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-rw-r--r--docs/dev/reference/confint.mkinfit.html225
1 files changed, 123 insertions, 102 deletions
diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html
index 5b683355..745f2dc4 100644
--- a/docs/dev/reference/confint.mkinfit.html
+++ b/docs/dev/reference/confint.mkinfit.html
@@ -79,7 +79,7 @@ method of Venzon and Moolgavkar (1988)." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
</span>
</div>
@@ -127,7 +127,7 @@ method of Venzon and Moolgavkar (1988)." />
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
- <a href="http://github.com/jranke/mkin/">
+ <a href="https://github.com/jranke/mkin/">
<span class="fab fa fab fa-github fa-lg"></span>
</a>
@@ -146,7 +146,7 @@ method of Venzon and Moolgavkar (1988)." />
<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='http://github.com/jranke/mkin/blob/master/R/confint.mkinfit.R'><code>R/confint.mkinfit.R</code></a></small>
+ <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/confint.mkinfit.R'><code>R/confint.mkinfit.R</code></a></small>
<div class="hidden name"><code>confint.mkinfit.Rd</code></div>
</div>
@@ -162,20 +162,20 @@ method of Venzon and Moolgavkar (1988).</p>
</div>
<pre class="usage"><span class='co'># S3 method for mkinfit</span>
-<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(
- <span class='no'>object</span>,
- <span class='no'>parm</span>,
- <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>,
- <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1</span> - <span class='no'>level</span>,
- <span class='no'>cutoff</span>,
- <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"quadratic"</span>, <span class='st'>"profile"</span>),
- <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>backtransform</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>cores</span> <span class='kw'>=</span> <span class='kw pkg'>parallel</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span>(),
- <span class='kw'>rel_tol</span> <span class='kw'>=</span> <span class='fl'>0.01</span>,
- <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='no'>...</span>
-)</pre>
+<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>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'>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'>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></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -257,68 +257,79 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
87–94.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
+ <pre class="examples"><div class='input'><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 class='fu'><a href='https://rdrr.io/r/stats/confint.html'>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>
+</div><div class='output co'>#&gt; 2.5% 97.5%
#&gt; parent_0 71.8242430 93.1600766
#&gt; k_parent 0.2109541 0.4440528
#&gt; sigma 1.9778868 7.3681380</div><div class='input'>
<span class='co'># \dontrun{</span>
-<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>)</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; 2.5% 97.5%
+<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>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>
+</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; 2.5% 97.5%
#&gt; parent_0 73.0641834 92.1392181
#&gt; k_parent 0.2170293 0.4235348
#&gt; sigma 3.1307772 8.0628314</div><div class='input'>
<span class='co'># Set the number of cores for the profiling method for further examples</span>
-<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span>(<span class='st'>"NOT_CRAN"</span>), <span class='st'>"true"</span>)) {
- <span class='no'>n_cores</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>parallel</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span>() - <span class='fl'>1</span>
-} <span class='kw'>else</span> {
- <span class='no'>n_cores</span> <span class='kw'>&lt;-</span> <span class='fl'>1</span>
-}
-<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span>(<span class='st'>"TRAVIS"</span>) <span class='kw'>!=</span> <span class='st'>""</span>) <span class='no'>n_cores</span> <span class='kw'>=</span> <span class='fl'>1</span>
-<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span>()[<span class='st'>"sysname"</span>] <span class='kw'>==</span> <span class='st'>"Windows"</span>) <span class='no'>n_cores</span> <span class='kw'>=</span> <span class='fl'>1</span>
-
-<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
- <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='no'>f_d_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; user system elapsed
-#&gt; 3.810 0.964 3.430 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span>
+<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>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 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'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>1</span>
+<span class='op'>}</span> <span class='kw'>else</span> <span class='op'>{</span>
+ <span class='va'>n_cores</span> <span class='op'>&lt;-</span> <span class='fl'>1</span>
+<span class='op'>}</span>
+<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>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 class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>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 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='mkinsub.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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</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='mkinsub.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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</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 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'>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 class='fu'><a href='https://rdrr.io/r/base/system.time.html'>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'>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>
+</div><div class='output co'>#&gt; user system elapsed
+#&gt; 3.829 1.000 3.519 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span>
<span class='co'># If we additionally exclude parent_0 (the confidence of which is often of</span>
<span class='co'># minor interest), we get a nice performance improvement from about 50</span>
<span class='co'># seconds to about 12 seconds if we use at least four cores</span>
-<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile_no_parent_0</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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='kw'>cores</span> <span class='kw'>=</span> <span class='no'>n_cores</span>))</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; <span class='warning'>Warning: scheduled cores 2, 1, 3 encountered errors in user code, all values of the jobs will be affected</span></div><div class='output co'>#&gt; <span class='error'>Error in dimnames(x) &lt;- dn: length of 'dimnames' [2] not equal to array extent</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.015 0.029 0.198</span></div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#&gt; 2.5% 97.5%
+<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>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'>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 class='fu'><a href='https://rdrr.io/r/base/c.html'>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>
+</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; <span class='warning'>Warning: scheduled cores 2, 1, 3 encountered errors in user code, all values of the jobs will be affected</span></div><div class='output co'>#&gt; <span class='error'>Error in dimnames(x) &lt;- dn: length of 'dimnames' [2] not equal to array extent</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.011 0.029 0.241</span></div><div class='input'><span class='va'>ci_profile</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
#&gt; parent_0 96.456003640 1.027703e+02
#&gt; k_parent 0.090911032 1.071578e-01
-#&gt; k_m1 0.003892605 6.702778e-03
+#&gt; k_m1 0.003892606 6.702775e-03
#&gt; f_parent_to_m1 0.471328495 5.611550e-01
-#&gt; sigma 2.535612399 3.985263e+00</div><div class='input'><span class='no'>ci_quadratic_transformed</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)
-<span class='no'>ci_quadratic_transformed</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403839460 1.027931e+02
-#&gt; k_parent 0.090823790 1.072543e-01
-#&gt; k_m1 0.004012216 6.897547e-03
-#&gt; f_parent_to_m1 0.469118713 5.595960e-01
-#&gt; sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>ci_quadratic_untransformed</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-<span class='no'>ci_quadratic_untransformed</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403839413 1.027931e+02
-#&gt; k_parent 0.090491931 1.069035e-01
-#&gt; k_m1 0.003835483 6.685819e-03
-#&gt; f_parent_to_m1 0.469113365 5.598386e-01
+#&gt; sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>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 class='va'>ci_quadratic_transformed</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 96.403833585 102.79311650
+#&gt; k_parent 0.090823771 0.10725430
+#&gt; k_m1 0.004012219 0.00689755
+#&gt; f_parent_to_m1 0.469118824 0.55959615
+#&gt; sigma 2.396089689 3.85491806</div><div class='input'><span class='va'>ci_quadratic_untransformed</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>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 class='va'>ci_quadratic_untransformed</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 96.403833589 1.027931e+02
+#&gt; k_parent 0.090491913 1.069035e-01
+#&gt; k_m1 0.003835485 6.685823e-03
+#&gt; f_parent_to_m1 0.469113477 5.598387e-01
#&gt; sigma 2.396089689 3.854918e+00</div><div class='input'><span class='co'># Against the expectation based on Bates and Watts (1988), the confidence</span>
<span class='co'># intervals based on the internal parameter transformation are less</span>
<span class='co'># congruent with the likelihood based intervals. Note the superiority of the</span>
<span class='co'># interval based on the untransformed fit for k_m1_sink</span>
-<span class='no'>rel_diffs_transformed</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_transformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>)
-<span class='no'>rel_diffs_untransformed</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_untransformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>)
-<span class='no'>rel_diffs_transformed</span> <span class='kw'>&lt;</span> <span class='no'>rel_diffs_untransformed</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 TRUE TRUE
+<span class='va'>rel_diffs_transformed</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>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 class='va'>rel_diffs_untransformed</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>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 class='va'>rel_diffs_transformed</span> <span class='op'>&lt;</span> <span class='va'>rel_diffs_untransformed</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 FALSE FALSE
#&gt; k_parent TRUE TRUE
#&gt; k_m1 FALSE FALSE
#&gt; f_parent_to_m1 TRUE FALSE
-#&gt; sigma FALSE FALSE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_transformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; sigma TRUE FALSE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_transformed</span>, <span class='fl'>3</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
#&gt; parent_0 0.000541 0.000222
#&gt; k_parent 0.000960 0.000900
#&gt; k_m1 0.030700 0.029100
#&gt; f_parent_to_m1 0.004690 0.002780
-#&gt; sigma 0.055000 0.032700</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_untransformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; sigma 0.055000 0.032700</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_untransformed</span>, <span class='fl'>3</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
#&gt; parent_0 0.000541 0.000222
#&gt; k_parent 0.004610 0.002370
#&gt; k_m1 0.014700 0.002530
@@ -326,66 +337,76 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
#&gt; sigma 0.055000 0.032700</div><div class='input'>
<span class='co'># Investigate a case with formation fractions</span>
-<span class='no'>f_d_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><span class='no'>ci_profile_ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='no'>n_cores</span>)</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='input'><span class='no'>ci_profile_ff</span></div><div class='output co'>#&gt; 2.5% 97.5%
+<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'>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 class='va'>ci_profile_ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>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>
+</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='input'><span class='va'>ci_profile_ff</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
#&gt; parent_0 96.456003640 1.027703e+02
#&gt; k_parent 0.090911032 1.071578e-01
-#&gt; k_m1 0.003892605 6.702778e-03
+#&gt; k_m1 0.003892606 6.702775e-03
#&gt; f_parent_to_m1 0.471328495 5.611550e-01
-#&gt; sigma 2.535612399 3.985263e+00</div><div class='input'><span class='no'>ci_quadratic_transformed_ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)
-<span class='no'>ci_quadratic_transformed_ff</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403839460 1.027931e+02
-#&gt; k_parent 0.090823790 1.072543e-01
-#&gt; k_m1 0.004012216 6.897547e-03
-#&gt; f_parent_to_m1 0.469118713 5.595960e-01
-#&gt; sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>ci_quadratic_untransformed_ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-<span class='no'>ci_quadratic_untransformed_ff</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403839413 1.027931e+02
-#&gt; k_parent 0.090491931 1.069035e-01
-#&gt; k_m1 0.003835483 6.685819e-03
-#&gt; f_parent_to_m1 0.469113365 5.598386e-01
-#&gt; sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>rel_diffs_transformed_ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_transformed_ff</span> - <span class='no'>ci_profile_ff</span>)/<span class='no'>ci_profile_ff</span>)
-<span class='no'>rel_diffs_untransformed_ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_untransformed_ff</span> - <span class='no'>ci_profile_ff</span>)/<span class='no'>ci_profile_ff</span>)
+#&gt; sigma 2.535612399 3.985263e+00</div><div class='input'><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'>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 class='va'>ci_quadratic_transformed_ff</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 96.403833585 102.79311650
+#&gt; k_parent 0.090823771 0.10725430
+#&gt; k_m1 0.004012219 0.00689755
+#&gt; f_parent_to_m1 0.469118824 0.55959615
+#&gt; sigma 2.396089689 3.85491806</div><div class='input'><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'>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 class='va'>ci_quadratic_untransformed_ff</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 96.403833589 1.027931e+02
+#&gt; k_parent 0.090491913 1.069035e-01
+#&gt; k_m1 0.003835485 6.685823e-03
+#&gt; f_parent_to_m1 0.469113477 5.598387e-01
+#&gt; sigma 2.396089689 3.854918e+00</div><div class='input'><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'>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 class='va'>rel_diffs_untransformed_ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>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 class='co'># While the confidence interval for the parent rate constant is closer to</span>
<span class='co'># the profile based interval when using the internal parameter</span>
<span class='co'># transformation, the interval for the metabolite rate constant is 'better</span>
<span class='co'># without internal parameter transformation.</span>
-<span class='no'>rel_diffs_transformed_ff</span> <span class='kw'>&lt;</span> <span class='no'>rel_diffs_untransformed_ff</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 TRUE TRUE
+<span class='va'>rel_diffs_transformed_ff</span> <span class='op'>&lt;</span> <span class='va'>rel_diffs_untransformed_ff</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 FALSE FALSE
#&gt; k_parent TRUE TRUE
#&gt; k_m1 FALSE FALSE
#&gt; f_parent_to_m1 TRUE FALSE
-#&gt; sigma FALSE FALSE</div><div class='input'><span class='no'>rel_diffs_transformed_ff</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.0005408080 0.0002217794
-#&gt; k_parent 0.0009596417 0.0009003876
-#&gt; k_m1 0.0307277370 0.0290579182
-#&gt; f_parent_to_m1 0.0046884130 0.0027782556
-#&gt; sigma 0.0550252516 0.0327066836</div><div class='input'><span class='no'>rel_diffs_untransformed_ff</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.0005408085 0.0002217799
-#&gt; k_parent 0.0046100096 0.0023730229
-#&gt; k_m1 0.0146746469 0.0025301011
-#&gt; f_parent_to_m1 0.0046997599 0.0023460223
+#&gt; sigma TRUE FALSE</div><div class='input'><span class='va'>rel_diffs_transformed_ff</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 0.0005408689 0.0002217234
+#&gt; k_parent 0.0009598532 0.0009001864
+#&gt; k_m1 0.0307283044 0.0290588365
+#&gt; f_parent_to_m1 0.0046881768 0.0027780063
+#&gt; sigma 0.0550252516 0.0327066836</div><div class='input'><span class='va'>rel_diffs_untransformed_ff</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 0.0005408689 0.0002217233
+#&gt; k_parent 0.0046102155 0.0023732281
+#&gt; k_m1 0.0146740688 0.0025291817
+#&gt; f_parent_to_m1 0.0046995211 0.0023457712
#&gt; sigma 0.0550252516 0.0327066836</div><div class='input'>
<span class='co'># The profiling for the following fit does not finish in a reasonable time,</span>
<span class='co'># therefore we use the quadratic approximation</span>
-<span class='no'>m_synth_DFOP_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
- <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
- <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
- <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='no'>DFOP_par_c</span> <span class='kw'>&lt;-</span> <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>
-<span class='no'>f_tc_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>, <span class='no'>DFOP_par_c</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>,
- <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='st'>"direct"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 94.59613833 106.19939215
-#&gt; k_M1 0.03760542 0.04490759
-#&gt; k_M2 0.00856874 0.01087675
-#&gt; f_parent_to_M1 0.02146166 0.62023888
-#&gt; f_parent_to_M2 0.01516502 0.37975343
-#&gt; k1 0.27389751 0.33388078
-#&gt; k2 0.01861456 0.02250379
-#&gt; g 0.67194349 0.73583256
-#&gt; sigma_low 0.25128383 0.83992146
-#&gt; rsd_high 0.04041100 0.07662001</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='st'>"parent_0"</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 94.59614 106.1994</div><div class='input'># }
+<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='mkinsub.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'>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>,
+ M1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
+ M2 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</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 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 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>,
+ 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 class='fu'><a href='https://rdrr.io/r/stats/confint.html'>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>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 94.596126334 106.19944007
+#&gt; k_M1 0.037605408 0.04490759
+#&gt; k_M2 0.008568739 0.01087675
+#&gt; f_parent_to_M1 0.021463787 0.62023881
+#&gt; f_parent_to_M2 0.015166531 0.37975349
+#&gt; k1 0.273897467 0.33388084
+#&gt; k2 0.018614555 0.02250379
+#&gt; g 0.671943606 0.73583278
+#&gt; sigma_low 0.251283766 0.83992113
+#&gt; rsd_high 0.040411014 0.07662005</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>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>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 94.59613 106.1994</div><div class='input'><span class='co'># }</span>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -402,7 +423,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
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