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authorJohannes Ranke <jranke@uni-bremen.de>2020-12-21 06:02:10 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-12-21 06:02:10 +0100
commitd28ce9f8ad6f9573e403ebd8eb637ecd5e5b0e02 (patch)
tree0a4d2a924eaf319dd686cc99f1705be3a5e2afe0 /docs/dev
parent49280ed2e27ec072232684b27f9b05d7f3cc12c7 (diff)
plot.mixed: Possibility to overlay predictions
Diffstat (limited to 'docs/dev')
-rw-r--r--docs/dev/pkgdown.yml2
-rw-r--r--docs/dev/reference/Rplot001.pngbin1011 -> 19395 bytes
-rw-r--r--docs/dev/reference/plot.mixed.mmkin-3.pngbin163488 -> 163536 bytes
-rw-r--r--docs/dev/reference/plot.mixed.mmkin-4.pngbin0 -> 166687 bytes
-rw-r--r--docs/dev/reference/plot.mixed.mmkin.html23
-rw-r--r--docs/dev/reference/saem.html57
6 files changed, 47 insertions, 35 deletions
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index b3124589..85a358df 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
web_only/NAFTA_examples: NAFTA_examples.html
web_only/benchmarks: benchmarks.html
web_only/compiled_models: compiled_models.html
-last_built: 2020-12-19T11:24Z
+last_built: 2020-12-21T04:57Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index 17a35806..bca41e2c 100644
--- a/docs/dev/reference/Rplot001.png
+++ b/docs/dev/reference/Rplot001.png
Binary files differ
diff --git a/docs/dev/reference/plot.mixed.mmkin-3.png b/docs/dev/reference/plot.mixed.mmkin-3.png
index 3055c0c9..5e00afe6 100644
--- a/docs/dev/reference/plot.mixed.mmkin-3.png
+++ b/docs/dev/reference/plot.mixed.mmkin-3.png
Binary files differ
diff --git a/docs/dev/reference/plot.mixed.mmkin-4.png b/docs/dev/reference/plot.mixed.mmkin-4.png
new file mode 100644
index 00000000..6a5f3b9c
--- /dev/null
+++ b/docs/dev/reference/plot.mixed.mmkin-4.png
Binary files differ
diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html
index 90ba9184..55c411e7 100644
--- a/docs/dev/reference/plot.mixed.mmkin.html
+++ b/docs/dev/reference/plot.mixed.mmkin.html
@@ -121,7 +121,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -156,6 +156,7 @@
xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>,
resplot <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'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>,
+ pred_over <span class='op'>=</span> <span class='cn'>NULL</span>,
ymax <span class='op'>=</span> <span class='st'>"auto"</span>,
maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>,
@@ -206,6 +207,11 @@ variables in the model.</p></td>
predicted values?</p></td>
</tr>
<tr>
+ <th>pred_over</th>
+ <td><p>Named list of alternative predictions as obtained
+from <a href='mkinpredict.html'>mkinpredict</a> with a compatible <a href='mkinmod.html'>mkinmod</a>.</p></td>
+ </tr>
+ <tr>
<th>ymax</th>
<td><p>Vector of maximum y axis values</p></td>
</tr>
@@ -275,13 +281,20 @@ corresponding model prediction lines for the different datasets.</p></td>
<span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-3</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span>
</div><div class='img'><img src='plot.mixed.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'>
-<span class='va'>f_saem</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
+<span class='va'>f_saem</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span>, transformations <span class='op'>=</span> <span class='st'>"saemix"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Fri Dec 11 15:37:36 2020"
+#&gt; [1] "Mon Dec 21 05:58:23 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Fri Dec 11 15:37:45 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span>
-</div><div class='img'><img src='plot.mixed.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
+#&gt; [1] "Mon Dec 21 05:58:30 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span>
+</div><div class='img'><img src='plot.mixed.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='co'># We can overlay the two variants if we generate predictions</span>
+<span class='va'>pred_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>dfop_sfo</span>,
+ <span class='va'>f_nlme</span><span class='op'>$</span><span class='va'>bparms.optim</span><span class='op'>[</span><span class='op'>-</span><span class='fl'>1</span><span class='op'>]</span>,
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='va'>f_nlme</span><span class='op'>$</span><span class='va'>bparms.optim</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span>, A1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>,
+ <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>180</span>, by <span class='op'>=</span> <span class='fl'>0.2</span><span class='op'>)</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span>, pred_over <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>nlme <span class='op'>=</span> <span class='va'>pred_nlme</span><span class='op'>)</span><span class='op'>)</span>
+</div><div class='img'><img src='plot.mixed.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index 67468f89..1e92e3fb 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -123,7 +123,7 @@ Expectation Maximisation algorithm (SAEM)." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -157,6 +157,7 @@ Expectation Maximisation algorithm (SAEM).</p>
<span class='fu'>saem</span><span class='op'>(</span>
<span class='va'>object</span>,
transformations <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'>"mkin"</span>, <span class='st'>"saemix"</span><span class='op'>)</span>,
+ degparms_start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/numeric.html'>numeric</a></span><span class='op'>(</span><span class='op'>)</span>,
solution_type <span class='op'>=</span> <span class='st'>"auto"</span>,
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>,
@@ -173,6 +174,7 @@ Expectation Maximisation algorithm (SAEM).</p>
<span class='va'>object</span>,
solution_type <span class='op'>=</span> <span class='st'>"auto"</span>,
transformations <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'>"mkin"</span>, <span class='st'>"saemix"</span><span class='op'>)</span>,
+ degparms_start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/numeric.html'>numeric</a></span><span class='op'>(</span><span class='op'>)</span>,
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
@@ -200,6 +202,11 @@ supported in cases where the initial concentration of the parent is not fixed,
SFO or DFOP is used for the parent and there is either no metabolite or one.</p></td>
</tr>
<tr>
+ <th>degparms_start</th>
+ <td><p>Parameter values given as a named numeric vector will
+be used to override the starting values obtained from the 'mmkin' object.</p></td>
+ </tr>
+ <tr>
<th>solution_type</th>
<td><p>Possibility to specify the solution type in case the
automatic choice is not desired</p></td>
@@ -260,36 +267,33 @@ 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] "Wed Dec 16 18:27:30 2020"
+#&gt; [1] "Mon Dec 21 05:58:33 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Dec 16 18:27:31 2020"</div><div class='input'>
+#&gt; [1] "Mon Dec 21 05:58:34 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 Dec 16 18:27:33 2020"
+#&gt; [1] "Mon Dec 21 05:58:36 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Dec 16 18:27:35 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] "Mon Dec 21 05:58:37 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 Dec 16 18:27:35 2020"
+#&gt; [1] "Mon Dec 21 05:58:38 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Dec 16 18:27:37 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] "Mon Dec 21 05:58:40 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 Dec 16 18:27:37 2020"
+#&gt; [1] "Mon Dec 21 05:58:40 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Dec 16 18:27:40 2020"</div><div class='input'>
+#&gt; [1] "Mon Dec 21 05:58:43 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>
</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
@@ -326,13 +330,11 @@ 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] "Wed Dec 16 18:27:43 2020"
+#&gt; [1] "Mon Dec 21 05:58:46 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Dec 16 18:27:48 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'>
+#&gt; [1] "Mon Dec 21 05:58:51 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; <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>,
@@ -350,15 +352,15 @@ 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] "Wed Dec 16 18:27:50 2020"
+#&gt; [1] "Mon Dec 21 05:58:53 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Dec 16 18:27:55 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] "Mon Dec 21 05:58:58 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 Dec 16 18:27:56 2020"
+#&gt; [1] "Mon Dec 21 05:58:59 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Dec 16 18:28:05 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
+#&gt; [1] "Mon Dec 21 05:59:08 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:
@@ -373,8 +375,6 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; 170 observations of 2 variable(s) grouped in 5 datasets
#&gt;
#&gt; Likelihood computed by importance sampling
-#&gt;
-#&gt; LL by is "-407.78 (df=13)"
#&gt; AIC BIC logLik
#&gt; 841.6 836.5 -407.8
#&gt;
@@ -400,12 +400,11 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; SD.log_k2 1.90634 0.70934 3.1033
#&gt; SD.g_qlogis 0.44771 -0.86417 1.7596</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_dfop_sfo</span><span class='op'>)</span>
</div><div class='img'><img src='saem-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt;
-#&gt; LL by is "-407.78 (df=13)"</div><div class='output co'>#&gt; saemix version used for fitting: 3.1.9000
+</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 Dec 16 18:28:06 2020
-#&gt; Date of summary: Wed Dec 16 18:28:06 2020
+#&gt; Date of fit: Mon Dec 21 05:59:09 2020
+#&gt; Date of summary: Mon Dec 21 05:59:09 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -420,7 +419,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 9.889 s using 300, 100 iterations
+#&gt; Fitted in 9.836 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Constant variance
#&gt;

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