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-rw-r--r--docs/dev/reference/saem.html49
1 files changed, 19 insertions, 30 deletions
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index a832e911..59589378 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -162,7 +162,6 @@ Expectation Maximisation algorithm (SAEM).</p>
control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>displayProgress <span class='op'>=</span> <span class='cn'>FALSE</span>, print <span class='op'>=</span> <span class='cn'>FALSE</span>, save <span class='op'>=</span> <span class='cn'>FALSE</span>, save.graphs <span class='op'>=</span>
<span class='cn'>FALSE</span><span class='op'>)</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>
@@ -221,11 +220,6 @@ automatic choice is not desired</p></td>
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>
- <td><p>Should we suppress any plotting that is done
-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>
@@ -267,36 +261,33 @@ 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] "Mon Jan 11 12:42:01 2021"
+#&gt; [1] "Mon Jan 25 14:41:42 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 11 12:42:03 2021"</div><div class='input'>
+#&gt; [1] "Mon Jan 25 14:41:43 2021"</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] "Mon Jan 11 12:42:04 2021"
+#&gt; [1] "Mon Jan 25 14:41:45 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 11 12:42:06 2021"</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] "Mon Jan 25 14:41:46 2021"</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] "Mon Jan 11 12:42:06 2021"
+#&gt; [1] "Mon Jan 25 14:41:47 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 11 12:42:08 2021"</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] "Mon Jan 25 14:41:49 2021"</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] "Mon Jan 11 12:42:09 2021"
+#&gt; [1] "Mon Jan 25 14:41:49 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 11 12:42:12 2021"</div><div class='input'>
+#&gt; [1] "Mon Jan 25 14:41:52 2021"</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>
</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='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_sfo</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_dfop</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; Likelihoods computed by importance sampling </div><div class='output co'>#&gt; AIC BIC
-#&gt; 1 624.2484 622.2956
-#&gt; 2 467.7096 464.9757
-#&gt; 3 495.4373 491.9222</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='error'>Error in compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)): 'compare.saemix' requires at least two models.</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Plotting convergence plots</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"individual.fit"</span><span class='op'>)</span>
</div><div class='img'><img src='saem-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Plotting individual fits</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"npde"</span><span class='op'>)</span>
</div><div class='img'><img src='saem-2.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Simulating data using nsim = 1000 simulated datasets
@@ -333,13 +324,11 @@ 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] "Mon Jan 11 12:42:14 2021"
+#&gt; [1] "Mon Jan 25 14:41:55 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 11 12:42:19 2021"</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'>
+#&gt; [1] "Mon Jan 25 14:42:00 2021"</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; <span class='error'>Error in compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)): 'compare.saemix' requires at least two models.</span></div><div class='input'>
<span class='va'>sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fomc_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
@@ -357,15 +346,15 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='co'># 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] "Mon Jan 11 12:42:22 2021"
+#&gt; [1] "Mon Jan 25 14:42:02 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 11 12:42:27 2021"</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] "Mon Jan 25 14:42:07 2021"</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] "Mon Jan 11 12:42:28 2021"
+#&gt; [1] "Mon Jan 25 14:42:08 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 11 12:42:37 2021"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
+#&gt; [1] "Mon Jan 25 14:42:17 2021"</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:
@@ -408,8 +397,8 @@ using <a href='mmkin.html'>mmkin</a>.</p>
</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: Mon Jan 11 12:42:38 2021
-#&gt; Date of summary: Mon Jan 11 12:42:38 2021
+#&gt; Date of fit: Mon Jan 25 14:42:18 2021
+#&gt; Date of summary: Mon Jan 25 14:42:18 2021
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -424,7 +413,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 10.092 s using 300, 100 iterations
+#&gt; Fitted in 9.954 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Constant variance
#&gt;

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