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authorJohannes Ranke <jranke@uni-bremen.de>2021-01-25 14:45:04 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-01-25 14:45:04 +0100
commit737fc7f352bbb853b01ff6e3c6ec21a528da901e (patch)
tree52b17ee5c0000de32d64dc3d4c4a8175868c78b3 /docs/dev
parent9756a9e7e7911caf97bc6a1533926e4e6a58ceda (diff)
Change default ylab in plot.mkinfit, explicit ylab for plot.mmkin
See NEWS.md. Closes #12
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/Rplot006.pngbin56330 -> 24624 bytes
-rw-r--r--docs/dev/reference/Rplot007.pngbin25161 -> 25074 bytes
-rw-r--r--docs/dev/reference/plot.mkinfit-1.pngbin53731 -> 53151 bytes
-rw-r--r--docs/dev/reference/plot.mkinfit-2.pngbin73830 -> 73247 bytes
-rw-r--r--docs/dev/reference/plot.mkinfit-3.pngbin69215 -> 67810 bytes
-rw-r--r--docs/dev/reference/plot.mkinfit-4.pngbin73285 -> 72295 bytes
-rw-r--r--docs/dev/reference/plot.mkinfit-5.pngbin68646 -> 66920 bytes
-rw-r--r--docs/dev/reference/plot.mkinfit-6.pngbin74042 -> 73078 bytes
-rw-r--r--docs/dev/reference/plot.mkinfit-7.pngbin75294 -> 73909 bytes
-rw-r--r--docs/dev/reference/plot.mkinfit.html4
-rw-r--r--docs/dev/reference/plot.mmkin-1.pngbin50628 -> 49402 bytes
-rw-r--r--docs/dev/reference/plot.mmkin-2.pngbin50911 -> 49753 bytes
-rw-r--r--docs/dev/reference/plot.mmkin-3.pngbin47267 -> 46090 bytes
-rw-r--r--docs/dev/reference/plot.mmkin-4.pngbin34181 -> 33266 bytes
-rw-r--r--docs/dev/reference/plot.mmkin-5.pngbin58620 -> 57777 bytes
-rw-r--r--docs/dev/reference/plot.mmkin.html7
-rw-r--r--docs/dev/reference/saem.html49
19 files changed, 28 insertions, 34 deletions
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index 3591cac8..2963e810 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: 2021-01-11T11:41Z
+last_built: 2021-01-25T13:41Z
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/Rplot006.png b/docs/dev/reference/Rplot006.png
index 921e0394..da52f580 100644
--- a/docs/dev/reference/Rplot006.png
+++ b/docs/dev/reference/Rplot006.png
Binary files differ
diff --git a/docs/dev/reference/Rplot007.png b/docs/dev/reference/Rplot007.png
index fcca232c..fce3b6ee 100644
--- a/docs/dev/reference/Rplot007.png
+++ b/docs/dev/reference/Rplot007.png
Binary files differ
diff --git a/docs/dev/reference/plot.mkinfit-1.png b/docs/dev/reference/plot.mkinfit-1.png
index fc195031..e5da9f1c 100644
--- a/docs/dev/reference/plot.mkinfit-1.png
+++ b/docs/dev/reference/plot.mkinfit-1.png
Binary files differ
diff --git a/docs/dev/reference/plot.mkinfit-2.png b/docs/dev/reference/plot.mkinfit-2.png
index fa99f680..376c812f 100644
--- a/docs/dev/reference/plot.mkinfit-2.png
+++ b/docs/dev/reference/plot.mkinfit-2.png
Binary files differ
diff --git a/docs/dev/reference/plot.mkinfit-3.png b/docs/dev/reference/plot.mkinfit-3.png
index 28789544..c976d4b1 100644
--- a/docs/dev/reference/plot.mkinfit-3.png
+++ b/docs/dev/reference/plot.mkinfit-3.png
Binary files differ
diff --git a/docs/dev/reference/plot.mkinfit-4.png b/docs/dev/reference/plot.mkinfit-4.png
index 77b3422f..c8bc00fe 100644
--- a/docs/dev/reference/plot.mkinfit-4.png
+++ b/docs/dev/reference/plot.mkinfit-4.png
Binary files differ
diff --git a/docs/dev/reference/plot.mkinfit-5.png b/docs/dev/reference/plot.mkinfit-5.png
index b4b6528b..bc44de88 100644
--- a/docs/dev/reference/plot.mkinfit-5.png
+++ b/docs/dev/reference/plot.mkinfit-5.png
Binary files differ
diff --git a/docs/dev/reference/plot.mkinfit-6.png b/docs/dev/reference/plot.mkinfit-6.png
index f71f1769..eb8cbd92 100644
--- a/docs/dev/reference/plot.mkinfit-6.png
+++ b/docs/dev/reference/plot.mkinfit-6.png
Binary files differ
diff --git a/docs/dev/reference/plot.mkinfit-7.png b/docs/dev/reference/plot.mkinfit-7.png
index 98fee908..92a664f4 100644
--- a/docs/dev/reference/plot.mkinfit-7.png
+++ b/docs/dev/reference/plot.mkinfit-7.png
Binary files differ
diff --git a/docs/dev/reference/plot.mkinfit.html b/docs/dev/reference/plot.mkinfit.html
index c7eda78f..c5bfb528 100644
--- a/docs/dev/reference/plot.mkinfit.html
+++ b/docs/dev/reference/plot.mkinfit.html
@@ -123,7 +123,7 @@ observed data together with the solution of the fitted model." />
<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>
@@ -157,7 +157,7 @@ observed data together with the solution of the fitted model.</p>
fit <span class='op'>=</span> <span class='va'>x</span>,
obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
- ylab <span class='op'>=</span> <span class='st'>"Observed"</span>,
+ ylab <span class='op'>=</span> <span class='st'>"Residue"</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'>fit</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>,
ylim <span class='op'>=</span> <span class='st'>"default"</span>,
col_obs <span class='op'>=</span> <span class='fl'>1</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'>obs_vars</span><span class='op'>)</span>,
diff --git a/docs/dev/reference/plot.mmkin-1.png b/docs/dev/reference/plot.mmkin-1.png
index 438d5a53..f12b7907 100644
--- a/docs/dev/reference/plot.mmkin-1.png
+++ b/docs/dev/reference/plot.mmkin-1.png
Binary files differ
diff --git a/docs/dev/reference/plot.mmkin-2.png b/docs/dev/reference/plot.mmkin-2.png
index ee04b3c4..e3127554 100644
--- a/docs/dev/reference/plot.mmkin-2.png
+++ b/docs/dev/reference/plot.mmkin-2.png
Binary files differ
diff --git a/docs/dev/reference/plot.mmkin-3.png b/docs/dev/reference/plot.mmkin-3.png
index e06ed002..5448976e 100644
--- a/docs/dev/reference/plot.mmkin-3.png
+++ b/docs/dev/reference/plot.mmkin-3.png
Binary files differ
diff --git a/docs/dev/reference/plot.mmkin-4.png b/docs/dev/reference/plot.mmkin-4.png
index 5869df55..9a25fc50 100644
--- a/docs/dev/reference/plot.mmkin-4.png
+++ b/docs/dev/reference/plot.mmkin-4.png
Binary files differ
diff --git a/docs/dev/reference/plot.mmkin-5.png b/docs/dev/reference/plot.mmkin-5.png
index 927c573b..82b422b5 100644
--- a/docs/dev/reference/plot.mmkin-5.png
+++ b/docs/dev/reference/plot.mmkin-5.png
Binary files differ
diff --git a/docs/dev/reference/plot.mmkin.html b/docs/dev/reference/plot.mmkin.html
index 32da836d..ee80c6e4 100644
--- a/docs/dev/reference/plot.mmkin.html
+++ b/docs/dev/reference/plot.mmkin.html
@@ -125,7 +125,7 @@ the fit of at least one model to the same dataset is shown." />
<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>
@@ -160,6 +160,7 @@ the fit of at least one model to the same dataset is shown.</p>
main <span class='op'>=</span> <span class='st'>"auto"</span>,
legends <span class='op'>=</span> <span class='fl'>1</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'>"time"</span>, <span class='st'>"errmod"</span><span class='op'>)</span>,
+ ylab <span class='op'>=</span> <span class='st'>"Residue"</span>,
standardized <span class='op'>=</span> <span class='cn'>FALSE</span>,
show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span>,
errmin_var <span class='op'>=</span> <span class='st'>"All data"</span>,
@@ -193,6 +194,10 @@ column.</p></td>
values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td>
</tr>
<tr>
+ <th>ylab</th>
+ <td><p>Label for the y axis.</p></td>
+ </tr>
+ <tr>
<th>standardized</th>
<td><p>Should the residuals be standardized? This option
is passed to <code><a href='mkinresplot.html'>mkinresplot</a></code>, it only takes effect if
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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