diff options
Diffstat (limited to 'docs/dev/reference/saem.html')
| -rw-r--r-- | docs/dev/reference/saem.html | 95 |
1 files changed, 53 insertions, 42 deletions
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index f1b4c421..f9cdf1c8 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -164,6 +164,9 @@ Expectation Maximisation algorithm (SAEM).</p> <span class='va'>...</span> <span class='op'>)</span> +<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_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> @@ -201,6 +204,14 @@ used.</p></td> <td><p>Should we suppress any plotting that is done by the saemix function?</p></td> </tr> + <tr> + <th>x</th> + <td><p>An saem.mmkin object to print</p></td> + </tr> + <tr> + <th>digits</th> + <td><p>Number of digits to use for printing</p></td> + </tr> </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> @@ -230,27 +241,27 @@ 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] "Mon Nov 9 17:18:28 2020" +#> [1] "Tue Nov 10 05:12:21 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 17:18:30 2020"</div><div class='input'> +#> [1] "Tue Nov 10 05:12:23 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 9 17:18:31 2020" +#> [1] "Tue Nov 10 05:12:24 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 17:18:33 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] "Tue Nov 10 05:12:26 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 9 17:18:33 2020" +#> [1] "Tue Nov 10 05:12:26 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 17:18:35 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] "Tue Nov 10 05:12:28 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 9 17:18:36 2020" +#> [1] "Tue Nov 10 05:12:29 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 17:18:39 2020"</div><div class='input'> +#> [1] "Tue Nov 10 05:12:32 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> @@ -296,10 +307,10 @@ 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 9 17:18:41 2020" +#> [1] "Tue Nov 10 05:12:34 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 17:18:46 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] "Tue Nov 10 05:12:39 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 #> 1 467.7644 465.0305 #> 2 469.4862 466.3617</div><div class='input'> @@ -319,20 +330,20 @@ 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] "Mon Nov 9 17:18:48 2020" +#> [1] "Tue Nov 10 05:12:42 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 17:18:53 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] "Tue Nov 10 05:12:47 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 9 17:18:54 2020" +#> [1] "Tue Nov 10 05:12:48 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 17:19:03 2020"</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> +#> [1] "Tue Nov 10 05:12:57 2020"</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'>#> 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 9 17:19:04 2020 -#> Date of summary: Mon Nov 9 17:19:04 2020 +#> Date of fit: Tue Nov 10 05:12:58 2020 +#> Date of summary: Tue Nov 10 05:12:58 2020 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -347,7 +358,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 9.941 s using 300, 100 iterations +#> Fitted in 10.382 s using 300, 100 iterations #> #> Variance model: Constant variance #> @@ -363,17 +374,17 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> Results: #> #> Likelihood computed by importance sampling -#> AIC BIC logLik -#> 841.3208 836.2435 -407.6604 +#> AIC BIC logLik +#> 841.3 836.2 -407.7 #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> est. lower upper -#> parent_0 93.7514328489 91.113651 96.3892150 -#> log_k_A1 -6.1262333211 -8.432492 -3.8199749 -#> f_parent_qlogis -0.9739851652 -1.371984 -0.5759863 -#> log_k1 -2.4818388836 -3.746899 -1.2167788 -#> log_k2 -3.6138616567 -5.294149 -1.9335743 -#> g_qlogis -0.0004613666 -1.063179 1.0622564 +#> est. lower upper +#> parent_0 93.7514328 91.114 96.389 +#> log_k_A1 -6.1262333 -8.432 -3.820 +#> f_parent_qlogis -0.9739852 -1.372 -0.576 +#> log_k1 -2.4818389 -3.747 -1.217 +#> log_k2 -3.6138617 -5.294 -1.934 +#> g_qlogis -0.0004614 -1.063 1.062 #> #> Correlation: #> prnt_0 lg__A1 f_prn_ log_k1 log_k2 @@ -384,26 +395,26 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> g_qlogis -0.068 -0.016 0.011 -0.181 -0.181 #> #> Random effects: -#> est. lower upper -#> SD.parent_0 2.7857084 0.7825105 4.7889063 -#> SD.log_k_A1 2.1412505 0.4425207 3.8399803 -#> SD.f_parent_qlogis 0.4463087 0.1609059 0.7317116 -#> SD.log_k1 1.4097204 0.5240566 2.2953842 -#> SD.log_k2 1.8739067 0.6979362 3.0498773 -#> SD.g_qlogis 0.4559301 -0.8149852 1.7268453 +#> est. lower upper +#> SD.parent_0 2.7857 0.7825 4.7889 +#> SD.log_k_A1 2.1413 0.4425 3.8400 +#> SD.f_parent_qlogis 0.4463 0.1609 0.7317 +#> SD.log_k1 1.4097 0.5241 2.2954 +#> SD.log_k2 1.8739 0.6979 3.0499 +#> SD.g_qlogis 0.4559 -0.8150 1.7268 #> #> Variance model: -#> est. lower upper -#> a.1 1.882757 1.665681 2.099832 +#> est. lower upper +#> a.1 1.883 1.666 2.1 #> #> Backtransformed parameters with asymmetric confidence intervals: -#> est. lower upper -#> parent_0 93.751432849 9.111365e+01 96.38921497 -#> k_A1 0.002184795 2.176784e-04 0.02192835 -#> f_parent_to_A1 0.274086887 2.022995e-01 0.35985666 -#> k1 0.083589373 2.359079e-02 0.29618269 -#> k2 0.026947583 5.020885e-03 0.14463032 -#> g 0.499884658 2.567024e-01 0.74312150 +#> est. lower upper +#> parent_0 93.751433 9.111e+01 96.38921 +#> k_A1 0.002185 2.177e-04 0.02193 +#> f_parent_to_A1 0.274087 2.023e-01 0.35986 +#> k1 0.083589 2.359e-02 0.29618 +#> k2 0.026948 5.021e-03 0.14463 +#> g 0.499885 2.567e-01 0.74312 #> #> Resulting formation fractions: #> ff |