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-rw-r--r--docs/dev/reference/saem.html56
1 files changed, 28 insertions, 28 deletions
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index 59589378..4578db2a 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -74,7 +74,7 @@ Expectation Maximisation algorithm (SAEM)." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span>
</span>
</div>
@@ -261,27 +261,27 @@ 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] "Mon Jan 25 14:41:42 2021"
+#&gt; [1] "Sat Feb 6 18:29:26 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 25 14:41:43 2021"</div><div class='input'>
+#&gt; [1] "Sat Feb 6 18:29:27 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 25 14:41:45 2021"
+#&gt; [1] "Sat Feb 6 18:29:28 2021"
#&gt; ....
#&gt; Minimisation finished
-#&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>
+#&gt; [1] "Sat Feb 6 18:29:30 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 25 14:41:47 2021"
+#&gt; [1] "Sat Feb 6 18:29:30 2021"
#&gt; ....
#&gt; Minimisation finished
-#&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>
+#&gt; [1] "Sat Feb 6 18:29:32 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 25 14:41:49 2021"
+#&gt; [1] "Sat Feb 6 18:29:32 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 25 14:41:52 2021"</div><div class='input'>
+#&gt; [1] "Sat Feb 6 18:29:35 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>
@@ -324,10 +324,10 @@ 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] "Mon Jan 25 14:41:55 2021"
+#&gt; [1] "Sat Feb 6 18:29:37 2021"
#&gt; ....
#&gt; Minimisation finished
-#&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>
+#&gt; [1] "Sat Feb 6 18:29:42 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>
@@ -346,15 +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 25 14:42:02 2021"
+#&gt; [1] "Sat Feb 6 18:29:44 2021"
#&gt; ....
#&gt; Minimisation finished
-#&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>
+#&gt; [1] "Sat Feb 6 18:29:48 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 25 14:42:08 2021"
+#&gt; [1] "Sat Feb 6 18:29:49 2021"
#&gt; ....
#&gt; Minimisation finished
-#&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>
+#&gt; [1] "Sat Feb 6 18:29:57 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:
@@ -395,10 +395,10 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&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; saemix version used for fitting: 3.1.9000
-#&gt; mkin version used for pre-fitting: 0.9.50.4
+#&gt; mkin version used for pre-fitting: 1.0.1.9000
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Jan 25 14:42:18 2021
-#&gt; Date of summary: Mon Jan 25 14:42:18 2021
+#&gt; Date of fit: Sat Feb 6 18:29:57 2021
+#&gt; Date of summary: Sat Feb 6 18:29:58 2021
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -413,7 +413,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 9.954 s using 300, 100 iterations
+#&gt; Fitted in 8.539 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Constant variance
#&gt;
@@ -489,12 +489,12 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; Dataset 6 parent 3 69.2 71.32042 2.12042 1.883 1.125873
#&gt; Dataset 6 parent 6 58.1 56.45256 -1.64744 1.883 -0.874739
#&gt; Dataset 6 parent 6 56.6 56.45256 -0.14744 1.883 -0.078288
-#&gt; Dataset 6 parent 10 44.4 44.48523 0.08523 1.883 0.045256
+#&gt; Dataset 6 parent 10 44.4 44.48523 0.08523 1.883 0.045257
#&gt; Dataset 6 parent 10 43.4 44.48523 1.08523 1.883 0.576224
#&gt; Dataset 6 parent 20 33.3 29.75774 -3.54226 1.883 -1.880826
#&gt; Dataset 6 parent 20 29.2 29.75774 0.55774 1.883 0.296141
#&gt; Dataset 6 parent 34 17.6 19.35710 1.75710 1.883 0.932966
-#&gt; Dataset 6 parent 34 18.0 19.35710 1.35710 1.883 0.720578
+#&gt; Dataset 6 parent 34 18.0 19.35710 1.35710 1.883 0.720579
#&gt; Dataset 6 parent 55 10.5 10.48443 -0.01557 1.883 -0.008266
#&gt; Dataset 6 parent 55 9.3 10.48443 1.18443 1.883 0.628895
#&gt; Dataset 6 parent 90 4.5 3.78622 -0.71378 1.883 -0.378995
@@ -560,9 +560,9 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; Dataset 8 parent 1 64.9 67.73197 2.83197 1.883 1.503686
#&gt; Dataset 8 parent 1 66.2 67.73197 1.53197 1.883 0.813428
#&gt; Dataset 8 parent 3 43.5 41.58448 -1.91552 1.883 -1.017081
-#&gt; Dataset 8 parent 3 44.1 41.58448 -2.51552 1.883 -1.335661
+#&gt; Dataset 8 parent 3 44.1 41.58448 -2.51552 1.883 -1.335662
#&gt; Dataset 8 parent 8 18.3 19.62286 1.32286 1.883 0.702395
-#&gt; Dataset 8 parent 8 18.1 19.62286 1.52286 1.883 0.808589
+#&gt; Dataset 8 parent 8 18.1 19.62286 1.52286 1.883 0.808588
#&gt; Dataset 8 parent 14 10.2 10.77819 0.57819 1.883 0.306999
#&gt; Dataset 8 parent 14 10.8 10.77819 -0.02181 1.883 -0.011582
#&gt; Dataset 8 parent 27 4.9 3.26977 -1.63023 1.883 -0.865599
@@ -575,13 +575,13 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; Dataset 8 A1 1 7.7 7.61539 -0.08461 1.883 -0.044923
#&gt; Dataset 8 A1 3 15.0 15.47954 0.47954 1.883 0.254622
#&gt; Dataset 8 A1 3 15.1 15.47954 0.37954 1.883 0.201525
-#&gt; Dataset 8 A1 8 21.2 20.22616 -0.97384 1.883 -0.517076
+#&gt; Dataset 8 A1 8 21.2 20.22616 -0.97384 1.883 -0.517075
#&gt; Dataset 8 A1 8 21.1 20.22616 -0.87384 1.883 -0.463979
#&gt; Dataset 8 A1 14 19.7 20.00067 0.30067 1.883 0.159645
#&gt; Dataset 8 A1 14 18.9 20.00067 1.10067 1.883 0.584419
-#&gt; Dataset 8 A1 27 17.5 16.38142 -1.11858 1.883 -0.593929
-#&gt; Dataset 8 A1 27 15.9 16.38142 0.48142 1.883 0.255619
-#&gt; Dataset 8 A1 48 9.5 10.25357 0.75357 1.883 0.400123
+#&gt; Dataset 8 A1 27 17.5 16.38142 -1.11858 1.883 -0.593928
+#&gt; Dataset 8 A1 27 15.9 16.38142 0.48142 1.883 0.255620
+#&gt; Dataset 8 A1 48 9.5 10.25357 0.75357 1.883 0.400124
#&gt; Dataset 8 A1 48 9.8 10.25357 0.45357 1.883 0.240833
#&gt; Dataset 8 A1 70 6.2 5.95728 -0.24272 1.883 -0.128878
#&gt; Dataset 8 A1 70 6.1 5.95728 -0.14272 1.883 -0.075781
@@ -622,7 +622,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; Dataset 9 A1 91 10.0 10.09177 0.09177 1.883 0.048727
#&gt; Dataset 9 A1 91 9.5 10.09177 0.59177 1.883 0.314211
#&gt; Dataset 9 A1 120 9.1 7.91379 -1.18621 1.883 -0.629841
-#&gt; Dataset 9 A1 120 9.0 7.91379 -1.08621 1.883 -0.576745
+#&gt; Dataset 9 A1 120 9.0 7.91379 -1.08621 1.883 -0.576744
#&gt; Dataset 10 parent 0 96.1 93.65257 -2.44743 1.883 -1.299505
#&gt; Dataset 10 parent 0 94.3 93.65257 -0.64743 1.883 -0.343763
#&gt; Dataset 10 parent 8 73.9 77.85906 3.95906 1.883 2.102132

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