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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-19 15:41:24 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-19 15:41:24 +0100
commitdb9ae6a0c9cecb92048fde6f06af1da183c09b5f (patch)
treef0ea97545549c71bd7aa3d13afed422fd402f0e6 /docs/dev/reference/saem.html
parent6441a9f35d66f2c4d38c0036f99cd8f509d76f3b (diff)
Depend on parallel, doc improvements
By depending on parallel instead of importing it, functions to set up and stop a cluster are always available when mkin is loaded. The use of multicore processing in mmkin on Windows is now documented in the help file, which brings mkin closer to a version 1.0 #9.
Diffstat (limited to 'docs/dev/reference/saem.html')
-rw-r--r--docs/dev/reference/saem.html244
1 files changed, 218 insertions, 26 deletions
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index d0c3495a..948e1378 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -247,27 +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 19:47:58 2020"
+#&gt; [1] "Thu Nov 19 14:51:31 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 19:48:00 2020"</div><div class='input'>
+#&gt; [1] "Thu Nov 19 14:51:33 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 19:48:01 2020"
+#&gt; [1] "Thu Nov 19 14:51:34 2020"
#&gt; ....
#&gt; Minimisation finished
-#&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>
+#&gt; [1] "Thu Nov 19 14:51:36 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 19:48:03 2020"
+#&gt; [1] "Thu Nov 19 14:51:36 2020"
#&gt; ....
#&gt; Minimisation finished
-#&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>
+#&gt; [1] "Thu Nov 19 14:51:38 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 19:48:06 2020"
+#&gt; [1] "Thu Nov 19 14:51:39 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Wed Nov 11 19:48:08 2020"</div><div class='input'>
+#&gt; [1] "Thu Nov 19 14:51:42 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>
@@ -313,10 +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 19:48:11 2020"
+#&gt; [1] "Thu Nov 19 14:51:44 2020"
#&gt; ....
#&gt; Minimisation finished
-#&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>
+#&gt; [1] "Thu Nov 19 14:51:49 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'>
@@ -327,7 +327,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='va'>dfop_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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.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'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># The following fit uses analytical solutions for SFO-SFO and DFOP-SFO,</span>
-<span class='co'># and compiled ODEs for FOMC, both are fast</span>
+<span class='co'># and compiled ODEs for FOMC that are much slower</span>
<span class='va'>f_mmkin</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/list.html'>list</a></span><span class='op'>(</span>
<span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>sfo_sfo</span>, <span class='st'>"FOMC-SFO"</span> <span class='op'>=</span> <span class='va'>fomc_sfo</span>, <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>,
<span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
@@ -336,15 +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 19:48:18 2020"
+#&gt; [1] "Thu Nov 19 14:51:52 2020"
#&gt; ....
#&gt; Minimisation finished
-#&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>
+#&gt; [1] "Thu Nov 19 14:51:57 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 19:48:23 2020"
+#&gt; [1] "Thu Nov 19 14:51:57 2020"
#&gt; ....
#&gt; Minimisation finished
-#&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>
+#&gt; [1] "Thu Nov 19 14:52:06 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:
@@ -359,8 +359,6 @@ 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;
@@ -385,13 +383,12 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; SD.log_k1 1.42027 0.52714 2.3134
#&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'>FALSE</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='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; R version used for fitting: 4.0.3
-#&gt; Date of fit: Wed Nov 11 19:48:33 2020
-#&gt; Date of summary: Wed Nov 11 19:48:33 2020
+#&gt; Date of fit: Thu Nov 19 14:52:07 2020
+#&gt; Date of summary: Thu Nov 19 14:52:07 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -406,7 +403,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 9.564 s using 300, 100 iterations
+#&gt; Fitted in 10.034 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Constant variance
#&gt;
@@ -472,11 +469,206 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; Estimated disappearance times:
#&gt; DT50 DT90 DT50back DT50_k1 DT50_k2
#&gt; parent 14.11 59.53 17.92 8.717 25.03
-#&gt; A1 319.21 1060.38 NA NA NA</div><div class='input'>
+#&gt; A1 319.21 1060.38 NA NA NA
+#&gt;
+#&gt; Data:
+#&gt; ds name time observed predicted residual std standardized
+#&gt; Dataset 6 parent 0 97.2 95.79523 -1.40477 1.883 -0.745888
+#&gt; Dataset 6 parent 0 96.4 95.79523 -0.60477 1.883 -0.321114
+#&gt; Dataset 6 parent 3 71.1 71.32042 0.22042 1.883 0.117035
+#&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 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 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
+#&gt; Dataset 6 parent 90 4.7 3.78622 -0.91378 1.883 -0.485188
+#&gt; Dataset 6 parent 112 3.0 1.99608 -1.00392 1.883 -0.533048
+#&gt; Dataset 6 parent 112 3.4 1.99608 -1.40392 1.883 -0.745435
+#&gt; Dataset 6 parent 132 2.3 1.11539 -1.18461 1.883 -0.628990
+#&gt; Dataset 6 parent 132 2.7 1.11539 -1.58461 1.883 -0.841377
+#&gt; Dataset 6 A1 3 4.3 4.66132 0.36132 1.883 0.191849
+#&gt; Dataset 6 A1 3 4.6 4.66132 0.06132 1.883 0.032559
+#&gt; Dataset 6 A1 6 7.0 7.41087 0.41087 1.883 0.218157
+#&gt; Dataset 6 A1 6 7.2 7.41087 0.21087 1.883 0.111964
+#&gt; Dataset 6 A1 10 8.2 9.50878 1.30878 1.883 0.694921
+#&gt; Dataset 6 A1 10 8.0 9.50878 1.50878 1.883 0.801114
+#&gt; Dataset 6 A1 20 11.0 11.69902 0.69902 1.883 0.371157
+#&gt; Dataset 6 A1 20 13.7 11.69902 -2.00098 1.883 -1.062455
+#&gt; Dataset 6 A1 34 11.5 12.67784 1.17784 1.883 0.625396
+#&gt; Dataset 6 A1 34 12.7 12.67784 -0.02216 1.883 -0.011765
+#&gt; Dataset 6 A1 55 14.9 12.78556 -2.11444 1.883 -1.122701
+#&gt; Dataset 6 A1 55 14.5 12.78556 -1.71444 1.883 -0.910314
+#&gt; Dataset 6 A1 90 12.1 11.52954 -0.57046 1.883 -0.302898
+#&gt; Dataset 6 A1 90 12.3 11.52954 -0.77046 1.883 -0.409092
+#&gt; Dataset 6 A1 112 9.9 10.43825 0.53825 1.883 0.285793
+#&gt; Dataset 6 A1 112 10.2 10.43825 0.23825 1.883 0.126503
+#&gt; Dataset 6 A1 132 8.8 9.42830 0.62830 1.883 0.333609
+#&gt; Dataset 6 A1 132 7.8 9.42830 1.62830 1.883 0.864577
+#&gt; Dataset 7 parent 0 93.6 90.91477 -2.68523 1.883 -1.425772
+#&gt; Dataset 7 parent 0 92.3 90.91477 -1.38523 1.883 -0.735514
+#&gt; Dataset 7 parent 3 87.0 84.76874 -2.23126 1.883 -1.184726
+#&gt; Dataset 7 parent 3 82.2 84.76874 2.56874 1.883 1.363919
+#&gt; Dataset 7 parent 7 74.0 77.62735 3.62735 1.883 1.926003
+#&gt; Dataset 7 parent 7 73.9 77.62735 3.72735 1.883 1.979100
+#&gt; Dataset 7 parent 14 64.2 67.52266 3.32266 1.883 1.764224
+#&gt; Dataset 7 parent 14 69.5 67.52266 -1.97734 1.883 -1.049904
+#&gt; Dataset 7 parent 30 54.0 52.41949 -1.58051 1.883 -0.839202
+#&gt; Dataset 7 parent 30 54.6 52.41949 -2.18051 1.883 -1.157783
+#&gt; Dataset 7 parent 60 41.1 39.36582 -1.73418 1.883 -0.920794
+#&gt; Dataset 7 parent 60 38.4 39.36582 0.96582 1.883 0.512818
+#&gt; Dataset 7 parent 90 32.5 33.75388 1.25388 1.883 0.665771
+#&gt; Dataset 7 parent 90 35.5 33.75388 -1.74612 1.883 -0.927132
+#&gt; Dataset 7 parent 120 28.1 30.41716 2.31716 1.883 1.230335
+#&gt; Dataset 7 parent 120 29.0 30.41716 1.41716 1.883 0.752464
+#&gt; Dataset 7 parent 180 26.5 25.66046 -0.83954 1.883 -0.445767
+#&gt; Dataset 7 parent 180 27.6 25.66046 -1.93954 1.883 -1.029832
+#&gt; Dataset 7 A1 3 3.9 2.69355 -1.20645 1.883 -0.640585
+#&gt; Dataset 7 A1 3 3.1 2.69355 -0.40645 1.883 -0.215811
+#&gt; Dataset 7 A1 7 6.9 5.81807 -1.08193 1.883 -0.574470
+#&gt; Dataset 7 A1 7 6.6 5.81807 -0.78193 1.883 -0.415180
+#&gt; Dataset 7 A1 14 10.4 10.22529 -0.17471 1.883 -0.092767
+#&gt; Dataset 7 A1 14 8.3 10.22529 1.92529 1.883 1.022265
+#&gt; Dataset 7 A1 30 14.4 16.75484 2.35484 1.883 1.250345
+#&gt; Dataset 7 A1 30 13.7 16.75484 3.05484 1.883 1.622022
+#&gt; Dataset 7 A1 60 22.1 22.22540 0.12540 1.883 0.066583
+#&gt; Dataset 7 A1 60 22.3 22.22540 -0.07460 1.883 -0.039610
+#&gt; Dataset 7 A1 90 27.5 24.38799 -3.11201 1.883 -1.652376
+#&gt; Dataset 7 A1 90 25.4 24.38799 -1.01201 1.883 -0.537344
+#&gt; Dataset 7 A1 120 28.0 25.53294 -2.46706 1.883 -1.309927
+#&gt; Dataset 7 A1 120 26.6 25.53294 -1.06706 1.883 -0.566572
+#&gt; Dataset 7 A1 180 25.8 26.94943 1.14943 1.883 0.610309
+#&gt; Dataset 7 A1 180 25.3 26.94943 1.64943 1.883 0.875793
+#&gt; Dataset 8 parent 0 91.9 91.53246 -0.36754 1.883 -0.195151
+#&gt; Dataset 8 parent 0 90.8 91.53246 0.73246 1.883 0.388914
+#&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 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 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
+#&gt; Dataset 8 parent 27 3.3 3.26977 -0.03023 1.883 -0.016051
+#&gt; Dataset 8 parent 48 1.6 0.48024 -1.11976 1.883 -0.594557
+#&gt; Dataset 8 parent 48 1.5 0.48024 -1.01976 1.883 -0.541460
+#&gt; Dataset 8 parent 70 1.1 0.06438 -1.03562 1.883 -0.549881
+#&gt; Dataset 8 parent 70 0.9 0.06438 -0.83562 1.883 -0.443688
+#&gt; Dataset 8 A1 1 9.6 7.61539 -1.98461 1.883 -1.053761
+#&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 21.1 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 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
+#&gt; Dataset 9 parent 0 99.8 97.47274 -2.32726 1.883 -1.235697
+#&gt; Dataset 9 parent 0 98.3 97.47274 -0.82726 1.883 -0.439246
+#&gt; Dataset 9 parent 1 77.1 79.72257 2.62257 1.883 1.392500
+#&gt; Dataset 9 parent 1 77.2 79.72257 2.52257 1.883 1.339404
+#&gt; Dataset 9 parent 3 59.0 56.26497 -2.73503 1.883 -1.452212
+#&gt; Dataset 9 parent 3 58.1 56.26497 -1.83503 1.883 -0.974342
+#&gt; Dataset 9 parent 8 27.4 31.66985 4.26985 1.883 2.267151
+#&gt; Dataset 9 parent 8 29.2 31.66985 2.46985 1.883 1.311410
+#&gt; Dataset 9 parent 14 19.1 22.39789 3.29789 1.883 1.751071
+#&gt; Dataset 9 parent 14 29.6 22.39789 -7.20211 1.883 -3.824090
+#&gt; Dataset 9 parent 27 10.1 14.21758 4.11758 1.883 2.186301
+#&gt; Dataset 9 parent 27 18.2 14.21758 -3.98242 1.883 -2.114537
+#&gt; Dataset 9 parent 48 4.5 7.27921 2.77921 1.883 1.475671
+#&gt; Dataset 9 parent 48 9.1 7.27921 -1.82079 1.883 -0.966780
+#&gt; Dataset 9 parent 70 2.3 3.61470 1.31470 1.883 0.698065
+#&gt; Dataset 9 parent 70 2.9 3.61470 0.71470 1.883 0.379485
+#&gt; Dataset 9 parent 91 2.0 1.85303 -0.14697 1.883 -0.078038
+#&gt; Dataset 9 parent 91 1.8 1.85303 0.05303 1.883 0.028155
+#&gt; Dataset 9 parent 120 2.0 0.73645 -1.26355 1.883 -0.670906
+#&gt; Dataset 9 parent 120 2.2 0.73645 -1.46355 1.883 -0.777099
+#&gt; Dataset 9 A1 1 4.2 3.87843 -0.32157 1.883 -0.170743
+#&gt; Dataset 9 A1 1 3.9 3.87843 -0.02157 1.883 -0.011453
+#&gt; Dataset 9 A1 3 7.4 8.90535 1.50535 1.883 0.799291
+#&gt; Dataset 9 A1 3 7.9 8.90535 1.00535 1.883 0.533807
+#&gt; Dataset 9 A1 8 14.5 13.75172 -0.74828 1.883 -0.397312
+#&gt; Dataset 9 A1 8 13.7 13.75172 0.05172 1.883 0.027462
+#&gt; Dataset 9 A1 14 14.2 14.97541 0.77541 1.883 0.411715
+#&gt; Dataset 9 A1 14 12.2 14.97541 2.77541 1.883 1.473650
+#&gt; Dataset 9 A1 27 13.7 14.94728 1.24728 1.883 0.662266
+#&gt; Dataset 9 A1 27 13.2 14.94728 1.74728 1.883 0.927750
+#&gt; Dataset 9 A1 48 13.6 13.66078 0.06078 1.883 0.032272
+#&gt; Dataset 9 A1 48 15.4 13.66078 -1.73922 1.883 -0.923470
+#&gt; Dataset 9 A1 70 10.4 11.84899 1.44899 1.883 0.769365
+#&gt; Dataset 9 A1 70 11.6 11.84899 0.24899 1.883 0.132204
+#&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 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
+#&gt; Dataset 10 parent 8 73.9 77.85906 3.95906 1.883 2.102132
+#&gt; Dataset 10 parent 14 69.4 70.17143 0.77143 1.883 0.409606
+#&gt; Dataset 10 parent 14 73.1 70.17143 -2.92857 1.883 -1.554974
+#&gt; Dataset 10 parent 21 65.6 63.99188 -1.60812 1.883 -0.853862
+#&gt; Dataset 10 parent 21 65.3 63.99188 -1.30812 1.883 -0.694572
+#&gt; Dataset 10 parent 41 55.9 54.64292 -1.25708 1.883 -0.667467
+#&gt; Dataset 10 parent 41 54.4 54.64292 0.24292 1.883 0.128985
+#&gt; Dataset 10 parent 63 47.0 49.61303 2.61303 1.883 1.387433
+#&gt; Dataset 10 parent 63 49.3 49.61303 0.31303 1.883 0.166207
+#&gt; Dataset 10 parent 91 44.7 45.17807 0.47807 1.883 0.253839
+#&gt; Dataset 10 parent 91 46.7 45.17807 -1.52193 1.883 -0.808096
+#&gt; Dataset 10 parent 120 42.1 41.27970 -0.82030 1.883 -0.435552
+#&gt; Dataset 10 parent 120 41.3 41.27970 -0.02030 1.883 -0.010778
+#&gt; Dataset 10 A1 8 3.3 3.99294 0.69294 1.883 0.367929
+#&gt; Dataset 10 A1 8 3.4 3.99294 0.59294 1.883 0.314832
+#&gt; Dataset 10 A1 14 3.9 5.92756 2.02756 1.883 1.076570
+#&gt; Dataset 10 A1 14 2.9 5.92756 3.02756 1.883 1.607538
+#&gt; Dataset 10 A1 21 6.4 7.47313 1.07313 1.883 0.569799
+#&gt; Dataset 10 A1 21 7.2 7.47313 0.27313 1.883 0.145025
+#&gt; Dataset 10 A1 41 9.1 9.76819 0.66819 1.883 0.354786
+#&gt; Dataset 10 A1 41 8.5 9.76819 1.26819 1.883 0.673367
+#&gt; Dataset 10 A1 63 11.7 10.94733 -0.75267 1.883 -0.399643
+#&gt; Dataset 10 A1 63 12.0 10.94733 -1.05267 1.883 -0.558933
+#&gt; Dataset 10 A1 91 13.3 11.93773 -1.36227 1.883 -0.723321
+#&gt; Dataset 10 A1 91 13.2 11.93773 -1.26227 1.883 -0.670224
+#&gt; Dataset 10 A1 120 14.3 12.77666 -1.52334 1.883 -0.808847
+#&gt; Dataset 10 A1 120 12.1 12.77666 0.67666 1.883 0.359282</div><div class='input'>
<span class='co'># Using a single core, the following takes about 6 minutes as we do not have an</span>
<span class='co'># analytical solution. Using 10 cores it is slower instead of faster</span>
-<span class='co'>#f_saem_fomc &lt;- saem(f_mmkin["FOMC-SFO", ], cores = 1)</span>
-<span class='co'># }</span>
+<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</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Running main SAEM algorithm
+#&gt; [1] "Thu Nov 19 14:52:08 2020"
+#&gt; DLSODA- At current T (=R1), MXSTEP (=I1) steps
+#&gt; taken on this call before reaching TOUT
+#&gt; In above message, I1 = 5000
+#&gt;
+#&gt; In above message, R1 = 0.00156238
+#&gt;
+#&gt; DLSODA- At T (=R1) and step size H (=R2), the
+#&gt; corrector convergence failed repeatedly
+#&gt; or with ABS(H) = HMIN
+#&gt; In above message, R1 = 0, R2 = 1.1373e-10
+#&gt;
+#&gt; DLSODA- At current T (=R1), MXSTEP (=I1) steps
+#&gt; taken on this call before reaching TOUT
+#&gt; In above message, I1 = 5000
+#&gt;
+#&gt; In above message, R1 = 2.24752e-06
+#&gt;
+#&gt; ....
+#&gt; Minimisation finished
+#&gt; [1] "Thu Nov 19 14:59:05 2020"</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>
+</div><div class='img'><img src='saem-6.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
</div></pre>
</div>
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