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Diffstat (limited to 'docs/dev/reference/saem.html')
| -rw-r--r-- | docs/dev/reference/saem.html | 50 |
1 files changed, 28 insertions, 22 deletions
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index bc54e1e1..d0c3495a 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -141,7 +141,7 @@ Expectation Maximisation algorithm (SAEM)." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Fit nonlinear mixed models with SAEM</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/saemix.R'><code>R/saemix.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/saem.R'><code>R/saem.R</code></a></small> <div class="hidden name"><code>saem.Rd</code></div> </div> @@ -161,6 +161,7 @@ Expectation Maximisation algorithm (SAEM).</p> cores <span class='op'>=</span> <span class='fl'>1</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> @@ -185,19 +186,19 @@ Expectation Maximisation algorithm (SAEM).</p> </tr> <tr> <th>...</th> - <td><p>Further parameters passed to <a href='https://rdrr.io/pkg/saemix/man/saemixData.html'>saemix::saemixData</a> -and <a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix::saemixModel</a>.</p></td> + <td><p>Further parameters passed to <a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix::saemixModel</a>.</p></td> </tr> <tr> <th>cores</th> <td><p>The number of cores to be used for multicore processing using <code><a href='https://rdrr.io/r/parallel/mclapply.html'>parallel::mclapply()</a></code>. Using more than 1 core is experimental and may -lead to uncontrolled forking, apparently depending on the BLAS version +lead to excessive forking, apparently depending on the BLAS version used.</p></td> </tr> <tr> <th>verbose</th> - <td><p>Should we print information about created objects?</p></td> + <td><p>Should we print information about created objects of +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> @@ -205,6 +206,11 @@ used.</p></td> 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> + </tr> + <tr> <th>x</th> <td><p>An saem.mmkin object to print</p></td> </tr> @@ -241,27 +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 09:36:41 2020" +#> [1] "Wed Nov 11 19:47:58 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:36:43 2020"</div><div class='input'> +#> [1] "Wed Nov 11 19:48:00 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 09:36:44 2020" +#> [1] "Wed Nov 11 19:48:01 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:36:45 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] "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> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 09:36:46 2020" +#> [1] "Wed Nov 11 19:48:03 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:36:48 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] "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> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 09:36:48 2020" +#> [1] "Wed Nov 11 19:48:06 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:36:51 2020"</div><div class='input'> +#> [1] "Wed Nov 11 19:48:08 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> @@ -307,10 +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 09:36:54 2020" +#> [1] "Wed Nov 11 19:48:11 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:36:59 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] "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> </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'> @@ -330,15 +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 09:37:01 2020" +#> [1] "Wed Nov 11 19:48:18 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:37:06 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] "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> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Wed Nov 11 09:37:06 2020" +#> [1] "Wed Nov 11 19:48:23 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:37:15 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span> +#> [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> <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: @@ -384,8 +390,8 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> LL by is "-407.78 (df=13)"</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 09:37:16 2020 -#> Date of summary: Wed Nov 11 09:37:16 2020 +#> Date of fit: Wed Nov 11 19:48:33 2020 +#> Date of summary: Wed Nov 11 19:48:33 2020 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -400,7 +406,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 9.691 s using 300, 100 iterations +#> Fitted in 9.564 s using 300, 100 iterations #> #> Variance model: Constant variance #> |