2 0.015165617 0.37975348</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k1 0.273897348 0.33388101</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k2 0.018614554 0.02250378</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> g 0.671943411 0.73583305</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma_low 0.251283495 0.83992077</span>
+<span class="r-out co"><span class="r-pr">#&gt;</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">#&gt;</span> 2.5% 97.5%</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 94.59621 106.1994</span>
-<span class="r-in"><span class="co"># }</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 94.59604 106.1995</span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>
</div>
@@ -361,7 +392,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>
</footer></div>

Contact - Imprint