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Diffstat (limited to 'docs')
-rw-r--r--docs/news/index.html2
-rw-r--r--docs/pkgdown.yml2
-rw-r--r--docs/reference/confint.mkinfit.html20
-rw-r--r--docs/reference/mmkin.html16
-rw-r--r--docs/reference/nlme.html4
-rw-r--r--docs/reference/parms.html6
-rw-r--r--docs/reference/saemix-1.pngbin37443 -> 31551 bytes
-rw-r--r--docs/reference/saemix-2.pngbin38557 -> 58815 bytes
-rw-r--r--docs/reference/saemix.html135
9 files changed, 80 insertions, 105 deletions
diff --git a/docs/news/index.html b/docs/news/index.html
index 149fc98e..c26652e9 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -148,6 +148,8 @@
<ul>
<li><p>‘parms’: Add a method for mmkin objects</p></li>
<li><p>‘saemix_model’, ‘saemix_data’: Helper functions to fit nonlinear mixed-effects models for mmkin row objects using the saemix package</p></li>
+<li><p>‘mmkin’ and ‘confint(method = ’profile’): Use all cores detected by parallel::detectCores() per default</p></li>
+<li><p>‘confint(method = ’profile’): Choose accuracy based on ‘rel_tol’ argument, relative to the bounds obtained by the quadratic approximation</p></li>
</ul>
</div>
<div id="mkin-0-9-50-2-2020-05-12" class="section level1">
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 0bb01ef4..a8b168ce 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
NAFTA_examples: web_only/NAFTA_examples.html
benchmarks: web_only/benchmarks.html
compiled_models: web_only/compiled_models.html
-last_built: 2020-05-25T10:48Z
+last_built: 2020-05-26T16:38Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html
index 190494bc..0686c7bb 100644
--- a/docs/reference/confint.mkinfit.html
+++ b/docs/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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span>
</span>
</div>
@@ -116,6 +116,9 @@ method of Venzon and Moolgavkar (1988)." />
<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>
+ </li>
</ul>
</li>
<li>
@@ -168,7 +171,8 @@ method of Venzon and Moolgavkar (1988).</p>
<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'>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>
@@ -224,6 +228,12 @@ their confidence intervals?</p></td>
On Windows machines, cores &gt; 1 is currently not supported.</p></td>
</tr>
<tr>
+ <th>rel_tol</th>
+ <td><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></td>
+ </tr>
+ <tr>
<th>quiet</th>
<td><p>Should we suppress the message "Profiling the likelihood"</p></td>
</tr>
@@ -270,13 +280,13 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
<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'>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; 3.410 0.000 3.412 </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='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; 3.689 0.991 3.361 </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 1, 2, 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: Länge von 'dimnames' [2] ungleich der Arrayausdehnung</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.008 0.044 0.201</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/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: 0.007 0.042 0.193</span></div><div class='input'><span class='no'>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
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 3be3b4b9..9628c017 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -75,7 +75,7 @@ datasets specified in its first two arguments." />
</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">0.9.50.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span>
</span>
</div>
@@ -112,6 +112,9 @@ datasets specified in its first two arguments." />
<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>
+ </li>
</ul>
</li>
<li>
@@ -152,7 +155,7 @@ datasets specified in its first two arguments.</p>
<pre class="usage"><span class='fu'>mmkin</span>(
<span class='kw'>models</span> <span class='kw'>=</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='no'>datasets</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'>cores</span> <span class='kw'>=</span> <span class='fu'>detectCores</span>(),
<span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='no'>...</span>
)</pre>
@@ -176,7 +179,8 @@ data for <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
<td><p>The number of cores to be used for multicore processing. This
is only used when the <code>cluster</code> argument is <code>NULL</code>. On Windows
machines, cores &gt; 1 is not supported, you need to use the <code>cluster</code>
-argument to use multiple logical processors.</p></td>
+argument to use multiple logical processors. Per default, all cores
+detected by <code><a href='https://rdrr.io/r/parallel/detectCores.html'>parallel::detectCores()</a></code> are used.</p></td>
</tr>
<tr>
<th>cluster</th>
@@ -215,9 +219,9 @@ plotting.</p></div>
<span class='no'>time_default</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.0</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</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='no'>time_default</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 4.520 0.374 1.284 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 5.076 0.004 5.083 </div><div class='input'>
+<span class='no'>time_default</span></div><div class='output co'>#&gt; user system elapsed
+#&gt; 4.457 0.561 1.328 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; user system elapsed
+#&gt; 5.031 0.004 5.038 </div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
#&gt; 0.7340478 0.2659522 0.7505691 0.2494309
diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html
index b2d415dc..3462e52e 100644
--- a/docs/reference/nlme.html
+++ b/docs/reference/nlme.html
@@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span>
</span>
</div>
@@ -178,7 +178,7 @@ datasets. They are used internally by the <code><a href='nlme.mmkin.html'>nlme.m
<p>If random is FALSE (default), a named vector containing mean values
of the fitted degradation model parameters. If random is TRUE, a list with
fixed and random effects, in the format required by the start argument of
-nlme for the case of a single grouping variable ds?</p>
+nlme for the case of a single grouping variable ds.</p>
<p>A <code><a href='https://rdrr.io/pkg/nlme/man/groupedData.html'>groupedData</a></code> object</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
diff --git a/docs/reference/parms.html b/docs/reference/parms.html
index 432bbc88..2fe91c26 100644
--- a/docs/reference/parms.html
+++ b/docs/reference/parms.html
@@ -195,7 +195,8 @@ such matrices is returned.</p>
<span class='no'>ds</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>],
<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)]))
<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>ds</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>6</span>:<span class='fl'>10</span>)
-<span class='no'>fits</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='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='co'># \dontrun{</span>
+<span class='no'>fits</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='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)
<span class='fu'>parms</span>(<span class='no'>fits</span>[<span class='st'>"SFO"</span>, ])</div><div class='output co'>#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
#&gt; parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450
#&gt; k_parent_sink 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421
@@ -259,7 +260,8 @@ such matrices is returned.</p>
#&gt; log_k2 -3.5206791 -5.85402317 -2.5794240 -3.4233253 -5.676532
#&gt; g_ilr -0.1463234 0.07627854 0.4719196 0.4477805 -0.460676
#&gt; sigma 1.3569047 2.22130220 1.3416908 2.8715985 1.942068
-#&gt; </div></pre>
+#&gt; </div><div class='input'># }
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
diff --git a/docs/reference/saemix-1.png b/docs/reference/saemix-1.png
index 529588ce..0d79300d 100644
--- a/docs/reference/saemix-1.png
+++ b/docs/reference/saemix-1.png
Binary files differ
diff --git a/docs/reference/saemix-2.png b/docs/reference/saemix-2.png
index b85f878f..04de70b5 100644
--- a/docs/reference/saemix-2.png
+++ b/docs/reference/saemix-2.png
Binary files differ
diff --git a/docs/reference/saemix.html b/docs/reference/saemix.html
index 1737a21c..d3eb216c 100644
--- a/docs/reference/saemix.html
+++ b/docs/reference/saemix.html
@@ -153,7 +153,7 @@ list of mkinfit objects that have been obtained by fitting the same model to
a list of datasets.</p>
</div>
- <pre class="usage"><span class='fu'>saemix_model</span>(<span class='no'>object</span>)
+ <pre class="usage"><span class='fu'>saemix_model</span>(<span class='no'>object</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='fu'>saemix_data</span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre>
@@ -165,6 +165,11 @@ a list of datasets.</p>
<td><p>An mmkin row object containing several fits of the same model to different datasets</p></td>
</tr>
<tr>
+ <th>cores</th>
+ <td><p>The number of cores to be used for multicore processing.
+On Windows machines, cores &gt; 1 is currently not supported.</p></td>
+ </tr>
+ <tr>
<th>...</th>
<td><p>Further parameters passed to <a href='https://rdrr.io/pkg/saemix/man/saemixData.html'>saemix::saemixData</a></p></td>
</tr>
@@ -174,21 +179,22 @@ a list of datasets.</p>
<p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixModel-class.html'>saemix::SaemixModel</a> object.</p>
<p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixData-class.html'>saemix::SaemixData</a> object.</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Starting values for the fixed effects (population mean parameters, argument psi0 of
+<code><a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix::saemixModel()</a></code> are the mean values of the parameters found using
+mmkin. Starting variances of the random effects (argument omega.init) are the
+variances of the deviations of the parameters from these mean values.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>ds</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>],
<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)]))
<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>ds</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>6</span>:<span class='fl'>10</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'>"A1"</span>),
- <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f_mmkin</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/list.html'>list</a></span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>sfo_sfo</span>), <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>5</span>)
-<span class='co'># \dontrun{</span>
-<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>saemix</span>)) {
- <span class='no'>m_saemix</span> <span class='kw'>&lt;-</span> <span class='fu'>saemix_model</span>(<span class='no'>f_mmkin</span>)
- <span class='no'>d_saemix</span> <span class='kw'>&lt;-</span> <span class='fu'>saemix_data</span>(<span class='no'>f_mmkin</span>)
- <span class='no'>saemix_options</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>, <span class='kw'>save</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>save.graphs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
- <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span>(<span class='no'>m_saemix</span>, <span class='no'>d_saemix</span>, <span class='no'>saemix_options</span>)
-}</div><div class='output co'>#&gt; <span class='message'>Loading required package: saemix</span></div><div class='output co'>#&gt; <span class='message'>Package saemix, version 3.1.9000</span>
-#&gt; <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='output co'>#&gt;
+ <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># \dontrun{</span>
+<span class='no'>f_mmkin</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/list.html'>list</a></span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>sfo_sfo</span>), <span class='no'>ds</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/library.html'>library</a></span>(<span class='no'>saemix</span>)</div><div class='output co'>#&gt; <span class='message'>Package saemix, version 3.1.9000</span>
+#&gt; <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><span class='no'>m_saemix</span> <span class='kw'>&lt;-</span> <span class='fu'>saemix_model</span>(<span class='no'>f_mmkin</span>)</div><div class='output co'>#&gt;
#&gt;
#&gt; The following SaemixModel object was successfully created:
#&gt;
@@ -224,12 +230,12 @@ a list of datasets.</p>
#&gt; out_values &lt;- out_wide[out_index]
#&gt; }
#&gt; return(out_values)
-#&gt; }, mc.cores = 15)
+#&gt; }, mc.cores = cores)
#&gt; res &lt;- unlist(res_list)
#&gt; return(res)
#&gt; }
-#&gt; &lt;bytecode: 0x555559875398&gt;
-#&gt; &lt;environment: 0x55555973a248&gt;
+#&gt; &lt;bytecode: 0x555559668108&gt;
+#&gt; &lt;environment: 0x555559677c08&gt;
#&gt; Nb of parameters: 4
#&gt; parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1
#&gt; distribution:
@@ -248,8 +254,7 @@ a list of datasets.</p>
#&gt; No covariate in the model.
#&gt; Initial values
#&gt; parent_0 log_k_parent log_k_A1 f_parent_ilr_1
-#&gt; Pop.CondInit 86.53449 -3.207005 -3.060308 -1.920449
-#&gt;
+#&gt; Pop.CondInit 86.53449 -3.207005 -3.060308 -1.920449</div><div class='input'><span class='no'>d_saemix</span> <span class='kw'>&lt;-</span> <span class='fu'>saemix_data</span>(<span class='no'>f_mmkin</span>)</div><div class='output co'>#&gt;
#&gt;
#&gt; The following SaemixData object was successfully created:
#&gt;
@@ -257,12 +262,14 @@ a list of datasets.</p>
#&gt; longitudinal data for use with the SAEM algorithm
#&gt; Dataset ds_saemix
#&gt; Structured data: value ~ time + name | ds
-#&gt; X variable for graphs: time ()
-#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon May 25 12:48:51 2020"
-#&gt; .</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; .</div><div class='img'><img src='saemix-2.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; .</div><div class='img'><img src='saemix-3.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; .</div><div class='img'><img src='saemix-4.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt;
+#&gt; X variable for graphs: time () </div><div class='input'><span class='no'>saemix_options</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>,
+ <span class='kw'>save</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>save.graphs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>displayProgress</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>nbiter.saemix</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>200</span>, <span class='fl'>80</span>))
+<span class='no'>f_saemix</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span>(<span class='no'>m_saemix</span>, <span class='no'>d_saemix</span>, <span class='no'>saemix_options</span>)</div><div class='output co'>#&gt; Running main SAEM algorithm
+#&gt; [1] "Tue May 26 18:25:16 2020"
+#&gt; ..
#&gt; Minimisation finished
-#&gt; [1] "Mon May 25 12:56:39 2020"</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by the SAEM algorithm
+#&gt; [1] "Tue May 26 18:31:09 2020"</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by the SAEM algorithm
#&gt; -----------------------------------
#&gt; ---- Data ----
#&gt; -----------------------------------
@@ -322,12 +329,12 @@ a list of datasets.</p>
#&gt; out_values &lt;- out_wide[out_index]
#&gt; }
#&gt; return(out_values)
-#&gt; }, mc.cores = 15)
+#&gt; }, mc.cores = cores)
#&gt; res &lt;- unlist(res_list)
#&gt; return(res)
#&gt; }
-#&gt; &lt;bytecode: 0x555559875398&gt;
-#&gt; &lt;environment: 0x55555973a248&gt;
+#&gt; &lt;bytecode: 0x555559668108&gt;
+#&gt; &lt;environment: 0x555559677c08&gt;
#&gt; Nb of parameters: 4
#&gt; parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1
#&gt; distribution:
@@ -353,7 +360,7 @@ a list of datasets.</p>
#&gt; Estimation of individual parameters (MAP)
#&gt; Estimation of standard errors and linearised log-likelihood
#&gt; Estimation of log-likelihood by importance sampling
-#&gt; Number of iterations: K1=300, K2=100
+#&gt; Number of iterations: K1=200, K2=80
#&gt; Number of chains: 10
#&gt; Seed: 123456
#&gt; Number of MCMC iterations for IS: 5000
@@ -369,19 +376,19 @@ a list of datasets.</p>
#&gt; ----------------- Fixed effects ------------------
#&gt; ----------------------------------------------------
#&gt; Parameter Estimate SE CV(%)
-#&gt; [1,] parent_0 86.21 1.51 1.7
+#&gt; [1,] parent_0 86.14 1.61 1.9
#&gt; [2,] log_k_parent -3.21 0.59 18.5
-#&gt; [3,] log_k_A1 -4.64 0.29 6.3
-#&gt; [4,] f_parent_ilr_1 -0.32 0.30 93.2
-#&gt; [5,] a.1 4.69 0.27 5.8
+#&gt; [3,] log_k_A1 -4.66 0.30 6.4
+#&gt; [4,] f_parent_ilr_1 -0.33 0.30 91.7
+#&gt; [5,] a.1 4.68 0.27 5.8
#&gt; ----------------------------------------------------
#&gt; ----------- Variance of random effects -----------
#&gt; ----------------------------------------------------
#&gt; Parameter Estimate SE CV(%)
-#&gt; parent_0 omega2.parent_0 6.07 7.08 117
-#&gt; log_k_parent omega2.log_k_parent 1.75 1.11 63
+#&gt; parent_0 omega2.parent_0 7.71 8.14 106
+#&gt; log_k_parent omega2.log_k_parent 1.76 1.12 63
#&gt; log_k_A1 omega2.log_k_A1 0.26 0.26 101
-#&gt; f_parent_ilr_1 omega2.f_parent_ilr_1 0.38 0.27 71
+#&gt; f_parent_ilr_1 omega2.f_parent_ilr_1 0.39 0.28 71
#&gt; ----------------------------------------------------
#&gt; ------ Correlation matrix of random effects ------
#&gt; ----------------------------------------------------
@@ -399,66 +406,16 @@ a list of datasets.</p>
#&gt; --------------- Statistical criteria -------------
#&gt; ----------------------------------------------------
#&gt; Likelihood computed by linearisation
-#&gt; -2LL= 1064.397
-#&gt; AIC = 1082.397
-#&gt; BIC = 1078.882
+#&gt; -2LL= 1064.364
+#&gt; AIC = 1082.364
+#&gt; BIC = 1078.848
#&gt;
#&gt; Likelihood computed by importance sampling
-#&gt; -2LL= 1063.161
-#&gt; AIC = 1081.161
-#&gt; BIC = 1077.646
-#&gt; ----------------------------------------------------</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by the SAEM algorithm
-#&gt; -----------------------------------------
-#&gt; ---- Data and Model ----
-#&gt; -----------------------------------------
-#&gt; Data
-#&gt; Dataset ds_saemix
-#&gt; Longitudinal data: value ~ time + name | ds
-#&gt;
-#&gt; Model:
-#&gt; Mixed model generated from mmkin object
-#&gt; 4 parameters: parent_0 log_k_parent log_k_A1 f_parent_ilr_1
-#&gt; error model: constant
-#&gt; No covariate
-#&gt;
-#&gt; Key options
-#&gt; Estimation of individual parameters (MAP)
-#&gt; Estimation of standard errors and linearised log-likelihood
-#&gt; Estimation of log-likelihood by importance sampling
-#&gt; Number of iterations: K1=300, K2=100
-#&gt; Number of chains: 10
-#&gt; Seed: 123456
-#&gt; Number of MCMC iterations for IS: 5000
-#&gt; Input/output
-#&gt; results not saved
-#&gt; no graphs
-#&gt; ----------------------------------------------------
-#&gt; ---- Results ----
-#&gt; Fixed effects
-#&gt; Parameter Estimate SE CV(%)
-#&gt; parent_0 86.214 1.506 1.75
-#&gt; log_k_parent -3.210 0.593 18.47
-#&gt; log_k_A1 -4.643 0.294 6.34
-#&gt; f_parent_ilr_1 -0.322 0.300 93.24
-#&gt; a.1 4.689 0.270 5.76
-#&gt;
-#&gt; Variance of random effects
-#&gt; Parameter Estimate SE CV(%)
-#&gt; omega2.parent_0 6.068 7.078 116.7
-#&gt; omega2.log_k_parent 1.752 1.111 63.4
-#&gt; omega2.log_k_A1 0.256 0.257 100.5
-#&gt; omega2.f_parent_ilr_1 0.385 0.273 70.8
-#&gt;
-#&gt; Statistical criteria
-#&gt; Likelihood computed by linearisation
-#&gt; -2LL= 1064.397
-#&gt; AIC= 1082.397
-#&gt; BIC= 1078.882
-#&gt; Likelihood computed by importance sampling
-#&gt; -2LL= 1063.161
-#&gt; AIC= 1081.161
-#&gt; BIC= 1077.646 </div><div class='input'># }
-</div><div class='img'><img src='saemix-5.png' alt='' width='700' height='433' /></div></pre>
+#&gt; -2LL= 1063.462
+#&gt; AIC = 1081.462
+#&gt; BIC = 1077.947
+#&gt; ----------------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span>(<span class='no'>f_saemix</span>, <span class='kw'>plot.type</span> <span class='kw'>=</span> <span class='st'>"convergence"</span>)</div><div class='output co'>#&gt; Plotting convergence plots</div><div class='img'><img src='saemix-2.png' alt='' width='700' height='433' /></div><div class='input'># }
+</div></pre>
</div>
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