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authorJohannes Ranke <jranke@uni-bremen.de>2019-11-01 15:34:28 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2019-11-01 15:34:28 +0100
commitce73c044b949154e3bc3e715b9b79e1360b3f794 (patch)
tree28f477a3142f1efa463a8d8569f924b9064e8637 /docs
parente7c65ee913d4a84da0957d2ebb89abfbc444de56 (diff)
Make the 'quadratic' the default for 'confint'
Also the documentation was improved here and there
Diffstat (limited to 'docs')
-rw-r--r--docs/404.html2
-rw-r--r--docs/articles/index.html2
-rw-r--r--docs/authors.html2
-rw-r--r--docs/index.html2
-rw-r--r--docs/news/index.html11
-rw-r--r--docs/reference/AIC.mmkin.html17
-rw-r--r--docs/reference/confint.mkinfit.html109
-rw-r--r--docs/reference/index.html2
-rw-r--r--docs/reference/parms.html19
-rw-r--r--docs/reference/residuals.mkinfit.html4
-rw-r--r--docs/reference/update.mkinfit-1.pngbin0 -> 28678 bytes
-rw-r--r--docs/reference/update.mkinfit-2.pngbin0 -> 28541 bytes
-rw-r--r--docs/reference/update.mkinfit.html350
13 files changed, 118 insertions, 402 deletions
diff --git a/docs/404.html b/docs/404.html
index f10cadb9..2a71e496 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -67,7 +67,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.7</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.8</span>
</span>
</div>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 76d7bc69..ac5f5df1 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -67,7 +67,7 @@
</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">0.9.49.7</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.8</span>
</span>
</div>
diff --git a/docs/authors.html b/docs/authors.html
index cb970788..fb50f268 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -67,7 +67,7 @@
</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">0.9.49.7</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.8</span>
</span>
</div>
diff --git a/docs/index.html b/docs/index.html
index 5a618e57..231ef39f 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -38,7 +38,7 @@
</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">0.9.49.7</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.8</span>
</span>
</div>
diff --git a/docs/news/index.html b/docs/news/index.html
index 5d1fc00f..baddfc96 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -67,7 +67,7 @@
</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">0.9.49.7</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.8</span>
</span>
</div>
@@ -129,6 +129,14 @@
</div>
+ <div id="mkin-0-9-49-8-unreleased" class="section level1">
+<h1 class="page-header">
+<a href="#mkin-0-9-49-8-unreleased" class="anchor"></a>mkin 0.9.49.8 (unreleased)<small> Unreleased </small>
+</h1>
+<ul>
+<li>‘confint.mkinfit’: Make the quadratic approximation the default, as the likelihood profiling takes too much time for any with more than three parameters</li>
+</ul>
+</div>
<div id="mkin-0-9-49-7-2019-11-01" class="section level1">
<h1 class="page-header">
<a href="#mkin-0-9-49-7-2019-11-01" class="anchor"></a>mkin 0.9.49.7 (2019-11-01)<small> Unreleased </small>
@@ -735,6 +743,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
+ <li><a href="#mkin-0-9-49-8-unreleased">0.9.49.8</a></li>
<li><a href="#mkin-0-9-49-7-2019-11-01">0.9.49.7</a></li>
<li><a href="#mkin-0-9-49-6-2019-10-31">0.9.49.6</a></li>
<li><a href="#mkin-0-9-49-5-2019-07-04">0.9.49.5</a></li>
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html
index 7ca12302..6b782456 100644
--- a/docs/reference/AIC.mmkin.html
+++ b/docs/reference/AIC.mmkin.html
@@ -70,7 +70,7 @@ same dataset." />
</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">0.9.49.7</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.8</span>
</span>
</div>
@@ -173,7 +173,10 @@ column.</p></td>
<span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>),
<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"FOCUS A"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_A</span>,
<span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</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; <span class='warning'>Warning: Optimisation did not converge:</span>
-#&gt; <span class='warning'>false convergence (8)</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>f</span>[<span class='fl'>1</span>, <span class='st'>"FOCUS A"</span>]) <span class='co'># We get a single number for a single fit</span></div><div class='output co'>#&gt; [1] 55.28197</div><div class='input'>
+#&gt; <span class='warning'>false convergence (8)</span></div><div class='input'> <span class='co'># We get a warning because the FOMC model does not converge for the</span>
+ <span class='co'># FOCUS A dataset, as it is well described by SFO</span>
+
+ <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>f</span>[<span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span>]) <span class='co'># We get a single number for a single fit</span></div><div class='output co'>#&gt; [1] 55.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>f</span><span class='kw'>[[</span><span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span>]]) <span class='co'># or when extracting an mkinfit object</span></div><div class='output co'>#&gt; [1] 55.28197</div><div class='input'>
<span class='co'># For FOCUS A, the models fit almost equally well, so the higher the number</span>
<span class='co'># of parameters, the higher (worse) the AIC</span>
<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>])</div><div class='output co'>#&gt; df AIC
@@ -182,12 +185,18 @@ column.</p></td>
#&gt; DFOP 5 59.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>], <span class='kw'>k</span> <span class='kw'>=</span> <span class='fl'>0</span>) <span class='co'># If we do not penalize additional parameters, we get nearly the same</span></div><div class='output co'>#&gt; df AIC
#&gt; SFO 3 49.28197
#&gt; FOMC 4 49.28202
-#&gt; DFOP 5 49.28197</div><div class='input'>
+#&gt; DFOP 5 49.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>]) <span class='co'># Comparing the BIC gives a very similar picture</span></div><div class='output co'>#&gt; df BIC
+#&gt; SFO 3 55.52030
+#&gt; FOMC 4 57.59979
+#&gt; DFOP 5 59.67918</div><div class='input'>
<span class='co'># For FOCUS C, the more complex models fit better</span>
<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='output co'>#&gt; df AIC
#&gt; SFO 3 59.29336
#&gt; FOMC 4 44.68652
-#&gt; DFOP 5 29.02372</div><div class='input'>
+#&gt; DFOP 5 29.02372</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='output co'>#&gt; df BIC
+#&gt; SFO 3 59.88504
+#&gt; FOMC 4 45.47542
+#&gt; DFOP 5 30.00984</div><div class='input'>
</div></pre>
</div>
diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html
index 54696ff5..6015fbf6 100644
--- a/docs/reference/confint.mkinfit.html
+++ b/docs/reference/confint.mkinfit.html
@@ -36,9 +36,14 @@
<meta property="og:title" content="Confidence intervals for parameters of mkinfit objects — confint.mkinfit" />
-<meta property="og:description" content="The default method 'profile' is based on the profile likelihood for each
-parameter. The method uses two nested optimisations. The speed of the method
-could likely be improved by using the method of Venzon and Moolgavkar (1988)." />
+<meta property="og:description" content="The default method 'quadratic' is based on the quadratic approximation of
+the curvature of the likelihood function at the maximum likelihood parameter
+estimates.
+The alternative method 'profile' is based on the profile likelihood for each
+parameter. The method uses two nested optimisations and can take a very long
+time, even if parallelized by specifying 'cores' on unixoid platforms. The
+speed of the method could likely be improved by using the method of Venzon
+and Moolgavkar (1988)." />
<meta name="twitter:card" content="summary" />
@@ -71,7 +76,7 @@ could likely be improved by using the 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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.8</span>
</span>
</div>
@@ -135,14 +140,19 @@ could likely be improved by using the method of Venzon and Moolgavkar (1988)." /
</div>
<div class="ref-description">
- <p>The default method 'profile' is based on the profile likelihood for each
-parameter. The method uses two nested optimisations. The speed of the method
-could likely be improved by using the method of Venzon and Moolgavkar (1988).</p>
+ <p>The default method 'quadratic' is based on the quadratic approximation of
+the curvature of the likelihood function at the maximum likelihood parameter
+estimates.
+The alternative method 'profile' is based on the profile likelihood for each
+parameter. The method uses two nested optimisations and can take a very long
+time, even if parallelized by specifying 'cores' on unixoid platforms. The
+speed of the method could likely be improved by using the method of Venzon
+and Moolgavkar (1988).</p>
</div>
<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'>"profile"</span>, <span class='st'>"quadratic"</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='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
@@ -174,11 +184,11 @@ cutoff value overrides arguments 'level' and 'alpha'</p></td>
</tr>
<tr>
<th>method</th>
- <td><p>The 'profile' method searches the parameter space for the
-cutoff of the confidence intervals by means of a likelihood ratio test.
-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.</p></td>
+ <td><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></td>
</tr>
<tr>
<th>transformed</th>
@@ -231,20 +241,27 @@ machines, cores &gt; 1 is not supported.</p></td>
#&gt; parent_0 73.0641834 92.1392181
#&gt; k_parent_sink 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>)
-<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'>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 verstrichen
-#&gt; 51.646 0.000 51.673 </div><div class='input'><span class='co'># The following does not save much time, as parent_0 takes up most of the time</span>
-<span class='co'># system.time(ci_profile &lt;- confint(f_d_1, cores = 5))</span>
-<span class='co'># system.time(ci_profile &lt;- confint(f_d_1,</span>
-<span class='co'># c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = 1))</span>
-<span class='co'># If we exclude parent_0 (the confidence of which is often of minor interest), we get a nice</span>
-<span class='co'># performance improvement from about 30 seconds to about 12 seconds</span>
-<span class='co'># system.time(ci_profile_no_parent_0 &lt;- confint(f_d_1, </span>
-<span class='co'># c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = 4))</span>
-<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='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 verstrichen
+#&gt; 51.297 0.000 51.328 </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; User System verstrichen
+#&gt; 0.006 0.003 11.435 </div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#&gt; 2.5% 97.5%
#&gt; parent_0 96.456003650 1.027703e+02
#&gt; k_parent_sink 0.040762501 5.549764e-02
#&gt; k_parent_m1 0.046786482 5.500879e-02
@@ -267,29 +284,26 @@ machines, cores &gt; 1 is not supported.</p></td>
<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></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.0005407854 0.0002218012
-#&gt; k_parent_sink 0.0066452394 0.0083795930
-#&gt; k_parent_m1 0.0001833903 0.0020092090
-#&gt; k_m1_sink 0.0307278240 0.0290580487
-#&gt; sigma 0.0550252516 0.0327066836</div><div class='input'><span class='no'>rel_diffs_untransformed</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.0005407854 0.0002218011
-#&gt; k_parent_sink 0.0067996407 0.0025717594
-#&gt; k_parent_m1 0.0037382781 0.0011843074
-#&gt; k_m1_sink 0.0146745610 0.0025299672
-#&gt; sigma 0.0550252516 0.0327066836</div><div class='input'>
-<span class='co'># Set the number of cores 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'>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 FALSE FALSE
+#&gt; k_parent_sink TRUE FALSE
+#&gt; k_parent_m1 TRUE FALSE
+#&gt; k_m1_sink FALSE 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; parent_0 0.000541 0.000222
+#&gt; k_parent_sink 0.006650 0.008380
+#&gt; k_parent_m1 0.000183 0.002010
+#&gt; k_m1_sink 0.030700 0.029100
+#&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; parent_0 0.000541 0.000222
+#&gt; k_parent_sink 0.006800 0.002570
+#&gt; k_parent_m1 0.003740 0.001180
+#&gt; k_m1_sink 0.014700 0.002530
+#&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>)
-<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'>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='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%
#&gt; parent_0 96.456003650 1.027703e+02
#&gt; k_parent 0.090911032 1.071578e-01
#&gt; k_m1 0.003892605 6.702778e-03
@@ -310,9 +324,14 @@ machines, cores &gt; 1 is not supported.</p></td>
<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>)
<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 intervals for the other parameters are 'better</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></div><div class='output co'>#&gt; 2.5% 97.5%
+<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
+#&gt; k_parent TRUE TRUE
+#&gt; k_m1 FALSE FALSE
+#&gt; f_parent_to_m1 TRUE FALSE
+#&gt; sigma FALSE TRUE</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 0.0005408012 0.0002217857
#&gt; k_parent 0.0009596303 0.0009003981
#&gt; k_m1 0.0307277425 0.0290579163
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 4279f6de..1c9975e0 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -67,7 +67,7 @@
</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">0.9.49.7</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.8</span>
</span>
</div>
diff --git a/docs/reference/parms.html b/docs/reference/parms.html
index 8ab26240..e3c52c53 100644
--- a/docs/reference/parms.html
+++ b/docs/reference/parms.html
@@ -71,7 +71,7 @@ considering the error structure that was assumed for the fit." />
</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">0.9.49.6</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.8</span>
</span>
</div>
@@ -167,12 +167,29 @@ as used internally during the optimisation?</p></td>
<p>A numeric vector of fitted model parameters</p>
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>fit</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>)</div><div class='output co'>#&gt; <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#&gt; Sum of squared residuals at call 1: 2388.077
+#&gt; Sum of squared residuals at call 3: 2388.077
+#&gt; Sum of squared residuals at call 4: 247.1962
+#&gt; Sum of squared residuals at call 7: 200.6791
+#&gt; Sum of squared residuals at call 10: 197.7231
+#&gt; Sum of squared residuals at call 11: 197.0872
+#&gt; Sum of squared residuals at call 14: 196.535
+#&gt; Sum of squared residuals at call 15: 196.535
+#&gt; Sum of squared residuals at call 16: 196.535
+#&gt; Sum of squared residuals at call 17: 196.5334
+#&gt; Sum of squared residuals at call 20: 196.5334
+#&gt; Sum of squared residuals at call 25: 196.5334
+#&gt; Negative log-likelihood at call 31: 26.64668</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='input'><span class='fu'>parms</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 k_parent_sink sigma
+#&gt; 82.4921598 0.3060633 4.6730124 </div><div class='input'><span class='fu'>parms</span>(<span class='no'>fit</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink sigma
+#&gt; 82.492160 -1.183963 4.673012 </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
+ <li><a href="#examples">Examples</a></li>
</ul>
</div>
diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html
index 7dd25012..96b02908 100644
--- a/docs/reference/residuals.mkinfit.html
+++ b/docs/reference/residuals.mkinfit.html
@@ -69,7 +69,7 @@
</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">0.9.49.6</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.7</span>
</span>
</div>
@@ -144,7 +144,7 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>object</th>
- <td><p>An <code><a href='mkinfit.html'>mkinfit</a></code> object</p></td>
+ <td><p>A <code><a href='mkinfit.html'>mkinfit</a></code> object</p></td>
</tr>
<tr>
<th>standardized</th>
diff --git a/docs/reference/update.mkinfit-1.png b/docs/reference/update.mkinfit-1.png
new file mode 100644
index 00000000..4cbefa56
--- /dev/null
+++ b/docs/reference/update.mkinfit-1.png
Binary files differ
diff --git a/docs/reference/update.mkinfit-2.png b/docs/reference/update.mkinfit-2.png
new file mode 100644
index 00000000..f432f6f8
--- /dev/null
+++ b/docs/reference/update.mkinfit-2.png
Binary files differ
diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html
index b9f6f9a9..bb93a61e 100644
--- a/docs/reference/update.mkinfit.html
+++ b/docs/reference/update.mkinfit.html
@@ -72,7 +72,7 @@ override these starting values." />
</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">0.9.49.6</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.8</span>
</span>
</div>
@@ -167,349 +167,11 @@ remove arguments given in the original call</p></td>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
-<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"DFOP"</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>)
-<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>fit</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)</div><div class='output co'>#&gt; $par
-#&gt; parent_0 log_k1 log_k2 g_ilr sigma_low rsd_high
-#&gt; 100.85489822 8.84468217 -2.29693632 -14.95263998 0.00375222 0.06763435
-#&gt;
-#&gt; $objective
-#&gt; [1] 19.40656
-#&gt;
-#&gt; $convergence
-#&gt; [1] 0
-#&gt;
-#&gt; $iterations
-#&gt; [1] 120
-#&gt;
-#&gt; $evaluations
-#&gt; function gradient
-#&gt; 144 847
-#&gt;
-#&gt; $message
-#&gt; [1] "relative convergence (4)"
-#&gt;
-#&gt; $logLik
-#&gt; [1] -19.40656
-#&gt;
-#&gt; $d_3_message
-#&gt; threestep
-#&gt; "Three-step fitting yielded a higher likelihood than direct fitting"
-#&gt;
-#&gt; $hessian
-#&gt; parent_0 log_k1 log_k2 g_ilr sigma_low
-#&gt; parent_0 3.662473e-01 -2.914408e-16 -7.241561e+01 -3.021629e-08 1.923504e+01
-#&gt; log_k1 -2.914408e-16 0.000000e+00 -2.215935e-13 -7.291307e-25 3.416474e-15
-#&gt; log_k2 -7.241561e+01 -2.215935e-13 3.127457e+04 6.766544e-06 -1.495826e+04
-#&gt; g_ilr -3.021629e-08 -7.291307e-25 6.766544e-06 3.122099e-09 -1.797429e-06
-#&gt; sigma_low 1.923504e+01 3.416474e-15 -1.495826e+04 -1.797429e-06 7.759299e+04
-#&gt; rsd_high 3.902119e+00 -1.801019e-16 -1.685343e+02 -3.750713e-07 3.984179e+03
-#&gt; rsd_high
-#&gt; parent_0 3.902119e+00
-#&gt; log_k1 -1.801019e-16
-#&gt; log_k2 -1.685343e+02
-#&gt; g_ilr -3.750713e-07
-#&gt; sigma_low 3.984179e+03
-#&gt; rsd_high 7.188991e+03
-#&gt;
-#&gt; $hessian_notrans
-#&gt; parent_0 k1 k2 g sigma_low
-#&gt; parent_0 3.662473e-01 -3.714445e-19 -7.201669e+02 -3.261485e+01 1.923504e+01
-#&gt; k1 -3.714445e-19 0.000000e+00 -4.258512e-15 7.218123e-21 4.355854e-18
-#&gt; k2 -7.201669e+02 -4.258512e-15 3.092510e+06 7.263235e+04 -1.456870e+05
-#&gt; g -3.261485e+01 7.218123e-21 7.263235e+04 3.291750e+03 -1.939948e+03
-#&gt; sigma_low 1.923504e+01 4.355854e-18 -1.456870e+05 -1.939948e+03 7.759299e+04
-#&gt; rsd_high 3.902119e+00 -2.259812e-19 -1.779680e+03 -4.048658e+02 3.984179e+03
-#&gt; rsd_high
-#&gt; parent_0 3.902119e+00
-#&gt; k1 -2.259812e-19
-#&gt; k2 -1.779680e+03
-#&gt; g -4.048658e+02
-#&gt; sigma_low 3.984179e+03
-#&gt; rsd_high 7.188991e+03
-#&gt;
-#&gt; $call
-#&gt; mkinfit(mkinmod = "DFOP", observed = subset(FOCUS_2006_D, value !=
-#&gt; 0), parms.ini = c(k1 = 0.699298911979803, k2 = 0.0899931270871125,
-#&gt; g = 0.0923391681138686), state.ini = c(parent = 101.948852047129),
-#&gt; quiet = TRUE, error_model = "tc")
-#&gt;
-#&gt; $error_model_algorithm
-#&gt; [1] "d_3"
-#&gt;
-#&gt; $solution_type
-#&gt; [1] "analytical"
-#&gt;
-#&gt; $transform_rates
-#&gt; [1] TRUE
-#&gt;
-#&gt; $transform_fractions
-#&gt; [1] TRUE
-#&gt;
-#&gt; $reweight.tol
-#&gt; [1] 1e-08
-#&gt;
-#&gt; $reweight.max.iter
-#&gt; [1] 10
-#&gt;
-#&gt; $control
-#&gt; $control$eval.max
-#&gt; [1] 300
-#&gt;
-#&gt; $control$iter.max
-#&gt; [1] 200
-#&gt;
-#&gt;
-#&gt; $calls
-#&gt; [1] 3105
-#&gt;
-#&gt; $time
-#&gt; User System verstrichen
-#&gt; 10.251 0.000 10.257
-#&gt;
-#&gt; $mkinmod
-#&gt; &lt;mkinmod&gt; model generated with
-#&gt; Use of formation fractions $use_of_ff: min
-#&gt; Specification $spec:
-#&gt; $parent
-#&gt; $type: DFOP; $sink: TRUE
-#&gt; Differential equations:
-#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
-#&gt; time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
-#&gt; * parent
-#&gt;
-#&gt; $observed
-#&gt; name time value
-#&gt; 1 parent 0 99.46
-#&gt; 2 parent 0 102.04
-#&gt; 3 parent 1 93.50
-#&gt; 4 parent 1 92.50
-#&gt; 5 parent 3 63.23
-#&gt; 6 parent 3 68.99
-#&gt; 7 parent 7 52.32
-#&gt; 8 parent 7 55.13
-#&gt; 9 parent 14 27.27
-#&gt; 10 parent 14 26.64
-#&gt; 11 parent 21 11.50
-#&gt; 12 parent 21 11.64
-#&gt; 13 parent 35 2.85
-#&gt; 14 parent 35 2.91
-#&gt; 15 parent 50 0.69
-#&gt; 16 parent 50 0.63
-#&gt; 17 parent 75 0.05
-#&gt; 18 parent 75 0.06
-#&gt;
-#&gt; $obs_vars
-#&gt; [1] "parent"
-#&gt;
-#&gt; $predicted
-#&gt; name time value
-#&gt; 1 parent 0.0000000 100.85489822
-#&gt; 2 parent 0.7575758 93.45650191
-#&gt; 3 parent 1.0000000 91.20560523
-#&gt; 4 parent 1.5151515 86.60082860
-#&gt; 5 parent 2.2727273 80.24806580
-#&gt; 6 parent 3.0000000 74.58828105
-#&gt; 7 parent 3.0303030 74.36132158
-#&gt; 8 parent 3.7878788 68.90641029
-#&gt; 9 parent 4.5454545 63.85165403
-#&gt; 10 parent 5.3030303 59.16769870
-#&gt; 11 parent 6.0606061 54.82734352
-#&gt; 12 parent 6.8181818 50.80538306
-#&gt; 13 parent 7.0000000 49.88485755
-#&gt; 14 parent 7.5757576 47.07846089
-#&gt; 15 parent 8.3333333 43.62493394
-#&gt; 16 parent 9.0909091 40.42474681
-#&gt; 17 parent 9.8484848 37.45931528
-#&gt; 18 parent 10.6060606 34.71141842
-#&gt; 19 parent 11.3636364 32.16509858
-#&gt; 20 parent 12.1212121 29.80556871
-#&gt; 21 parent 12.8787879 27.61912649
-#&gt; 22 parent 13.6363636 25.59307475
-#&gt; 23 parent 14.0000000 24.67405211
-#&gt; 24 parent 14.3939394 23.71564776
-#&gt; 25 parent 15.1515152 21.97594287
-#&gt; 26 parent 15.9090909 20.36385722
-#&gt; 27 parent 16.6666667 18.87002909
-#&gt; 28 parent 17.4242424 17.48578345
-#&gt; 29 parent 18.1818182 16.20308170
-#&gt; 30 parent 18.9393939 15.01447489
-#&gt; 31 parent 19.6969697 13.91306051
-#&gt; 32 parent 20.4545455 12.89244241
-#&gt; 33 parent 21.0000000 12.20428157
-#&gt; 34 parent 21.2121212 11.94669362
-#&gt; 35 parent 21.9696970 11.07032198
-#&gt; 36 parent 22.7272727 10.25823818
-#&gt; 37 parent 23.4848485 9.50572628
-#&gt; 38 parent 24.2424242 8.80841627
-#&gt; 39 parent 25.0000000 8.16225872
-#&gt; 40 parent 25.7575758 7.56350125
-#&gt; 41 parent 26.5151515 7.00866672
-#&gt; 42 parent 27.2727273 6.49453311
-#&gt; 43 parent 28.0303030 6.01811471
-#&gt; 44 parent 28.7878788 5.57664485
-#&gt; 45 parent 29.5454545 5.16755983
-#&gt; 46 parent 30.3030303 4.78848399
-#&gt; 47 parent 31.0606061 4.43721595
-#&gt; 48 parent 31.8181818 4.11171583
-#&gt; 49 parent 32.5757576 3.81009336
-#&gt; 50 parent 33.3333333 3.53059697
-#&gt; 51 parent 34.0909091 3.27160354
-#&gt; 52 parent 34.8484848 3.03160906
-#&gt; 53 parent 35.0000000 2.98576554
-#&gt; 54 parent 35.6060606 2.80921981
-#&gt; 55 parent 36.3636364 2.60314433
-#&gt; 56 parent 37.1212121 2.41218590
-#&gt; 57 parent 37.8787879 2.23523557
-#&gt; 58 parent 38.6363636 2.07126576
-#&gt; 59 parent 39.3939394 1.91932426
-#&gt; 60 parent 40.1515152 1.77852870
-#&gt; 61 parent 40.9090909 1.64806147
-#&gt; 62 parent 41.6666667 1.52716489
-#&gt; 63 parent 42.4242424 1.41513691
-#&gt; 64 parent 43.1818182 1.31132694
-#&gt; 65 parent 43.9393939 1.21513214
-#&gt; 66 parent 44.6969697 1.12599389
-#&gt; 67 parent 45.4545455 1.04339454
-#&gt; 68 parent 46.2121212 0.96685442
-#&gt; 69 parent 46.9696970 0.89592904
-#&gt; 70 parent 47.7272727 0.83020652
-#&gt; 71 parent 48.4848485 0.76930520
-#&gt; 72 parent 49.2424242 0.71287140
-#&gt; 73 parent 50.0000000 0.66057741
-#&gt; 74 parent 50.7575758 0.61211954
-#&gt; 75 parent 51.5151515 0.56721639
-#&gt; 76 parent 52.2727273 0.52560719
-#&gt; 77 parent 53.0303030 0.48705031
-#&gt; 78 parent 53.7878788 0.45132184
-#&gt; 79 parent 54.5454545 0.41821430
-#&gt; 80 parent 55.3030303 0.38753542
-#&gt; 81 parent 56.0606061 0.35910705
-#&gt; 82 parent 56.8181818 0.33276409
-#&gt; 83 parent 57.5757576 0.30835357
-#&gt; 84 parent 58.3333333 0.28573373
-#&gt; 85 parent 59.0909091 0.26477320
-#&gt; 86 parent 59.8484848 0.24535028
-#&gt; 87 parent 60.6060606 0.22735216
-#&gt; 88 parent 61.3636364 0.21067432
-#&gt; 89 parent 62.1212121 0.19521992
-#&gt; 90 parent 62.8787879 0.18089921
-#&gt; 91 parent 63.6363636 0.16762901
-#&gt; 92 parent 64.3939394 0.15533228
-#&gt; 93 parent 65.1515152 0.14393759
-#&gt; 94 parent 65.9090909 0.13337879
-#&gt; 95 parent 66.6666667 0.12359454
-#&gt; 96 parent 67.4242424 0.11452804
-#&gt; 97 parent 68.1818182 0.10612662
-#&gt; 98 parent 68.9393939 0.09834151
-#&gt; 99 parent 69.6969697 0.09112749
-#&gt; 100 parent 70.4545455 0.08444266
-#&gt; 101 parent 71.2121212 0.07824822
-#&gt; 102 parent 71.9696970 0.07250818
-#&gt; 103 parent 72.7272727 0.06718920
-#&gt; 104 parent 73.4848485 0.06226042
-#&gt; 105 parent 74.2424242 0.05769319
-#&gt; 106 parent 75.0000000 0.05346100
-#&gt;
-#&gt; $rss
-#&gt; function (P)
-#&gt; cost_function(P, OLS = TRUE, update_data = FALSE)
-#&gt; &lt;bytecode: 0x555558e48258&gt;
-#&gt; &lt;environment: 0x55555caa08e0&gt;
-#&gt;
-#&gt; $ll
-#&gt; function (P, fixed_degparms = FALSE, fixed_errparms = FALSE)
-#&gt; {
-#&gt; -cost_function(P, trans = FALSE, fixed_degparms = fixed_degparms,
-#&gt; fixed_errparms = fixed_errparms, OLS = FALSE, update_data = FALSE)
-#&gt; }
-#&gt; &lt;bytecode: 0x555558e47e30&gt;
-#&gt; &lt;environment: 0x55555caa08e0&gt;
-#&gt;
-#&gt; $start
-#&gt; value type
-#&gt; parent_0 101.94885205 state
-#&gt; k1 0.69929891 deparm
-#&gt; k2 0.08999313 deparm
-#&gt; g 0.09233917 deparm
-#&gt; sigma_low 0.10000000 error
-#&gt; rsd_high 0.10000000 error
-#&gt;
-#&gt; $start_transformed
-#&gt; value lower upper
-#&gt; parent_0 101.948852 -Inf Inf
-#&gt; log_k1 -0.357677 -Inf Inf
-#&gt; log_k2 -2.408022 -Inf Inf
-#&gt; g_ilr -1.616024 -Inf Inf
-#&gt; sigma_low 0.100000 0 Inf
-#&gt; rsd_high 0.100000 0 Inf
-#&gt;
-#&gt; $fixed
-#&gt; [1] value type
-#&gt; &lt;0 Zeilen&gt; (oder row.names mit Länge 0)
-#&gt;
-#&gt; $data
-#&gt; time variable observed predicted residual
-#&gt; 1 0 parent 99.46 100.8548982 -1.39489822
-#&gt; 2 0 parent 102.04 100.8548982 1.18510178
-#&gt; 3 1 parent 93.50 91.2056052 2.29439477
-#&gt; 4 1 parent 92.50 91.2056052 1.29439477
-#&gt; 5 3 parent 63.23 74.5882810 -11.35828105
-#&gt; 6 3 parent 68.99 74.5882810 -5.59828105
-#&gt; 7 7 parent 52.32 49.8848576 2.43514245
-#&gt; 8 7 parent 55.13 49.8848576 5.24514245
-#&gt; 9 14 parent 27.27 24.6740521 2.59594789
-#&gt; 10 14 parent 26.64 24.6740521 1.96594789
-#&gt; 11 21 parent 11.50 12.2042816 -0.70428157
-#&gt; 12 21 parent 11.64 12.2042816 -0.56428157
-#&gt; 13 35 parent 2.85 2.9857655 -0.13576554
-#&gt; 14 35 parent 2.91 2.9857655 -0.07576554
-#&gt; 15 50 parent 0.69 0.6605774 0.02942259
-#&gt; 16 50 parent 0.63 0.6605774 -0.03057741
-#&gt; 17 75 parent 0.05 0.0534610 -0.00346100
-#&gt; 18 75 parent 0.06 0.0534610 0.00653900
-#&gt;
-#&gt; $atol
-#&gt; [1] 1e-08
-#&gt;
-#&gt; $rtol
-#&gt; [1] 1e-10
-#&gt;
-#&gt; $err_mod
-#&gt; [1] "tc"
-#&gt;
-#&gt; $bparms.optim
-#&gt; parent_0 k1 k2 g
-#&gt; 1.008549e+02 6.937399e+03 1.005665e-01 6.551046e-10
-#&gt;
-#&gt; $bparms.fixed
-#&gt; numeric(0)
-#&gt;
-#&gt; $bparms.ode
-#&gt; k1 k2 g
-#&gt; 6.937399e+03 1.005665e-01 6.551046e-10
-#&gt;
-#&gt; $bparms.state
-#&gt; parent
-#&gt; 100.8549
-#&gt;
-#&gt; $errparms
-#&gt; sigma_low rsd_high
-#&gt; 0.00375222 0.06763435
-#&gt;
-#&gt; $df.residual
-#&gt; [1] 12
-#&gt;
-#&gt; $date
-#&gt; [1] "Fri Nov 1 10:10:42 2019"
-#&gt;
-#&gt; $version
-#&gt; [1] "0.9.49.6"
-#&gt;
-#&gt; $Rversion
-#&gt; [1] "3.6.1"
-#&gt;
-#&gt; attr(,"class")
-#&gt; [1] "mkinfit" "modFit" </div><div class='input'># }
+<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"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>)
+<span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 k_parent_sink sigma
+#&gt; 99.44423886 0.09793574 3.39632469 </div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_err</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='update.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>fit</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)
+<span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit_2</span>)</div><div class='output co'>#&gt; parent_0 k_parent_sink sigma_low rsd_high
+#&gt; 1.008549e+02 1.005665e-01 3.752222e-03 6.763434e-02 </div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_err</a></span>(<span class='no'>fit_2</span>)</div><div class='img'><img src='update.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'># }
</div></pre>
</div>
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