diff options
Diffstat (limited to 'docs/dev/reference/saem.html')
| -rw-r--r-- | docs/dev/reference/saem.html | 127 |
1 files changed, 65 insertions, 62 deletions
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index e4ebf5d9..73699e19 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -151,11 +151,13 @@ effects models created from <a href='mmkin.html'>mmkin</a> row objects using the Expectation Maximisation algorithm (SAEM).</p> </div> - <pre class="usage"><span class='fu'>saem</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>control</span>, <span class='va'>...</span><span class='op'>)</span> + <pre class="usage"><span class='fu'>saem</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span> <span class='co'># S3 method for mmkin</span> <span class='fu'>saem</span><span class='op'>(</span> <span class='va'>object</span>, + transformations <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'>"mkin"</span>, <span class='st'>"saemix"</span><span class='op'>)</span>, + solution_type <span class='op'>=</span> <span class='st'>"auto"</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>displayProgress <span class='op'>=</span> <span class='cn'>FALSE</span>, print <span class='op'>=</span> <span class='cn'>FALSE</span>, save <span class='op'>=</span> <span class='cn'>FALSE</span>, save.graphs <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, @@ -168,7 +170,14 @@ Expectation Maximisation algorithm (SAEM).</p> <span class='co'># S3 method for saem.mmkin</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, digits <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"digits"</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>3</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span> -<span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>object</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span> +<span class='fu'>saemix_model</span><span class='op'>(</span> + <span class='va'>object</span>, + solution_type <span class='op'>=</span> <span class='st'>"auto"</span>, + transformations <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'>"mkin"</span>, <span class='st'>"saemix"</span><span class='op'>)</span>, + cores <span class='op'>=</span> <span class='fl'>1</span>, + verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, + <span class='va'>...</span> +<span class='op'>)</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>object</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span></pre> @@ -181,19 +190,25 @@ Expectation Maximisation algorithm (SAEM).</p> <a href='mkinmod.html'>mkinmod</a> model to different datasets</p></td> </tr> <tr> - <th>control</th> - <td><p>Passed to <a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix::saemix</a></p></td> - </tr> - <tr> <th>...</th> <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 excessive forking, apparently depending on the BLAS version -used.</p></td> + <th>transformations</th> + <td><p>Per default, all parameter transformations are done +in mkin. If this argument is set to 'saemix', parameter transformations +are done in 'saemix' for the supported cases. Currently this is only +supported in cases where the initial concentration of the parent is not fixed, +SFO or DFOP is used for the parent and there is either no metabolite or one.</p></td> + </tr> + <tr> + <th>solution_type</th> + <td><p>Possibility to specify the solution type in case the +automatic choice is not desired</p></td> + </tr> + <tr> + <th>control</th> + <td><p>Passed to <a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix::saemix</a></p></td> </tr> <tr> <th>verbose</th> @@ -243,31 +258,31 @@ using <a href='mmkin.html'>mmkin</a>.</p> <span class='va'>ds</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</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'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span> -<span class='va'>f_mmkin_parent_p0_fixed</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>ds</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, +<span class='va'>f_mmkin_parent_p0_fixed</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>ds</span>, 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] "Mon Nov 30 15:53:02 2020" +#> [1] "Fri Dec 11 15:37:47 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 30 15:53:04 2020"</div><div class='input'> +#> [1] "Fri Dec 11 15:37:49 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] "Mon Nov 30 15:53:05 2020" +#> [1] "Fri Dec 11 15:37:51 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 30 15:53:07 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] "Fri Dec 11 15:37:52 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] "Mon Nov 30 15:53:07 2020" +#> [1] "Fri Dec 11 15:37:52 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 30 15:53:09 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] "Fri Dec 11 15:37:55 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] "Mon Nov 30 15:53:10 2020" +#> [1] "Fri Dec 11 15:37:55 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 30 15:53:13 2020"</div><div class='input'> +#> [1] "Fri Dec 11 15:37:58 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 +328,10 @@ 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] "Mon Nov 30 15:53:15 2020" +#> [1] "Fri Dec 11 15:38:01 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 30 15:53:20 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'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> +#> [1] "Fri Dec 11 15:38:06 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</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'> @@ -331,20 +346,21 @@ using <a href='mmkin.html'>mmkin</a>.</p> <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> -<span class='co'># These take about five seconds each on this system, as we use</span> -<span class='co'># analytical solutions written for saemix. When using the analytical</span> -<span class='co'># solutions written for mkin this took around four minutes</span> +<span class='co'># saem fits of SFO-SFO and DFOP-SFO to these data take about five seconds</span> +<span class='co'># each on this system, as we use analytical solutions written for saemix.</span> +<span class='co'># When using the analytical solutions written for mkin this took around</span> +<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] "Mon Nov 30 15:53:23 2020" +#> [1] "Fri Dec 11 15:38:09 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 30 15:53:28 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] "Fri Dec 11 15:38:14 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] "Mon Nov 30 15:53:29 2020" +#> [1] "Fri Dec 11 15:38:15 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 30 15:53:38 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span> +#> [1] "Fri Dec 11 15:38:24 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: @@ -387,8 +403,8 @@ 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: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Mon Nov 30 15:53:38 2020 -#> Date of summary: Mon Nov 30 15:53:39 2020 +#> Date of fit: Fri Dec 11 15:38:25 2020 +#> Date of summary: Fri Dec 11 15:38:25 2020 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -403,15 +419,15 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 9.963 s using 300, 100 iterations +#> Fitted in 10.096 s using 300, 100 iterations #> #> Variance model: Constant variance #> #> Mean of starting values for individual parameters: #> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 -#> 93.8101519 -9.7647455 -0.9711148 -1.8799371 -4.2708142 +#> 93.8102 -9.7647 -0.9711 -1.8799 -4.2708 #> g_qlogis -#> 0.1356441 +#> 0.1356 #> #> Fixed degradation parameter values: #> None @@ -422,7 +438,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> AIC BIC logLik #> 841.6 836.5 -407.8 #> -#> Optimised, transformed parameters with symmetric confidence intervals: +#> Optimised parameters: #> est. lower upper #> parent_0 93.76647 91.153 96.3798 #> log_k_A1 -6.13235 -8.458 -3.8068 @@ -452,7 +468,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> est. lower upper #> a.1 1.883 1.666 2.1 #> -#> Backtransformed parameters with asymmetric confidence intervals: +#> Backtransformed parameters: #> est. lower upper #> parent_0 93.766473 9.115e+01 96.37983 #> k_A1 0.002171 2.122e-04 0.02222 @@ -643,32 +659,19 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> 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='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] "Mon Nov 30 15:53:39 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] "Mon Nov 30 16:00:45 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> +<span class='co'># The following takes about 6 minutes</span> +<span class='co'>#f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve",</span> +<span class='co'># control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span> + +<span class='co'>#saemix::compare.saemix(list(</span> +<span class='co'># f_saem_dfop_sfo$so,</span> +<span class='co'># f_saem_dfop_sfo_deSolve$so))</span> + +<span class='co'># If the model supports it, we can also use eigenvalue based solutions, which</span> +<span class='co'># take a similar amount of time</span> +<span class='co'>#f_saem_sfo_sfo_eigen <- saem(f_mmkin["SFO-SFO", ], solution_type = "eigen",</span> +<span class='co'># control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span> +<span class='co'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |