diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-19 15:41:24 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-19 15:41:24 +0100 |
| commit | db9ae6a0c9cecb92048fde6f06af1da183c09b5f (patch) | |
| tree | f0ea97545549c71bd7aa3d13afed422fd402f0e6 /docs/dev/reference/saem.html | |
| parent | 6441a9f35d66f2c4d38c0036f99cd8f509d76f3b (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.html | 244 |
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'><-</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'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 19:47:58 2020" +#> [1] "Thu Nov 19 14:51:31 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 19:48:00 2020"</div><div class='input'> +#> [1] "Thu Nov 19 14:51:33 2020"</div><div class='input'> <span class='va'>f_mmkin_parent</span> <span class='op'><-</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'><-</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'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 19:48:01 2020" +#> [1] "Thu Nov 19 14:51:34 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 19:48:03 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</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> +#> [1] "Thu Nov 19 14:51:36 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</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'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 19:48:03 2020" +#> [1] "Thu Nov 19 14:51:36 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 19:48:05 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</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> +#> [1] "Thu Nov 19 14:51:38 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</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'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 19:48:06 2020" +#> [1] "Thu Nov 19 14:51:39 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 19:48:08 2020"</div><div class='input'> +#> [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'><-</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'><-</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'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 19:48:11 2020" +#> [1] "Thu Nov 19 14:51:44 2020" #> .... #> Minimisation finished -#> [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> +#> [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'>#> Likelihoods computed by importance sampling </div><div class='output co'>#> AIC BIC #> 1 467.7096 464.9757 #> 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'>#> <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'><-</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'>#> <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'><-</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'><-</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'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 19:48:18 2020" +#> [1] "Thu Nov 19 14:51:52 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 19:48:23 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</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> +#> [1] "Thu Nov 19 14:51:57 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</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'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 19:48:23 2020" +#> [1] "Thu Nov 19 14:51:57 2020" #> .... #> Minimisation finished -#> [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> +#> [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'>#> Kinetic nonlinear mixed-effects model fit by SAEM #> Structural model: @@ -359,8 +359,6 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> 170 observations of 2 variable(s) grouped in 5 datasets #> #> Likelihood computed by importance sampling -#> -#> LL by is "-407.78 (df=13)" #> AIC BIC logLik #> 841.6 836.5 -407.8 #> @@ -385,13 +383,12 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> SD.log_k1 1.42027 0.52714 2.3134 #> SD.log_k2 1.90634 0.70934 3.1033 #> 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'>#> -#> LL by is "-407.78 (df=13)"</div><div class='output co'>#> 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'>#> saemix version used for fitting: 3.1.9000 #> mkin version used for pre-fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Wed Nov 11 19:48:33 2020 -#> Date of summary: Wed Nov 11 19:48:33 2020 +#> Date of fit: Thu Nov 19 14:52:07 2020 +#> Date of summary: Thu Nov 19 14:52:07 2020 #> #> Equations: #> 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> #> #> Model predictions using solution type analytical #> -#> Fitted in 9.564 s using 300, 100 iterations +#> Fitted in 10.034 s using 300, 100 iterations #> #> Variance model: Constant variance #> @@ -472,11 +469,206 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> Estimated disappearance times: #> DT50 DT90 DT50back DT50_k1 DT50_k2 #> parent 14.11 59.53 17.92 8.717 25.03 -#> A1 319.21 1060.38 NA NA NA</div><div class='input'> +#> A1 319.21 1060.38 NA NA NA +#> +#> Data: +#> ds name time observed predicted residual std standardized +#> Dataset 6 parent 0 97.2 95.79523 -1.40477 1.883 -0.745888 +#> Dataset 6 parent 0 96.4 95.79523 -0.60477 1.883 -0.321114 +#> Dataset 6 parent 3 71.1 71.32042 0.22042 1.883 0.117035 +#> Dataset 6 parent 3 69.2 71.32042 2.12042 1.883 1.125873 +#> Dataset 6 parent 6 58.1 56.45256 -1.64744 1.883 -0.874739 +#> Dataset 6 parent 6 56.6 56.45256 -0.14744 1.883 -0.078288 +#> Dataset 6 parent 10 44.4 44.48523 0.08523 1.883 0.045256 +#> Dataset 6 parent 10 43.4 44.48523 1.08523 1.883 0.576224 +#> Dataset 6 parent 20 33.3 29.75774 -3.54226 1.883 -1.880826 +#> Dataset 6 parent 20 29.2 29.75774 0.55774 1.883 0.296141 +#> Dataset 6 parent 34 17.6 19.35710 1.75710 1.883 0.932966 +#> Dataset 6 parent 34 18.0 19.35710 1.35710 1.883 0.720578 +#> Dataset 6 parent 55 10.5 10.48443 -0.01557 1.883 -0.008266 +#> Dataset 6 parent 55 9.3 10.48443 1.18443 1.883 0.628895 +#> Dataset 6 parent 90 4.5 3.78622 -0.71378 1.883 -0.378995 +#> Dataset 6 parent 90 4.7 3.78622 -0.91378 1.883 -0.485188 +#> Dataset 6 parent 112 3.0 1.99608 -1.00392 1.883 -0.533048 +#> Dataset 6 parent 112 3.4 1.99608 -1.40392 1.883 -0.745435 +#> Dataset 6 parent 132 2.3 1.11539 -1.18461 1.883 -0.628990 +#> Dataset 6 parent 132 2.7 1.11539 -1.58461 1.883 -0.841377 +#> Dataset 6 A1 3 4.3 4.66132 0.36132 1.883 0.191849 +#> Dataset 6 A1 3 4.6 4.66132 0.06132 1.883 0.032559 +#> Dataset 6 A1 6 7.0 7.41087 0.41087 1.883 0.218157 +#> Dataset 6 A1 6 7.2 7.41087 0.21087 1.883 0.111964 +#> Dataset 6 A1 10 8.2 9.50878 1.30878 1.883 0.694921 +#> Dataset 6 A1 10 8.0 9.50878 1.50878 1.883 0.801114 +#> Dataset 6 A1 20 11.0 11.69902 0.69902 1.883 0.371157 +#> Dataset 6 A1 20 13.7 11.69902 -2.00098 1.883 -1.062455 +#> Dataset 6 A1 34 11.5 12.67784 1.17784 1.883 0.625396 +#> Dataset 6 A1 34 12.7 12.67784 -0.02216 1.883 -0.011765 +#> Dataset 6 A1 55 14.9 12.78556 -2.11444 1.883 -1.122701 +#> Dataset 6 A1 55 14.5 12.78556 -1.71444 1.883 -0.910314 +#> Dataset 6 A1 90 12.1 11.52954 -0.57046 1.883 -0.302898 +#> Dataset 6 A1 90 12.3 11.52954 -0.77046 1.883 -0.409092 +#> Dataset 6 A1 112 9.9 10.43825 0.53825 1.883 0.285793 +#> Dataset 6 A1 112 10.2 10.43825 0.23825 1.883 0.126503 +#> Dataset 6 A1 132 8.8 9.42830 0.62830 1.883 0.333609 +#> Dataset 6 A1 132 7.8 9.42830 1.62830 1.883 0.864577 +#> Dataset 7 parent 0 93.6 90.91477 -2.68523 1.883 -1.425772 +#> Dataset 7 parent 0 92.3 90.91477 -1.38523 1.883 -0.735514 +#> Dataset 7 parent 3 87.0 84.76874 -2.23126 1.883 -1.184726 +#> Dataset 7 parent 3 82.2 84.76874 2.56874 1.883 1.363919 +#> Dataset 7 parent 7 74.0 77.62735 3.62735 1.883 1.926003 +#> Dataset 7 parent 7 73.9 77.62735 3.72735 1.883 1.979100 +#> Dataset 7 parent 14 64.2 67.52266 3.32266 1.883 1.764224 +#> Dataset 7 parent 14 69.5 67.52266 -1.97734 1.883 -1.049904 +#> Dataset 7 parent 30 54.0 52.41949 -1.58051 1.883 -0.839202 +#> Dataset 7 parent 30 54.6 52.41949 -2.18051 1.883 -1.157783 +#> Dataset 7 parent 60 41.1 39.36582 -1.73418 1.883 -0.920794 +#> Dataset 7 parent 60 38.4 39.36582 0.96582 1.883 0.512818 +#> Dataset 7 parent 90 32.5 33.75388 1.25388 1.883 0.665771 +#> Dataset 7 parent 90 35.5 33.75388 -1.74612 1.883 -0.927132 +#> Dataset 7 parent 120 28.1 30.41716 2.31716 1.883 1.230335 +#> Dataset 7 parent 120 29.0 30.41716 1.41716 1.883 0.752464 +#> Dataset 7 parent 180 26.5 25.66046 -0.83954 1.883 -0.445767 +#> Dataset 7 parent 180 27.6 25.66046 -1.93954 1.883 -1.029832 +#> Dataset 7 A1 3 3.9 2.69355 -1.20645 1.883 -0.640585 +#> Dataset 7 A1 3 3.1 2.69355 -0.40645 1.883 -0.215811 +#> Dataset 7 A1 7 6.9 5.81807 -1.08193 1.883 -0.574470 +#> Dataset 7 A1 7 6.6 5.81807 -0.78193 1.883 -0.415180 +#> Dataset 7 A1 14 10.4 10.22529 -0.17471 1.883 -0.092767 +#> Dataset 7 A1 14 8.3 10.22529 1.92529 1.883 1.022265 +#> Dataset 7 A1 30 14.4 16.75484 2.35484 1.883 1.250345 +#> Dataset 7 A1 30 13.7 16.75484 3.05484 1.883 1.622022 +#> Dataset 7 A1 60 22.1 22.22540 0.12540 1.883 0.066583 +#> Dataset 7 A1 60 22.3 22.22540 -0.07460 1.883 -0.039610 +#> Dataset 7 A1 90 27.5 24.38799 -3.11201 1.883 -1.652376 +#> Dataset 7 A1 90 25.4 24.38799 -1.01201 1.883 -0.537344 +#> Dataset 7 A1 120 28.0 25.53294 -2.46706 1.883 -1.309927 +#> Dataset 7 A1 120 26.6 25.53294 -1.06706 1.883 -0.566572 +#> Dataset 7 A1 180 25.8 26.94943 1.14943 1.883 0.610309 +#> Dataset 7 A1 180 25.3 26.94943 1.64943 1.883 0.875793 +#> Dataset 8 parent 0 91.9 91.53246 -0.36754 1.883 -0.195151 +#> Dataset 8 parent 0 90.8 91.53246 0.73246 1.883 0.388914 +#> Dataset 8 parent 1 64.9 67.73197 2.83197 1.883 1.503686 +#> Dataset 8 parent 1 66.2 67.73197 1.53197 1.883 0.813428 +#> Dataset 8 parent 3 43.5 41.58448 -1.91552 1.883 -1.017081 +#> Dataset 8 parent 3 44.1 41.58448 -2.51552 1.883 -1.335661 +#> Dataset 8 parent 8 18.3 19.62286 1.32286 1.883 0.702395 +#> Dataset 8 parent 8 18.1 19.62286 1.52286 1.883 0.808589 +#> Dataset 8 parent 14 10.2 10.77819 0.57819 1.883 0.306999 +#> Dataset 8 parent 14 10.8 10.77819 -0.02181 1.883 -0.011582 +#> Dataset 8 parent 27 4.9 3.26977 -1.63023 1.883 -0.865599 +#> Dataset 8 parent 27 3.3 3.26977 -0.03023 1.883 -0.016051 +#> Dataset 8 parent 48 1.6 0.48024 -1.11976 1.883 -0.594557 +#> Dataset 8 parent 48 1.5 0.48024 -1.01976 1.883 -0.541460 +#> Dataset 8 parent 70 1.1 0.06438 -1.03562 1.883 -0.549881 +#> Dataset 8 parent 70 0.9 0.06438 -0.83562 1.883 -0.443688 +#> Dataset 8 A1 1 9.6 7.61539 -1.98461 1.883 -1.053761 +#> Dataset 8 A1 1 7.7 7.61539 -0.08461 1.883 -0.044923 +#> Dataset 8 A1 3 15.0 15.47954 0.47954 1.883 0.254622 +#> Dataset 8 A1 3 15.1 15.47954 0.37954 1.883 0.201525 +#> Dataset 8 A1 8 21.2 20.22616 -0.97384 1.883 -0.517076 +#> Dataset 8 A1 8 21.1 20.22616 -0.87384 1.883 -0.463979 +#> Dataset 8 A1 14 19.7 20.00067 0.30067 1.883 0.159645 +#> Dataset 8 A1 14 18.9 20.00067 1.10067 1.883 0.584419 +#> Dataset 8 A1 27 17.5 16.38142 -1.11858 1.883 -0.593929 +#> Dataset 8 A1 27 15.9 16.38142 0.48142 1.883 0.255619 +#> Dataset 8 A1 48 9.5 10.25357 0.75357 1.883 0.400123 +#> Dataset 8 A1 48 9.8 10.25357 0.45357 1.883 0.240833 +#> Dataset 8 A1 70 6.2 5.95728 -0.24272 1.883 -0.128878 +#> Dataset 8 A1 70 6.1 5.95728 -0.14272 1.883 -0.075781 +#> Dataset 9 parent 0 99.8 97.47274 -2.32726 1.883 -1.235697 +#> Dataset 9 parent 0 98.3 97.47274 -0.82726 1.883 -0.439246 +#> Dataset 9 parent 1 77.1 79.72257 2.62257 1.883 1.392500 +#> Dataset 9 parent 1 77.2 79.72257 2.52257 1.883 1.339404 +#> Dataset 9 parent 3 59.0 56.26497 -2.73503 1.883 -1.452212 +#> Dataset 9 parent 3 58.1 56.26497 -1.83503 1.883 -0.974342 +#> Dataset 9 parent 8 27.4 31.66985 4.26985 1.883 2.267151 +#> Dataset 9 parent 8 29.2 31.66985 2.46985 1.883 1.311410 +#> Dataset 9 parent 14 19.1 22.39789 3.29789 1.883 1.751071 +#> Dataset 9 parent 14 29.6 22.39789 -7.20211 1.883 -3.824090 +#> Dataset 9 parent 27 10.1 14.21758 4.11758 1.883 2.186301 +#> Dataset 9 parent 27 18.2 14.21758 -3.98242 1.883 -2.114537 +#> Dataset 9 parent 48 4.5 7.27921 2.77921 1.883 1.475671 +#> Dataset 9 parent 48 9.1 7.27921 -1.82079 1.883 -0.966780 +#> Dataset 9 parent 70 2.3 3.61470 1.31470 1.883 0.698065 +#> Dataset 9 parent 70 2.9 3.61470 0.71470 1.883 0.379485 +#> Dataset 9 parent 91 2.0 1.85303 -0.14697 1.883 -0.078038 +#> Dataset 9 parent 91 1.8 1.85303 0.05303 1.883 0.028155 +#> Dataset 9 parent 120 2.0 0.73645 -1.26355 1.883 -0.670906 +#> Dataset 9 parent 120 2.2 0.73645 -1.46355 1.883 -0.777099 +#> Dataset 9 A1 1 4.2 3.87843 -0.32157 1.883 -0.170743 +#> Dataset 9 A1 1 3.9 3.87843 -0.02157 1.883 -0.011453 +#> Dataset 9 A1 3 7.4 8.90535 1.50535 1.883 0.799291 +#> Dataset 9 A1 3 7.9 8.90535 1.00535 1.883 0.533807 +#> Dataset 9 A1 8 14.5 13.75172 -0.74828 1.883 -0.397312 +#> Dataset 9 A1 8 13.7 13.75172 0.05172 1.883 0.027462 +#> Dataset 9 A1 14 14.2 14.97541 0.77541 1.883 0.411715 +#> Dataset 9 A1 14 12.2 14.97541 2.77541 1.883 1.473650 +#> Dataset 9 A1 27 13.7 14.94728 1.24728 1.883 0.662266 +#> Dataset 9 A1 27 13.2 14.94728 1.74728 1.883 0.927750 +#> Dataset 9 A1 48 13.6 13.66078 0.06078 1.883 0.032272 +#> Dataset 9 A1 48 15.4 13.66078 -1.73922 1.883 -0.923470 +#> Dataset 9 A1 70 10.4 11.84899 1.44899 1.883 0.769365 +#> Dataset 9 A1 70 11.6 11.84899 0.24899 1.883 0.132204 +#> Dataset 9 A1 91 10.0 10.09177 0.09177 1.883 0.048727 +#> Dataset 9 A1 91 9.5 10.09177 0.59177 1.883 0.314211 +#> Dataset 9 A1 120 9.1 7.91379 -1.18621 1.883 -0.629841 +#> Dataset 9 A1 120 9.0 7.91379 -1.08621 1.883 -0.576745 +#> Dataset 10 parent 0 96.1 93.65257 -2.44743 1.883 -1.299505 +#> Dataset 10 parent 0 94.3 93.65257 -0.64743 1.883 -0.343763 +#> Dataset 10 parent 8 73.9 77.85906 3.95906 1.883 2.102132 +#> Dataset 10 parent 8 73.9 77.85906 3.95906 1.883 2.102132 +#> Dataset 10 parent 14 69.4 70.17143 0.77143 1.883 0.409606 +#> Dataset 10 parent 14 73.1 70.17143 -2.92857 1.883 -1.554974 +#> Dataset 10 parent 21 65.6 63.99188 -1.60812 1.883 -0.853862 +#> Dataset 10 parent 21 65.3 63.99188 -1.30812 1.883 -0.694572 +#> Dataset 10 parent 41 55.9 54.64292 -1.25708 1.883 -0.667467 +#> Dataset 10 parent 41 54.4 54.64292 0.24292 1.883 0.128985 +#> Dataset 10 parent 63 47.0 49.61303 2.61303 1.883 1.387433 +#> Dataset 10 parent 63 49.3 49.61303 0.31303 1.883 0.166207 +#> Dataset 10 parent 91 44.7 45.17807 0.47807 1.883 0.253839 +#> Dataset 10 parent 91 46.7 45.17807 -1.52193 1.883 -0.808096 +#> Dataset 10 parent 120 42.1 41.27970 -0.82030 1.883 -0.435552 +#> Dataset 10 parent 120 41.3 41.27970 -0.02030 1.883 -0.010778 +#> Dataset 10 A1 8 3.3 3.99294 0.69294 1.883 0.367929 +#> Dataset 10 A1 8 3.4 3.99294 0.59294 1.883 0.314832 +#> Dataset 10 A1 14 3.9 5.92756 2.02756 1.883 1.076570 +#> Dataset 10 A1 14 2.9 5.92756 3.02756 1.883 1.607538 +#> Dataset 10 A1 21 6.4 7.47313 1.07313 1.883 0.569799 +#> Dataset 10 A1 21 7.2 7.47313 0.27313 1.883 0.145025 +#> Dataset 10 A1 41 9.1 9.76819 0.66819 1.883 0.354786 +#> Dataset 10 A1 41 8.5 9.76819 1.26819 1.883 0.673367 +#> Dataset 10 A1 63 11.7 10.94733 -0.75267 1.883 -0.399643 +#> Dataset 10 A1 63 12.0 10.94733 -1.05267 1.883 -0.558933 +#> Dataset 10 A1 91 13.3 11.93773 -1.36227 1.883 -0.723321 +#> Dataset 10 A1 91 13.2 11.93773 -1.26227 1.883 -0.670224 +#> Dataset 10 A1 120 14.3 12.77666 -1.52334 1.883 -0.808847 +#> 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 <- saem(f_mmkin["FOMC-SFO", ], cores = 1)</span> -<span class='co'># }</span> +<span class='va'>f_saem_fomc</span> <span class='op'><-</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'>#> Running main SAEM algorithm +#> [1] "Thu Nov 19 14:52:08 2020" +#> DLSODA- At current T (=R1), MXSTEP (=I1) steps +#> taken on this call before reaching TOUT +#> In above message, I1 = 5000 +#> +#> In above message, R1 = 0.00156238 +#> +#> DLSODA- At T (=R1) and step size H (=R2), the +#> corrector convergence failed repeatedly +#> or with ABS(H) = HMIN +#> In above message, R1 = 0, R2 = 1.1373e-10 +#> +#> DLSODA- At current T (=R1), MXSTEP (=I1) steps +#> taken on this call before reaching TOUT +#> In above message, I1 = 5000 +#> +#> In above message, R1 = 2.24752e-06 +#> +#> .... +#> Minimisation finished +#> [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> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |