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| author | Johannes Ranke <jranke@uni-bremen.de> | 2021-08-04 16:37:52 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2021-08-04 16:37:52 +0200 |
| commit | 51fab94230e926cec690dc455964bd797a97b7c7 (patch) | |
| tree | e737a267d121034ea232d5aa8fdea2fad8bc9007 /docs/dev/reference/saem.html | |
| parent | 1bef803fc9d83989352f1b029d83e66918a0e58a (diff) | |
Improve AIC table in vignette
Diffstat (limited to 'docs/dev/reference/saem.html')
| -rw-r--r-- | docs/dev/reference/saem.html | 34 |
1 files changed, 17 insertions, 17 deletions
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 0334e0e1..620173b2 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -288,27 +288,27 @@ 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] "Thu Jul 29 12:14:07 2021" +#> [1] "Wed Aug 4 16:22:05 2021" #> .... #> Minimisation finished -#> [1] "Thu Jul 29 12:14:08 2021"</div><div class='input'> +#> [1] "Wed Aug 4 16:22:06 2021"</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] "Thu Jul 29 12:14:11 2021" +#> [1] "Wed Aug 4 16:22:08 2021" #> .... #> Minimisation finished -#> [1] "Thu Jul 29 12:14:12 2021"</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] "Wed Aug 4 16:22:10 2021"</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] "Thu Jul 29 12:14:12 2021" +#> [1] "Wed Aug 4 16:22:10 2021" #> .... #> Minimisation finished -#> [1] "Thu Jul 29 12:14:14 2021"</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] "Wed Aug 4 16:22:12 2021"</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] "Thu Jul 29 12:14:15 2021" +#> [1] "Wed Aug 4 16:22:12 2021" #> .... #> Minimisation finished -#> [1] "Thu Jul 29 12:14:18 2021"</div><div class='input'> +#> [1] "Wed Aug 4 16:22:16 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> @@ -357,10 +357,10 @@ 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] "Thu Jul 29 12:14:21 2021" +#> [1] "Wed Aug 4 16:22:19 2021" #> .... #> Minimisation finished -#> [1] "Thu Jul 29 12:14:27 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='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> +#> [1] "Wed Aug 4 16:22:24 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='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> </div><div class='output co'>#> <span class='message'>Likelihoods calculated by importance sampling</span></div><div class='output co'>#> AIC BIC #> 1 467.7096 464.9757 #> 2 469.6831 466.5586</div><div class='input'> @@ -381,15 +381,15 @@ 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'><-</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] "Thu Jul 29 12:14:31 2021" +#> [1] "Wed Aug 4 16:22:27 2021" #> .... #> Minimisation finished -#> [1] "Thu Jul 29 12:14:36 2021"</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] "Wed Aug 4 16:22:32 2021"</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] "Thu Jul 29 12:14:36 2021" +#> [1] "Wed Aug 4 16:22:33 2021" #> .... #> Minimisation finished -#> [1] "Thu Jul 29 12:14:46 2021"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span> +#> [1] "Wed Aug 4 16:22:42 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'>#> Kinetic nonlinear mixed-effects model fit by SAEM #> Structural model: @@ -432,8 +432,8 @@ using <a href='mmkin.html'>mmkin</a>.</p> </div><div class='output co'>#> saemix version used for fitting: 3.1.9000 #> mkin version used for pre-fitting: 1.0.5 #> R version used for fitting: 4.1.0 -#> Date of fit: Thu Jul 29 12:14:46 2021 -#> Date of summary: Thu Jul 29 12:14:46 2021 +#> Date of fit: Wed Aug 4 16:22:43 2021 +#> Date of summary: Wed Aug 4 16:22:43 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -448,7 +448,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 9.987 s using 300, 100 iterations +#> Fitted in 10.143 s using 300, 100 iterations #> #> Variance model: Constant variance #> |