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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-11 19:49:25 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-11 19:49:25 +0100
commitc0c82d9523da8965f5fb7a5f8cf1410750885d30 (patch)
tree8db6015dfa8eb14df8318b9661b07424bb92620f /docs/dev/reference/saem.html
parente13189e6a34d87fabf650c777d0432057bcacbb9 (diff)
Update static docs
Diffstat (limited to 'docs/dev/reference/saem.html')
-rw-r--r--docs/dev/reference/saem.html50
1 files changed, 28 insertions, 22 deletions
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index bc54e1e1..d0c3495a 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -141,7 +141,7 @@ Expectation Maximisation algorithm (SAEM)." />
<div class="col-md-9 contents">
<div class="page-header">
<h1>Fit nonlinear mixed models with SAEM</h1>
- <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/saemix.R'><code>R/saemix.R</code></a></small>
+ <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/saem.R'><code>R/saem.R</code></a></small>
<div class="hidden name"><code>saem.Rd</code></div>
</div>
@@ -161,6 +161,7 @@ Expectation Maximisation algorithm (SAEM).</p>
cores <span class='op'>=</span> <span class='fl'>1</span>,
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
suppressPlot <span class='op'>=</span> <span class='cn'>TRUE</span>,
+ quiet <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
@@ -185,19 +186,19 @@ Expectation Maximisation algorithm (SAEM).</p>
</tr>
<tr>
<th>...</th>
- <td><p>Further parameters passed to <a href='https://rdrr.io/pkg/saemix/man/saemixData.html'>saemix::saemixData</a>
-and <a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix::saemixModel</a>.</p></td>
+ <td><p>Further parameters passed to <a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix::saemixModel</a>.</p></td>
</tr>
<tr>
<th>cores</th>
<td><p>The number of cores to be used for multicore processing using
<code><a href='https://rdrr.io/r/parallel/mclapply.html'>parallel::mclapply()</a></code>. Using more than 1 core is experimental and may
-lead to uncontrolled forking, apparently depending on the BLAS version
+lead to excessive forking, apparently depending on the BLAS version
used.</p></td>
</tr>
<tr>
<th>verbose</th>
- <td><p>Should we print information about created objects?</p></td>
+ <td><p>Should we print information about created objects of
+type <a href='https://rdrr.io/pkg/saemix/man/SaemixModel-class.html'>saemix::SaemixModel</a> and <a href='https://rdrr.io/pkg/saemix/man/SaemixData-class.html'>saemix::SaemixData</a>?</p></td>
</tr>
<tr>
<th>suppressPlot</th>
@@ -205,6 +206,11 @@ used.</p></td>
by the saemix function?</p></td>
</tr>
<tr>
+ <th>quiet</th>
+ <td><p>Should we suppress the messages saemix prints at the beginning
+and the end of the optimisation process?</p></td>
+ </tr>
+ <tr>
<th>x</th>
<td><p>An saem.mmkin object to print</p></td>
</tr>
@@ -241,27 +247,27 @@ using <a href='mmkin.html'>mmkin</a>.</p>
state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>f_saem_p0_fixed</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed Nov 11 09:36:41 2020"
+#&gt; [1] "Wed Nov 11 19:47:58 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 09:36:43 2020"</div><div class='input'>
+#&gt; [1] "Wed Nov 11 19:48:00 2020"</div><div class='input'>
<span class='va'>f_mmkin_parent</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><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'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>f_saem_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed Nov 11 09:36:44 2020"
+#&gt; [1] "Wed Nov 11 19:48:01 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 09:36:45 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Wed Nov 11 19:48:03 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed Nov 11 09:36:46 2020"
+#&gt; [1] "Wed Nov 11 19:48:03 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 09:36:48 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Wed Nov 11 19:48:05 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed Nov 11 09:36:48 2020"
+#&gt; [1] "Wed Nov 11 19:48:06 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 09:36:51 2020"</div><div class='input'>
+#&gt; [1] "Wed Nov 11 19:48:08 2020"</div><div class='input'>
<span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span>
<span class='co'># functions from saemix</span>
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span>
@@ -307,10 +313,10 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='va'>f_mmkin_parent_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
<span class='va'>f_saem_fomc_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed Nov 11 09:36:54 2020"
+#&gt; [1] "Wed Nov 11 19:48:11 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 09:36:59 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
+#&gt; [1] "Wed Nov 11 19:48:16 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Likelihoods computed by importance sampling </div><div class='output co'>#&gt; AIC BIC
#&gt; 1 467.7096 464.9757
#&gt; 2 469.5208 466.3963</div><div class='input'>
@@ -330,15 +336,15 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='co'># solutions written for mkin this took around four minutes</span>
<span class='va'>f_saem_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed Nov 11 09:37:01 2020"
+#&gt; [1] "Wed Nov 11 19:48:18 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 09:37:06 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Wed Nov 11 19:48:23 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed Nov 11 09:37:06 2020"
+#&gt; [1] "Wed Nov 11 19:48:23 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 09:37:15 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
+#&gt; [1] "Wed Nov 11 19:48:32 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by SAEM
#&gt; Structural model:
@@ -384,8 +390,8 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; LL by is "-407.78 (df=13)"</div><div class='output co'>#&gt; saemix version used for fitting: 3.1.9000
#&gt; mkin version used for pre-fitting: 0.9.50.4
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Wed Nov 11 09:37:16 2020
-#&gt; Date of summary: Wed Nov 11 09:37:16 2020
+#&gt; Date of fit: Wed Nov 11 19:48:33 2020
+#&gt; Date of summary: Wed Nov 11 19:48:33 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -400,7 +406,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 9.691 s using 300, 100 iterations
+#&gt; Fitted in 9.564 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Constant variance
#&gt;

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