diff options
Diffstat (limited to 'docs/dev')
40 files changed, 972 insertions, 406 deletions
diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 4e31f4b7..3980ea88 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -146,6 +146,8 @@ <a href="#mkin-0-9-50-4-unreleased" class="anchor"></a>mkin 0.9.50.4 (unreleased)<small> Unreleased </small> </h1> <ul> +<li><p>‘transform_odeparms’, ‘backtransform_odeparms’: Use logit transformation for solitary fractions like the g parameter of the DFOP model, or formation fractions for a pathway to only one target variable</p></li> +<li><p>‘update’ method for ‘mmkin’ objects</p></li> <li><p>‘plot’, ‘summary’ and ‘print’ methods for ‘nlme.mmkin’ objects</p></li> <li><p>‘saemix_model’, ‘saemix_data’: Helper functions to fit nonlinear mixed-effects models for mmkin row objects using the saemix package</p></li> </ul> diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 6d59c7cb..7b186c37 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2020-11-05T07:25Z +last_built: 2020-11-05T22:53Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex 36b20f09..17a35806 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png Binary files differindex b568eb1c..a33ecd71 100644 --- a/docs/dev/reference/Rplot002.png +++ b/docs/dev/reference/Rplot002.png diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png Binary files differindex 53415e5d..dd7e24f3 100644 --- a/docs/dev/reference/Rplot003.png +++ b/docs/dev/reference/Rplot003.png diff --git a/docs/dev/reference/Rplot004.png b/docs/dev/reference/Rplot004.png Binary files differindex ea685493..2057f883 100644 --- a/docs/dev/reference/Rplot004.png +++ b/docs/dev/reference/Rplot004.png diff --git a/docs/dev/reference/Rplot005.png b/docs/dev/reference/Rplot005.png Binary files differindex aceec1b5..b9285d56 100644 --- a/docs/dev/reference/Rplot005.png +++ b/docs/dev/reference/Rplot005.png diff --git a/docs/dev/reference/Rplot006.png b/docs/dev/reference/Rplot006.png Binary files differindex b3c9f16f..511c6b00 100644 --- a/docs/dev/reference/Rplot006.png +++ b/docs/dev/reference/Rplot006.png diff --git a/docs/dev/reference/Rplot007.png b/docs/dev/reference/Rplot007.png Binary files differindex 225931c4..a0d6336e 100644 --- a/docs/dev/reference/Rplot007.png +++ b/docs/dev/reference/Rplot007.png diff --git a/docs/dev/reference/Rplot008.png b/docs/dev/reference/Rplot008.png Binary files differnew file mode 100644 index 00000000..5d1701b8 --- /dev/null +++ b/docs/dev/reference/Rplot008.png diff --git a/docs/dev/reference/Rplot009.png b/docs/dev/reference/Rplot009.png Binary files differnew file mode 100644 index 00000000..7788b2d0 --- /dev/null +++ b/docs/dev/reference/Rplot009.png diff --git a/docs/dev/reference/Rplot010.png b/docs/dev/reference/Rplot010.png Binary files differnew file mode 100644 index 00000000..86ddd790 --- /dev/null +++ b/docs/dev/reference/Rplot010.png diff --git a/docs/dev/reference/Rplot011.png b/docs/dev/reference/Rplot011.png Binary files differnew file mode 100644 index 00000000..30861f3e --- /dev/null +++ b/docs/dev/reference/Rplot011.png diff --git a/docs/dev/reference/Rplot012.png b/docs/dev/reference/Rplot012.png Binary files differnew file mode 100644 index 00000000..4286bb2a --- /dev/null +++ b/docs/dev/reference/Rplot012.png diff --git a/docs/dev/reference/Rplot013.png b/docs/dev/reference/Rplot013.png Binary files differnew file mode 100644 index 00000000..65903441 --- /dev/null +++ b/docs/dev/reference/Rplot013.png diff --git a/docs/dev/reference/Rplot014.png b/docs/dev/reference/Rplot014.png Binary files differnew file mode 100644 index 00000000..fe2cf0d9 --- /dev/null +++ b/docs/dev/reference/Rplot014.png diff --git a/docs/dev/reference/Rplot015.png b/docs/dev/reference/Rplot015.png Binary files differnew file mode 100644 index 00000000..65903441 --- /dev/null +++ b/docs/dev/reference/Rplot015.png diff --git a/docs/dev/reference/mkinfit-1.png b/docs/dev/reference/mkinfit-1.png Binary files differnew file mode 100644 index 00000000..eed9064f --- /dev/null +++ b/docs/dev/reference/mkinfit-1.png diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html index 39bd12cb..b46c2cce 100644 --- a/docs/dev/reference/mkinfit.html +++ b/docs/dev/reference/mkinfit.html @@ -307,12 +307,11 @@ a lower bound for the rates in the optimisation.</p></td> <tr> <th>transform_fractions</th> <td><p>Boolean specifying if formation fractions -constants should be transformed in the model specification used in the -fitting for better compliance with the assumption of normal distribution -of the estimator. The default (TRUE) is to do transformations. If TRUE, -the g parameter of the DFOP and HS models are also transformed, as they -can also be seen as compositional data. The transformation used for these -transformations is the <code><a href='ilr.html'>ilr()</a></code> transformation.</p></td> +should be transformed in the model specification used in the fitting for +better compliance with the assumption of normal distribution of the +estimator. The default (TRUE) is to do transformations. If TRUE, +the g parameter of the DFOP model is also transformed. Transformations +are described in <a href='transform_odeparms.html'>transform_odeparms</a>.</p></td> </tr> <tr> <th>quiet</th> @@ -433,15 +432,15 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> </div><div class='output co'>#> mkin version used for fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Thu Nov 5 08:25:42 2020 -#> Date of summary: Thu Nov 5 08:25:42 2020 +#> Date of fit: Thu Nov 5 23:14:40 2020 +#> Date of summary: Thu Nov 5 23:14:40 2020 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.049 s +#> Fitted using 222 model solutions performed in 0.05 s #> #> Error model: Constant variance #> @@ -521,8 +520,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 </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'># Fit the model quietly to the FOCUS example dataset D using defaults</span> <span class='va'>fit</span> <span class='op'><-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='co'># Since mkin 0.9.50.3, we get a warning about non-normality of residuals,</span> -<span class='co'># so we try an alternative error model</span> +<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> +</div><div class='img'><img src='mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># As lower parent values appear to have lower variance, we try an alternative error model</span> <span class='va'>fit.tc</span> <span class='op'><-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> <span class='co'># This avoids the warning, and the likelihood ratio test confirms it is preferable</span> <span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>fit.tc</span>, <span class='va'>fit</span><span class='op'>)</span> @@ -536,8 +535,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'># We can also allow for different variances of parent and metabolite as error model</span> <span class='va'>fit.obs</span> <span class='op'><-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span> -<span class='co'># This also avoids the warning about non-normality, but the two-component error model</span> -<span class='co'># has significantly higher likelihood</span> +<span class='co'># The two-component error model has significantly higher likelihood</span> <span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>fit.obs</span>, <span class='va'>fit.tc</span><span class='op'>)</span> </div><div class='output co'>#> Likelihood ratio test #> @@ -549,9 +547,9 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span><span class='op'>(</span><span class='va'>fit.tc</span><span class='op'>)</span> </div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma_low -#> 1.007343e+02 1.005562e-01 5.166712e-03 5.083933e-01 3.049891e-03 +#> 1.007343e+02 1.005562e-01 5.166712e-03 5.083933e-01 3.049884e-03 #> rsd_high -#> 7.928117e-02 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.tc</span><span class='op'>)</span> +#> 7.928118e-02 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.tc</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> parent_m1 parent_sink #> 0.5083933 0.4916067 @@ -559,7 +557,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> $distimes #> DT50 DT90 #> parent 6.89313 22.89848 -#> m1 134.15635 445.65776 +#> m1 134.15634 445.65772 #> </div><div class='input'> <span class='co'># We can show a quick (only one replication) benchmark for this case, as we</span> <span class='co'># have several alternative solution methods for the model. We skip</span> @@ -576,9 +574,9 @@ Degradation Data. <em>Environments</em> 6(12) 124 solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>}</span> </div><div class='output co'>#> <span class='message'>Loading required package: rbenchmark</span></div><div class='output co'>#> test relative elapsed -#> 3 analytical 1.000 0.746 -#> 1 deSolve_compiled 2.288 1.707 -#> 2 eigen 2.708 2.020</div><div class='input'><span class='co'># }</span> +#> 3 analytical 1.000 0.532 +#> 1 deSolve_compiled 1.765 0.939 +#> 2 eigen 2.229 1.186</div><div class='input'><span class='co'># }</span> <span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span> <span class='co'># \dontrun{</span> @@ -588,21 +586,22 @@ Degradation Data. <em>Environments</em> 6(12) 124 </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'>fit.FOMC_SFO</span> <span class='op'><-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>FOMC_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># Again, we get a warning and try a more sophisticated error model</span> <span class='va'>fit.FOMC_SFO.tc</span> <span class='op'><-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>FOMC_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> -<span class='co'># This model has a higher likelihood, but not significantly so</span> +</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> +#> <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'><span class='co'># This model has a higher likelihood, but not significantly so</span> <span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>fit.tc</span>, <span class='va'>fit.FOMC_SFO.tc</span><span class='op'>)</span> </div><div class='output co'>#> Likelihood ratio test #> #> Model 1: FOMC_SFO with error model tc and fixed parameter(s) m1_0 #> Model 2: SFO_SFO with error model tc and fixed parameter(s) m1_0 #> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 7 -64.829 -#> 2 6 -64.983 -1 0.3075 0.5792</div><div class='input'><span class='co'># Also, the missing standard error for log_beta and the t-tests for alpha</span> +#> 1 7 -64.870 +#> 2 6 -64.983 -1 0.2259 0.6346</div><div class='input'><span class='co'># Also, the missing standard error for log_beta and the t-tests for alpha</span> <span class='co'># and beta indicate overparameterisation</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.FOMC_SFO.tc</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#> mkin version used for fitting: 0.9.50.4 +</div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#> mkin version used for fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Thu Nov 5 08:25:56 2020 -#> Date of summary: Thu Nov 5 08:25:56 2020 +#> Date of fit: Thu Nov 5 23:14:51 2020 +#> Date of summary: Thu Nov 5 23:14:51 2020 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -611,7 +610,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> #> Model predictions using solution type deSolve #> -#> Fitted using 3611 model solutions performed in 2.673 s +#> Fitted using 4273 model solutions performed in 3.081 s #> #> Error model: Two-component variance function #> @@ -629,80 +628,85 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> rsd_high 0.10 error #> #> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> parent_0 100.750000 -Inf Inf -#> log_k_m1 -2.302585 -Inf Inf -#> f_parent_ilr_1 0.000000 -Inf Inf -#> log_alpha 0.000000 -Inf Inf -#> log_beta 2.302585 -Inf Inf -#> sigma_low 0.100000 0 Inf -#> rsd_high 0.100000 0 Inf +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_m1 -2.302585 -Inf Inf +#> f_parent_qlogis 0.000000 -Inf Inf +#> log_alpha 0.000000 -Inf Inf +#> log_beta 2.302585 -Inf Inf +#> sigma_low 0.100000 0 Inf +#> rsd_high 0.100000 0 Inf #> #> Fixed parameter values: #> value type #> m1_0 0 state #> +#> +#> Warning(s): +#> Optimisation did not converge: +#> iteration limit reached without convergence (10) +#> #> Results: #> -#> AIC BIC logLik -#> 143.658 155.1211 -64.82902 +#> AIC BIC logLik +#> 143.7396 155.2027 -64.86982 #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 101.600000 2.6390000 96.240000 107.000000 -#> log_k_m1 -5.284000 0.0928900 -5.473000 -5.095000 -#> f_parent_ilr_1 0.001008 0.0541900 -0.109500 0.111500 -#> log_alpha 5.522000 0.0077300 5.506000 5.538000 -#> log_beta 7.806000 NaN NaN NaN -#> sigma_low 0.002488 0.0002431 0.001992 0.002984 -#> rsd_high 0.079210 0.0093280 0.060180 0.098230 +#> Estimate Std. Error Lower Upper +#> parent_0 1.016e+02 1.90600 97.7400 105.5000 +#> log_k_m1 -5.285e+00 0.09286 -5.4740 -5.0950 +#> f_parent_qlogis 6.482e-04 0.06164 -0.1251 0.1264 +#> log_alpha 5.467e+00 NaN NaN NaN +#> log_beta 7.750e+00 NaN NaN NaN +#> sigma_low 0.000e+00 NaN NaN NaN +#> rsd_high 7.989e-02 NaN NaN NaN #> #> Parameter correlation: -#> parent_0 log_k_m1 f_parent_ilr_1 log_alpha log_beta sigma_low -#> parent_0 1.000000 -0.094697 -0.76654 0.70525 NaN 0.016099 -#> log_k_m1 -0.094697 1.000000 0.51404 -0.14347 NaN 0.001576 -#> f_parent_ilr_1 -0.766543 0.514038 1.00000 -0.61368 NaN 0.015465 -#> log_alpha 0.705247 -0.143468 -0.61368 1.00000 NaN 5.871780 -#> log_beta NaN NaN NaN NaN 1 NaN -#> sigma_low 0.016099 0.001576 0.01546 5.87178 NaN 1.000000 -#> rsd_high 0.006566 -0.011662 -0.05353 0.04845 NaN -0.652554 -#> rsd_high -#> parent_0 0.006566 -#> log_k_m1 -0.011662 -#> f_parent_ilr_1 -0.053525 -#> log_alpha 0.048451 -#> log_beta NaN -#> sigma_low -0.652554 -#> rsd_high 1.000000 +#> parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta +#> parent_0 1.0000000 -0.0002167 -0.6060 NaN NaN +#> log_k_m1 -0.0002167 1.0000000 0.5474 NaN NaN +#> f_parent_qlogis -0.6060320 0.5474423 1.0000 NaN NaN +#> log_alpha NaN NaN NaN 1 NaN +#> log_beta NaN NaN NaN NaN 1 +#> sigma_low NaN NaN NaN NaN NaN +#> rsd_high NaN NaN NaN NaN NaN +#> sigma_low rsd_high +#> parent_0 NaN NaN +#> log_k_m1 NaN NaN +#> f_parent_qlogis NaN NaN +#> log_alpha NaN NaN +#> log_beta NaN NaN +#> sigma_low 1 NaN +#> rsd_high NaN 1 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. #> Estimate t value Pr(>t) Lower Upper -#> parent_0 1.016e+02 32.7800 6.312e-26 9.624e+01 1.070e+02 -#> k_m1 5.072e-03 10.1200 1.216e-11 4.197e-03 6.130e-03 -#> f_parent_to_m1 5.004e-01 20.8300 4.318e-20 4.614e-01 5.394e-01 -#> alpha 2.502e+02 0.5624 2.889e-01 2.463e+02 2.542e+02 -#> beta 2.455e+03 0.5549 2.915e-01 NA NA -#> sigma_low 2.488e-03 0.4843 3.158e-01 1.992e-03 2.984e-03 -#> rsd_high 7.921e-02 8.4300 8.001e-10 6.018e-02 9.823e-02 +#> parent_0 1.016e+02 32.5400 7.812e-26 97.740000 1.055e+02 +#> k_m1 5.069e-03 10.0400 1.448e-11 0.004194 6.126e-03 +#> f_parent_to_m1 5.002e-01 20.7300 5.001e-20 0.468800 5.315e-01 +#> alpha 2.367e+02 0.6205 2.697e-01 NA NA +#> beta 2.322e+03 0.6114 2.727e-01 NA NA +#> sigma_low 0.000e+00 NaN NaN NaN NaN +#> rsd_high 7.989e-02 8.6630 4.393e-10 NaN NaN #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df -#> All data 6.781 5 14 -#> parent 7.141 3 6 -#> m1 4.640 2 8 +#> All data 6.782 5 14 +#> parent 7.142 3 6 +#> m1 4.639 2 8 #> #> Resulting formation fractions: #> ff -#> parent_m1 0.5004 -#> parent_sink 0.4996 +#> parent_m1 0.5002 +#> parent_sink 0.4998 #> #> Estimated disappearance times: -#> DT50 DT90 DT50back -#> parent 6.812 22.7 6.834 -#> m1 136.661 454.0 NA</div><div class='input'> +#> DT50 DT90 DT50back +#> parent 6.81 22.7 6.833 +#> m1 136.74 454.2 NA</div><div class='input'> <span class='co'># We can easily use starting parameters from the parent only fit (only for illustration)</span> <span class='va'>fit.FOMC</span> <span class='op'>=</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> <span class='va'>fit.FOMC_SFO</span> <span class='op'><-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>FOMC_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, diff --git a/docs/dev/reference/mmkin-1.png b/docs/dev/reference/mmkin-1.png Binary files differindex 135d5446..7b7da90a 100644 --- a/docs/dev/reference/mmkin-1.png +++ b/docs/dev/reference/mmkin-1.png diff --git a/docs/dev/reference/mmkin-2.png b/docs/dev/reference/mmkin-2.png Binary files differindex 40109afc..ce2b2af4 100644 --- a/docs/dev/reference/mmkin-2.png +++ b/docs/dev/reference/mmkin-2.png diff --git a/docs/dev/reference/mmkin-3.png b/docs/dev/reference/mmkin-3.png Binary files differindex bce34531..bb96f1b2 100644 --- a/docs/dev/reference/mmkin-3.png +++ b/docs/dev/reference/mmkin-3.png diff --git a/docs/dev/reference/mmkin-4.png b/docs/dev/reference/mmkin-4.png Binary files differindex 02976ced..351b21aa 100644 --- a/docs/dev/reference/mmkin-4.png +++ b/docs/dev/reference/mmkin-4.png diff --git a/docs/dev/reference/mmkin-5.png b/docs/dev/reference/mmkin-5.png Binary files differindex 56750342..c1c05eea 100644 --- a/docs/dev/reference/mmkin-5.png +++ b/docs/dev/reference/mmkin-5.png diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html index a5d7ba42..b0ca90f0 100644 --- a/docs/dev/reference/mmkin.html +++ b/docs/dev/reference/mmkin.html @@ -75,7 +75,7 @@ datasets specified in its first two arguments." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> @@ -123,7 +123,7 @@ datasets specified in its first two arguments." /> </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="http://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/"> <span class="fab fa fab fa-github fa-lg"></span> </a> @@ -143,7 +143,7 @@ datasets specified in its first two arguments." /> <div class="page-header"> <h1>Fit one or more kinetic models with one or more state variables to one or more datasets</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mmkin.R'><code>R/mmkin.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mmkin.R'><code>R/mmkin.R</code></a></small> <div class="hidden name"><code>mmkin.Rd</code></div> </div> @@ -152,13 +152,13 @@ more datasets</h1> datasets specified in its first two arguments.</p> </div> - <pre class="usage"><span class='fu'>mmkin</span>( - <span class='kw'>models</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), - <span class='no'>datasets</span>, - <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>detectCores</span>(), - <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='no'>...</span> -)</pre> + <pre class="usage"><span class='fu'>mmkin</span><span class='op'>(</span> + models <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'>datasets</span>, + cores <span class='op'>=</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span>, + cluster <span class='op'>=</span> <span class='cn'>NULL</span>, + <span class='va'>...</span> +<span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -201,45 +201,58 @@ first index (row index) and the dataset names for the second index (column index).</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <div class='dont-index'><p><code><a href='Extract.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for + <div class='dont-index'><p><code><a href='[.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for plotting.</p></div> + <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + + <p>Johannes Ranke</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'># \dontrun{</span> -<span class='no'>m_synth_SFO_lin</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M1"</span>), - <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M2"</span>), - <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>m_synth_FOMC_lin</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"FOMC"</span>, <span class='st'>"M1"</span>), - <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M2"</span>), - <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>models</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>SFO_lin</span> <span class='kw'>=</span> <span class='no'>m_synth_SFO_lin</span>, <span class='kw'>FOMC_lin</span> <span class='kw'>=</span> <span class='no'>m_synth_FOMC_lin</span>) -<span class='no'>datasets</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>synthetic_data_for_UBA_2014</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>) -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>datasets</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>) - -<span class='no'>time_default</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.0</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) -<span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> -#> <span class='warning'>false convergence (8)</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0117</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0174</span></div><div class='input'> -<span class='no'>time_default</span></div><div class='output co'>#> user system elapsed -#> 4.500 0.399 1.311 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> user system elapsed -#> 5.154 0.008 5.165 </div><div class='input'> -<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff +<span class='va'>m_synth_SFO_lin</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'>"SFO"</span>, <span class='st'>"M1"</span><span class='op'>)</span>, + M1 <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='st'>"M2"</span><span class='op'>)</span>, + M2 <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>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</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='va'>m_synth_FOMC_lin</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'>"FOMC"</span>, <span class='st'>"M1"</span><span class='op'>)</span>, + M1 <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='st'>"M2"</span><span class='op'>)</span>, + M2 <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>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</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='va'>models</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>SFO_lin <span class='op'>=</span> <span class='va'>m_synth_SFO_lin</span>, FOMC_lin <span class='op'>=</span> <span class='va'>m_synth_FOMC_lin</span><span class='op'>)</span> +<span class='va'>datasets</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'>synthetic_data_for_UBA_2014</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</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='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/names.html'>names</a></span><span class='op'>(</span><span class='va'>datasets</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'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>)</span> + +<span class='va'>time_default</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>fits.0</span> <span class='op'><-</span> <span class='fu'>mmkin</span><span class='op'>(</span><span class='va'>models</span>, <span class='va'>datasets</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> +<span class='va'>time_1</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>fits.4</span> <span class='op'><-</span> <span class='fu'>mmkin</span><span class='op'>(</span><span class='va'>models</span>, <span class='va'>datasets</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> + +<span class='va'>time_default</span> +</div><div class='output co'>#> user system elapsed +#> 4.706 0.488 1.375 </div><div class='input'><span class='va'>time_1</span> +</div><div class='output co'>#> user system elapsed +#> 5.232 0.005 5.238 </div><div class='input'> +<span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> +</div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink -#> 0.7340478 0.2659522 0.7505691 0.2494309 +#> 0.7340478 0.2659522 0.7505687 0.2494313 #> #> $distimes -#> DT50 DT90 -#> parent 0.8777688 2.915885 -#> M1 2.3257466 7.725963 -#> M2 33.7200800 112.015681 +#> DT50 DT90 +#> parent 0.877769 2.915885 +#> M1 2.325746 7.725960 +#> M2 33.720083 112.015691 #> </div><div class='input'> <span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span> -<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><div class='img'><img src='mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><div class='img'><img src='mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span> +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='op'>]</span><span class='op'>)</span> +</div><div class='img'><img src='mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='op'>]</span>, obs_var <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'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='img'><img src='mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span>, <span class='fl'>1</span><span class='op'>]</span><span class='op'>)</span> +</div><div class='img'><img src='mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span> <span class='co'># by plot.mkinfit and can be plotted using plot_sep</span> -<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]], <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]]) +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span>, sep_obs <span class='op'>=</span> <span class='cn'>TRUE</span>, show_residuals <span class='op'>=</span> <span class='cn'>TRUE</span>, show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='img'><img src='mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span> <span class='co'># allow to plot the observed variables separately</span> -<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'># } +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='fl'>1</span><span class='op'>]</span><span class='op'>)</span> +</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> </div></pre> </div> @@ -257,7 +270,7 @@ plotting.</p></div> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> diff --git a/docs/dev/reference/saemix-1.png b/docs/dev/reference/saemix-1.png Binary files differindex 696fa7d9..e5e01249 100644 --- a/docs/dev/reference/saemix-1.png +++ b/docs/dev/reference/saemix-1.png diff --git a/docs/dev/reference/saemix-10.png b/docs/dev/reference/saemix-10.png Binary files differnew file mode 100644 index 00000000..19aa6cfb --- /dev/null +++ b/docs/dev/reference/saemix-10.png diff --git a/docs/dev/reference/saemix-11.png b/docs/dev/reference/saemix-11.png Binary files differnew file mode 100644 index 00000000..454b9be0 --- /dev/null +++ b/docs/dev/reference/saemix-11.png diff --git a/docs/dev/reference/saemix-12.png b/docs/dev/reference/saemix-12.png Binary files differnew file mode 100644 index 00000000..c8b0fd71 --- /dev/null +++ b/docs/dev/reference/saemix-12.png diff --git a/docs/dev/reference/saemix-13.png b/docs/dev/reference/saemix-13.png Binary files differnew file mode 100644 index 00000000..e3538cb6 --- /dev/null +++ b/docs/dev/reference/saemix-13.png diff --git a/docs/dev/reference/saemix-2.png b/docs/dev/reference/saemix-2.png Binary files differindex 6525a36c..4bc3d0bc 100644 --- a/docs/dev/reference/saemix-2.png +++ b/docs/dev/reference/saemix-2.png diff --git a/docs/dev/reference/saemix-3.png b/docs/dev/reference/saemix-3.png Binary files differindex 86ae1f19..be6b0acb 100644 --- a/docs/dev/reference/saemix-3.png +++ b/docs/dev/reference/saemix-3.png diff --git a/docs/dev/reference/saemix-4.png b/docs/dev/reference/saemix-4.png Binary files differindex e0c5ce4a..fa4db812 100644 --- a/docs/dev/reference/saemix-4.png +++ b/docs/dev/reference/saemix-4.png diff --git a/docs/dev/reference/saemix-5.png b/docs/dev/reference/saemix-5.png Binary files differnew file mode 100644 index 00000000..2b7b8f46 --- /dev/null +++ b/docs/dev/reference/saemix-5.png diff --git a/docs/dev/reference/saemix-6.png b/docs/dev/reference/saemix-6.png Binary files differnew file mode 100644 index 00000000..af14b43b --- /dev/null +++ b/docs/dev/reference/saemix-6.png diff --git a/docs/dev/reference/saemix-7.png b/docs/dev/reference/saemix-7.png Binary files differnew file mode 100644 index 00000000..e3538cb6 --- /dev/null +++ b/docs/dev/reference/saemix-7.png diff --git a/docs/dev/reference/saemix-8.png b/docs/dev/reference/saemix-8.png Binary files differnew file mode 100644 index 00000000..35cc6c6e --- /dev/null +++ b/docs/dev/reference/saemix-8.png diff --git a/docs/dev/reference/saemix-9.png b/docs/dev/reference/saemix-9.png Binary files differnew file mode 100644 index 00000000..e3538cb6 --- /dev/null +++ b/docs/dev/reference/saemix-9.png diff --git a/docs/dev/reference/saemix.html b/docs/dev/reference/saemix.html index c8cf9fab..5dacefc9 100644 --- a/docs/dev/reference/saemix.html +++ b/docs/dev/reference/saemix.html @@ -190,16 +190,15 @@ mmkin. Starting variances of the random effects (argument omega.init) are the variances of the deviations of the parameters from these mean values.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><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'>sfo_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'>"SFO"</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'># \dontrun{</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='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> + <pre class="examples"><div class='input'><span class='co'># \dontrun{</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> </div><div class='output co'>#> <span class='message'>Package saemix, version 3.1.9000</span> -#> <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><span class='va'>m_saemix</span> <span class='op'><-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> +#> <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><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/pkg/saemix/man/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>, + 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'>m_saemix_p0_fixed</span> <span class='op'><-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> #> #> The following SaemixModel object was successfully created: @@ -208,59 +207,236 @@ variances of the deviations of the parameters from these mean values.</p> #> Model function: Mixed model generated from mmkin object Model type: structural #> function (psi, id, xidep) #> { -#> uid <- unique(id) -#> res_list <- parallel::mclapply(uid, function(i) { -#> transparms_optim <- psi[i, ] -#> names(transparms_optim) <- names(degparms_optim) -#> odeini_optim <- transparms_optim[odeini_optim_parm_names] -#> names(odeini_optim) <- gsub("_0$", "", odeini_optim_parm_names) -#> odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)] -#> ode_transparms_optim_names <- setdiff(names(transparms_optim), -#> odeini_optim_parm_names) -#> odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], -#> mkin_model, transform_rates = object[[1]]$transform_rates, -#> transform_fractions = object[[1]]$transform_fractions) -#> odeparms <- c(odeparms_optim, odeparms_fixed) -#> xidep_i <- subset(xidep, id == i) -#> if (analytical) { -#> out_values <- mkin_model$deg_func(xidep_i, odeini, -#> odeparms) -#> } -#> else { -#> i_time <- xidep_i$time -#> i_name <- xidep_i$name -#> out_wide <- mkinpredict(mkin_model, odeparms = odeparms, -#> odeini = odeini, solution_type = object[[1]]$solution_type, -#> outtimes = sort(unique(i_time))) -#> out_index <- cbind(as.character(i_time), as.character(i_name)) -#> out_values <- out_wide[out_index] -#> } -#> return(out_values) -#> }, mc.cores = cores) -#> res <- unlist(res_list) -#> return(res) +#> odeini_fixed/(xidep[, "time"]/exp(psi[id, 2]) + 1)^exp(psi[id, +#> 1]) +#> } +#> <bytecode: 0x5555599945b8> +#> <environment: 0x555559984388> +#> Nb of parameters: 2 +#> parameter names: log_alpha log_beta +#> distribution: +#> Parameter Distribution Estimated +#> [1,] log_alpha normal Estimated +#> [2,] log_beta normal Estimated +#> Variance-covariance matrix: +#> log_alpha log_beta +#> log_alpha 1 0 +#> log_beta 0 1 +#> Error model: constant , initial values: a.1=2.95893806804889 +#> No covariate in the model. +#> Initial values +#> log_alpha log_beta +#> Pop.CondInit -0.347996 1.66788</div><div class='input'><span class='va'>d_saemix_parent</span> <span class='op'><-</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span> +</div><div class='output co'>#> +#> +#> The following SaemixData object was successfully created: +#> +#> Object of class SaemixData +#> longitudinal data for use with the SAEM algorithm +#> Dataset ds_saemix +#> Structured data: value ~ time + name | ds +#> X variable for graphs: time () </div><div class='input'><span class='va'>saemix_options</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>seed <span class='op'>=</span> <span class='fl'>123456</span>, displayProgress <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>, nbiter.saemix <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='fl'>200</span>, <span class='fl'>80</span><span class='op'>)</span><span class='op'>)</span> +<span class='va'>f_saemix_p0_fixed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_p0_fixed</span>, <span class='va'>d_saemix_parent</span>, <span class='va'>saemix_options</span><span class='op'>)</span> +</div><div class='output co'>#> Running main SAEM algorithm +#> [1] "Thu Nov 5 23:53:29 2020" +#> .. +#> Minimisation finished +#> [1] "Thu Nov 5 23:53:30 2020"</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm +#> ----------------------------------- +#> ---- Data ---- +#> ----------------------------------- +#> Object of class SaemixData +#> longitudinal data for use with the SAEM algorithm +#> Dataset ds_saemix +#> Structured data: value ~ time + name | ds +#> X variable for graphs: time () +#> Dataset characteristics: +#> number of subjects: 5 +#> number of observations: 90 +#> average/min/max nb obs: 18.00 / 16 / 20 +#> First 10 lines of data: +#> ds time name value mdv cens occ ytype +#> 1 Dataset 6 0 parent 97.2 0 0 1 1 +#> 2 Dataset 6 0 parent 96.4 0 0 1 1 +#> 3 Dataset 6 3 parent 71.1 0 0 1 1 +#> 4 Dataset 6 3 parent 69.2 0 0 1 1 +#> 5 Dataset 6 6 parent 58.1 0 0 1 1 +#> 6 Dataset 6 6 parent 56.6 0 0 1 1 +#> 7 Dataset 6 10 parent 44.4 0 0 1 1 +#> 8 Dataset 6 10 parent 43.4 0 0 1 1 +#> 9 Dataset 6 20 parent 33.3 0 0 1 1 +#> 10 Dataset 6 20 parent 29.2 0 0 1 1 +#> ----------------------------------- +#> ---- Model ---- +#> ----------------------------------- +#> Nonlinear mixed-effects model +#> Model function: Mixed model generated from mmkin object Model type: structural +#> function (psi, id, xidep) +#> { +#> odeini_fixed/(xidep[, "time"]/exp(psi[id, 2]) + 1)^exp(psi[id, +#> 1]) +#> } +#> <bytecode: 0x5555599945b8> +#> <environment: 0x555559984388> +#> Nb of parameters: 2 +#> parameter names: log_alpha log_beta +#> distribution: +#> Parameter Distribution Estimated +#> [1,] log_alpha normal Estimated +#> [2,] log_beta normal Estimated +#> Variance-covariance matrix: +#> log_alpha log_beta +#> log_alpha 1 0 +#> log_beta 0 1 +#> Error model: constant , initial values: a.1=2.95893806804889 +#> No covariate in the model. +#> Initial values +#> log_alpha log_beta +#> Pop.CondInit -0.347996 1.66788 +#> ----------------------------------- +#> ---- Key algorithm options ---- +#> ----------------------------------- +#> Estimation of individual parameters (MAP) +#> Estimation of standard errors and linearised log-likelihood +#> Estimation of log-likelihood by importance sampling +#> Number of iterations: K1=200, K2=80 +#> Number of chains: 10 +#> Seed: 123456 +#> Number of MCMC iterations for IS: 5000 +#> Simulations: +#> nb of simulated datasets used for npde: 1000 +#> nb of simulated datasets used for VPC: 100 +#> Input/output +#> save the results to a file: FALSE +#> save the graphs to files: FALSE +#> ---------------------------------------------------- +#> ---- Results ---- +#> ---------------------------------------------------- +#> ----------------- Fixed effects ------------------ +#> ---------------------------------------------------- +#> Parameter Estimate SE CV(%) +#> log_alpha -0.33 0.30 91.6 +#> log_beta 1.70 0.21 12.4 +#> a a.1 3.15 0.25 7.9 +#> ---------------------------------------------------- +#> ----------- Variance of random effects ----------- +#> ---------------------------------------------------- +#> Parameter Estimate SE CV(%) +#> log_alpha omega2.log_alpha 0.44 0.28 65 +#> log_beta omega2.log_beta 0.18 0.14 79 +#> ---------------------------------------------------- +#> ------ Correlation matrix of random effects ------ +#> ---------------------------------------------------- +#> omega2.log_alpha omega2.log_beta +#> omega2.log_alpha 1 0 +#> omega2.log_beta 0 1 +#> ---------------------------------------------------- +#> --------------- Statistical criteria ------------- +#> ---------------------------------------------------- +#> Likelihood computed by linearisation +#> -2LL= 501.6082 +#> AIC = 511.6082 +#> BIC = 509.6554 +#> +#> Likelihood computed by importance sampling +#> -2LL= 501.7 +#> AIC = 511.7 +#> BIC = 509.7472 +#> ----------------------------------------------------</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'>m_saemix_sfo</span> <span class='op'><-</span> <span class='fu'>saemix_model</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'>#> +#> +#> The following SaemixModel object was successfully created: +#> +#> Nonlinear mixed-effects model +#> Model function: Mixed model generated from mmkin object Model type: structural +#> function (psi, id, xidep) +#> { +#> psi[id, 1] * exp(-exp(psi[id, 2]) * xidep[, "time"]) #> } -#> <bytecode: 0x55555d62aeb8> -#> <environment: 0x55555e35c170> +#> <bytecode: 0x55555998d588> +#> <environment: 0x55555c0f4ae8> +#> Nb of parameters: 2 +#> parameter names: parent_0 log_k_parent +#> distribution: +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_k_parent normal Estimated +#> Variance-covariance matrix: +#> parent_0 log_k_parent +#> parent_0 1 0 +#> log_k_parent 0 1 +#> Error model: constant , initial values: a.1=5.76827561471585 +#> No covariate in the model. +#> Initial values +#> parent_0 log_k_parent +#> Pop.CondInit 86.39406 -3.215063</div><div class='input'><span class='va'>m_saemix_fomc</span> <span class='op'><-</span> <span class='fu'>saemix_model</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'>#> +#> +#> The following SaemixModel object was successfully created: +#> +#> Nonlinear mixed-effects model +#> Model function: Mixed model generated from mmkin object Model type: structural +#> function (psi, id, xidep) +#> { +#> psi[id, 1]/(xidep[, "time"]/exp(psi[id, 3]) + 1)^exp(psi[id, +#> 2]) +#> } +#> <bytecode: 0x55555998dc50> +#> <environment: 0x5555595d7668> +#> Nb of parameters: 3 +#> parameter names: parent_0 log_alpha log_beta +#> distribution: +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_alpha normal Estimated +#> [3,] log_beta normal Estimated +#> Variance-covariance matrix: +#> parent_0 log_alpha log_beta +#> parent_0 1 0 0 +#> log_alpha 0 1 0 +#> log_beta 0 0 1 +#> Error model: constant , initial values: a.1=1.91976382242696 +#> No covariate in the model. +#> Initial values +#> parent_0 log_alpha log_beta +#> Pop.CondInit 94.43884 -0.2226095 2.048192</div><div class='input'><span class='va'>m_saemix_dfop</span> <span class='op'><-</span> <span class='fu'>saemix_model</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'>#> +#> +#> The following SaemixModel object was successfully created: +#> +#> Nonlinear mixed-effects model +#> Model function: Mixed model generated from mmkin object Model type: structural +#> function (psi, id, xidep) +#> { +#> g <- plogis(psi[id, 4]) +#> t = xidep[, "time"] +#> psi[id, 1] * (g * exp(-exp(psi[id, 2]) * t) + (1 - g) * exp(-exp(psi[id, +#> 3]) * t)) +#> } +#> <bytecode: 0x55555998e548> +#> <environment: 0x555558225bf0> #> Nb of parameters: 4 -#> parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1 +#> parameter names: parent_0 log_k1 log_k2 g_qlogis #> distribution: -#> Parameter Distribution Estimated -#> [1,] parent_0 normal Estimated -#> [2,] log_k_parent normal Estimated -#> [3,] log_k_A1 normal Estimated -#> [4,] f_parent_ilr_1 normal Estimated +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_k1 normal Estimated +#> [3,] log_k2 normal Estimated +#> [4,] g_qlogis normal Estimated #> Variance-covariance matrix: -#> parent_0 log_k_parent log_k_A1 f_parent_ilr_1 -#> parent_0 1 0 0 0 -#> log_k_parent 0 1 0 0 -#> log_k_A1 0 0 1 0 -#> f_parent_ilr_1 0 0 0 1 -#> Error model: constant , initial values: a.1=4.97259024646577 +#> parent_0 log_k1 log_k2 g_qlogis +#> parent_0 1 0 0 0 +#> log_k1 0 1 0 0 +#> log_k2 0 0 1 0 +#> g_qlogis 0 0 0 1 +#> Error model: constant , initial values: a.1=1.94671278396371 #> No covariate in the model. #> Initial values -#> parent_0 log_k_parent log_k_A1 f_parent_ilr_1 -#> Pop.CondInit 86.53449 -3.207005 -3.060308 -1.920449</div><div class='input'><span class='va'>d_saemix</span> <span class='op'><-</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span> +#> parent_0 log_k1 log_k2 g_qlogis +#> Pop.CondInit 94.08322 -1.834163 -4.210797 0.11002</div><div class='input'><span class='va'>d_saemix_parent</span> <span class='op'><-</span> <span class='fu'>saemix_data</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'>#> #> #> The following SaemixData object was successfully created: @@ -269,15 +445,12 @@ variances of the deviations of the parameters from these mean values.</p> #> longitudinal data for use with the SAEM algorithm #> Dataset ds_saemix #> Structured data: value ~ time + name | ds -#> X variable for graphs: time () </div><div class='input'><span class='va'>saemix_options</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>seed <span class='op'>=</span> <span class='fl'>123456</span>, - save <span class='op'>=</span> <span class='cn'>FALSE</span>, save.graphs <span class='op'>=</span> <span class='cn'>FALSE</span>, displayProgress <span class='op'>=</span> <span class='cn'>FALSE</span>, - nbiter.saemix <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='fl'>200</span>, <span class='fl'>80</span><span class='op'>)</span><span class='op'>)</span> -<span class='va'>f_saemix</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix</span>, <span class='va'>d_saemix</span>, <span class='va'>saemix_options</span><span class='op'>)</span> +#> X variable for graphs: time () </div><div class='input'><span class='va'>f_saemix_sfo</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_sfo</span>, <span class='va'>d_saemix_parent</span>, <span class='va'>saemix_options</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Thu Nov 5 08:26:39 2020" +#> [1] "Thu Nov 5 23:53:31 2020" #> .. #> Minimisation finished -#> [1] "Thu Nov 5 08:28:33 2020"</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm +#> [1] "Thu Nov 5 23:53:32 2020"</div><div class='img'><img src='saemix-2.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm #> ----------------------------------- #> ---- Data ---- #> ----------------------------------- @@ -288,8 +461,8 @@ variances of the deviations of the parameters from these mean values.</p> #> X variable for graphs: time () #> Dataset characteristics: #> number of subjects: 5 -#> number of observations: 170 -#> average/min/max nb obs: 34.00 / 30 / 38 +#> number of observations: 90 +#> average/min/max nb obs: 18.00 / 16 / 20 #> First 10 lines of data: #> ds time name value mdv cens occ ytype #> 1 Dataset 6 0 parent 97.2 0 0 1 1 @@ -309,59 +482,248 @@ variances of the deviations of the parameters from these mean values.</p> #> Model function: Mixed model generated from mmkin object Model type: structural #> function (psi, id, xidep) #> { -#> uid <- unique(id) -#> res_list <- parallel::mclapply(uid, function(i) { -#> transparms_optim <- psi[i, ] -#> names(transparms_optim) <- names(degparms_optim) -#> odeini_optim <- transparms_optim[odeini_optim_parm_names] -#> names(odeini_optim) <- gsub("_0$", "", odeini_optim_parm_names) -#> odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)] -#> ode_transparms_optim_names <- setdiff(names(transparms_optim), -#> odeini_optim_parm_names) -#> odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], -#> mkin_model, transform_rates = object[[1]]$transform_rates, -#> transform_fractions = object[[1]]$transform_fractions) -#> odeparms <- c(odeparms_optim, odeparms_fixed) -#> xidep_i <- subset(xidep, id == i) -#> if (analytical) { -#> out_values <- mkin_model$deg_func(xidep_i, odeini, -#> odeparms) -#> } -#> else { -#> i_time <- xidep_i$time -#> i_name <- xidep_i$name -#> out_wide <- mkinpredict(mkin_model, odeparms = odeparms, -#> odeini = odeini, solution_type = object[[1]]$solution_type, -#> outtimes = sort(unique(i_time))) -#> out_index <- cbind(as.character(i_time), as.character(i_name)) -#> out_values <- out_wide[out_index] -#> } -#> return(out_values) -#> }, mc.cores = cores) -#> res <- unlist(res_list) -#> return(res) +#> psi[id, 1] * exp(-exp(psi[id, 2]) * xidep[, "time"]) #> } -#> <bytecode: 0x55555d62aeb8> -#> <environment: 0x55555e35c170> +#> <bytecode: 0x55555998d588> +#> <environment: 0x55555c0f4ae8> +#> Nb of parameters: 2 +#> parameter names: parent_0 log_k_parent +#> distribution: +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_k_parent normal Estimated +#> Variance-covariance matrix: +#> parent_0 log_k_parent +#> parent_0 1 0 +#> log_k_parent 0 1 +#> Error model: constant , initial values: a.1=5.76827561471585 +#> No covariate in the model. +#> Initial values +#> parent_0 log_k_parent +#> Pop.CondInit 86.39406 -3.215063 +#> ----------------------------------- +#> ---- Key algorithm options ---- +#> ----------------------------------- +#> Estimation of individual parameters (MAP) +#> Estimation of standard errors and linearised log-likelihood +#> Estimation of log-likelihood by importance sampling +#> Number of iterations: K1=200, K2=80 +#> Number of chains: 10 +#> Seed: 123456 +#> Number of MCMC iterations for IS: 5000 +#> Simulations: +#> nb of simulated datasets used for npde: 1000 +#> nb of simulated datasets used for VPC: 100 +#> Input/output +#> save the results to a file: FALSE +#> save the graphs to files: FALSE +#> ---------------------------------------------------- +#> ---- Results ---- +#> ---------------------------------------------------- +#> ----------------- Fixed effects ------------------ +#> ---------------------------------------------------- +#> Parameter Estimate SE CV(%) +#> parent_0 85.8 1.85 2.2 +#> log_k_parent -3.2 0.59 18.3 +#> a a.1 6.2 0.49 7.9 +#> ---------------------------------------------------- +#> ----------- Variance of random effects ----------- +#> ---------------------------------------------------- +#> Parameter Estimate SE CV(%) +#> parent_0 omega2.parent_0 7.8 10.7 138 +#> log_k_parent omega2.log_k_parent 1.7 1.1 64 +#> ---------------------------------------------------- +#> ------ Correlation matrix of random effects ------ +#> ---------------------------------------------------- +#> omega2.parent_0 omega2.log_k_parent +#> omega2.parent_0 1 0 +#> omega2.log_k_parent 0 1 +#> ---------------------------------------------------- +#> --------------- Statistical criteria ------------- +#> ---------------------------------------------------- +#> Likelihood computed by linearisation +#> -2LL= 615.4074 +#> AIC = 625.4074 +#> BIC = 623.4546 +#> +#> Likelihood computed by importance sampling +#> -2LL= 614.4911 +#> AIC = 624.4911 +#> BIC = 622.5382 +#> ----------------------------------------------------</div><div class='input'><span class='va'>f_saemix_fomc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_fomc</span>, <span class='va'>d_saemix_parent</span>, <span class='va'>saemix_options</span><span class='op'>)</span> +</div><div class='output co'>#> Running main SAEM algorithm +#> [1] "Thu Nov 5 23:53:33 2020" +#> .. +#> Minimisation finished +#> [1] "Thu Nov 5 23:53:34 2020"</div><div class='img'><img src='saemix-3.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm +#> ----------------------------------- +#> ---- Data ---- +#> ----------------------------------- +#> Object of class SaemixData +#> longitudinal data for use with the SAEM algorithm +#> Dataset ds_saemix +#> Structured data: value ~ time + name | ds +#> X variable for graphs: time () +#> Dataset characteristics: +#> number of subjects: 5 +#> number of observations: 90 +#> average/min/max nb obs: 18.00 / 16 / 20 +#> First 10 lines of data: +#> ds time name value mdv cens occ ytype +#> 1 Dataset 6 0 parent 97.2 0 0 1 1 +#> 2 Dataset 6 0 parent 96.4 0 0 1 1 +#> 3 Dataset 6 3 parent 71.1 0 0 1 1 +#> 4 Dataset 6 3 parent 69.2 0 0 1 1 +#> 5 Dataset 6 6 parent 58.1 0 0 1 1 +#> 6 Dataset 6 6 parent 56.6 0 0 1 1 +#> 7 Dataset 6 10 parent 44.4 0 0 1 1 +#> 8 Dataset 6 10 parent 43.4 0 0 1 1 +#> 9 Dataset 6 20 parent 33.3 0 0 1 1 +#> 10 Dataset 6 20 parent 29.2 0 0 1 1 +#> ----------------------------------- +#> ---- Model ---- +#> ----------------------------------- +#> Nonlinear mixed-effects model +#> Model function: Mixed model generated from mmkin object Model type: structural +#> function (psi, id, xidep) +#> { +#> psi[id, 1]/(xidep[, "time"]/exp(psi[id, 3]) + 1)^exp(psi[id, +#> 2]) +#> } +#> <bytecode: 0x55555998dc50> +#> <environment: 0x5555595d7668> +#> Nb of parameters: 3 +#> parameter names: parent_0 log_alpha log_beta +#> distribution: +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_alpha normal Estimated +#> [3,] log_beta normal Estimated +#> Variance-covariance matrix: +#> parent_0 log_alpha log_beta +#> parent_0 1 0 0 +#> log_alpha 0 1 0 +#> log_beta 0 0 1 +#> Error model: constant , initial values: a.1=1.91976382242696 +#> No covariate in the model. +#> Initial values +#> parent_0 log_alpha log_beta +#> Pop.CondInit 94.43884 -0.2226095 2.048192 +#> ----------------------------------- +#> ---- Key algorithm options ---- +#> ----------------------------------- +#> Estimation of individual parameters (MAP) +#> Estimation of standard errors and linearised log-likelihood +#> Estimation of log-likelihood by importance sampling +#> Number of iterations: K1=200, K2=80 +#> Number of chains: 10 +#> Seed: 123456 +#> Number of MCMC iterations for IS: 5000 +#> Simulations: +#> nb of simulated datasets used for npde: 1000 +#> nb of simulated datasets used for VPC: 100 +#> Input/output +#> save the results to a file: FALSE +#> save the graphs to files: FALSE +#> ---------------------------------------------------- +#> ---- Results ---- +#> ---------------------------------------------------- +#> ----------------- Fixed effects ------------------ +#> ---------------------------------------------------- +#> Parameter Estimate SE CV(%) +#> parent_0 94.49 1.18 1.2 +#> log_alpha -0.21 0.30 142.0 +#> log_beta 2.06 0.21 10.4 +#> a a.1 2.28 0.19 8.2 +#> ---------------------------------------------------- +#> ----------- Variance of random effects ----------- +#> ---------------------------------------------------- +#> Parameter Estimate SE CV(%) +#> parent_0 omega2.parent_0 4.66 4.34 93 +#> log_alpha omega2.log_alpha 0.45 0.29 65 +#> log_beta omega2.log_beta 0.19 0.14 75 +#> ---------------------------------------------------- +#> ------ Correlation matrix of random effects ------ +#> ---------------------------------------------------- +#> omega2.parent_0 omega2.log_alpha omega2.log_beta +#> omega2.parent_0 1 0 0 +#> omega2.log_alpha 0 1 0 +#> omega2.log_beta 0 0 1 +#> ---------------------------------------------------- +#> --------------- Statistical criteria ------------- +#> ---------------------------------------------------- +#> Likelihood computed by linearisation +#> -2LL= 454.0598 +#> AIC = 468.0598 +#> BIC = 465.3259 +#> +#> Likelihood computed by importance sampling +#> -2LL= 453.7499 +#> AIC = 467.7499 +#> BIC = 465.016 +#> ----------------------------------------------------</div><div class='input'><span class='va'>f_saemix_dfop</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_dfop</span>, <span class='va'>d_saemix_parent</span>, <span class='va'>saemix_options</span><span class='op'>)</span> +</div><div class='output co'>#> Running main SAEM algorithm +#> [1] "Thu Nov 5 23:53:35 2020" +#> .. +#> Minimisation finished +#> [1] "Thu Nov 5 23:53:37 2020"</div><div class='img'><img src='saemix-4.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm +#> ----------------------------------- +#> ---- Data ---- +#> ----------------------------------- +#> Object of class SaemixData +#> longitudinal data for use with the SAEM algorithm +#> Dataset ds_saemix +#> Structured data: value ~ time + name | ds +#> X variable for graphs: time () +#> Dataset characteristics: +#> number of subjects: 5 +#> number of observations: 90 +#> average/min/max nb obs: 18.00 / 16 / 20 +#> First 10 lines of data: +#> ds time name value mdv cens occ ytype +#> 1 Dataset 6 0 parent 97.2 0 0 1 1 +#> 2 Dataset 6 0 parent 96.4 0 0 1 1 +#> 3 Dataset 6 3 parent 71.1 0 0 1 1 +#> 4 Dataset 6 3 parent 69.2 0 0 1 1 +#> 5 Dataset 6 6 parent 58.1 0 0 1 1 +#> 6 Dataset 6 6 parent 56.6 0 0 1 1 +#> 7 Dataset 6 10 parent 44.4 0 0 1 1 +#> 8 Dataset 6 10 parent 43.4 0 0 1 1 +#> 9 Dataset 6 20 parent 33.3 0 0 1 1 +#> 10 Dataset 6 20 parent 29.2 0 0 1 1 +#> ----------------------------------- +#> ---- Model ---- +#> ----------------------------------- +#> Nonlinear mixed-effects model +#> Model function: Mixed model generated from mmkin object Model type: structural +#> function (psi, id, xidep) +#> { +#> g <- plogis(psi[id, 4]) +#> t = xidep[, "time"] +#> psi[id, 1] * (g * exp(-exp(psi[id, 2]) * t) + (1 - g) * exp(-exp(psi[id, +#> 3]) * t)) +#> } +#> <bytecode: 0x55555998e548> +#> <environment: 0x555558225bf0> #> Nb of parameters: 4 -#> parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1 +#> parameter names: parent_0 log_k1 log_k2 g_qlogis #> distribution: -#> Parameter Distribution Estimated -#> [1,] parent_0 normal Estimated -#> [2,] log_k_parent normal Estimated -#> [3,] log_k_A1 normal Estimated -#> [4,] f_parent_ilr_1 normal Estimated +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_k1 normal Estimated +#> [3,] log_k2 normal Estimated +#> [4,] g_qlogis normal Estimated #> Variance-covariance matrix: -#> parent_0 log_k_parent log_k_A1 f_parent_ilr_1 -#> parent_0 1 0 0 0 -#> log_k_parent 0 1 0 0 -#> log_k_A1 0 0 1 0 -#> f_parent_ilr_1 0 0 0 1 -#> Error model: constant , initial values: a.1=4.97259024646577 +#> parent_0 log_k1 log_k2 g_qlogis +#> parent_0 1 0 0 0 +#> log_k1 0 1 0 0 +#> log_k2 0 0 1 0 +#> g_qlogis 0 0 0 1 +#> Error model: constant , initial values: a.1=1.94671278396371 #> No covariate in the model. #> Initial values -#> parent_0 log_k_parent log_k_A1 f_parent_ilr_1 -#> Pop.CondInit 86.53449 -3.207005 -3.060308 -1.920449 +#> parent_0 log_k1 log_k2 g_qlogis +#> Pop.CondInit 94.08322 -1.834163 -4.210797 0.11002 #> ----------------------------------- #> ---- Key algorithm options ---- #> ----------------------------------- @@ -383,69 +745,195 @@ variances of the deviations of the parameters from these mean values.</p> #> ---------------------------------------------------- #> ----------------- Fixed effects ------------------ #> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> parent_0 86.09 1.57 1.8 -#> log_k_parent -3.21 0.59 18.5 -#> log_k_A1 -4.69 0.31 6.6 -#> f_parent_ilr_1 -0.34 0.30 89.2 -#> a a.1 4.69 0.27 5.8 +#> Parameter Estimate SE CV(%) +#> parent_0 93.97 1.35 1.4 +#> log_k1 -2.37 0.58 24.5 +#> log_k2 -3.63 0.87 24.0 +#> g_qlogis -0.14 0.34 246.1 +#> a a.1 2.32 0.19 8.3 #> ---------------------------------------------------- #> ----------- Variance of random effects ----------- #> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> parent_0 omega2.parent_0 7.07 7.72 109 -#> log_k_parent omega2.log_k_parent 1.75 1.11 63 -#> log_k_A1 omega2.log_k_A1 0.28 0.28 99 -#> f_parent_ilr_1 omega2.f_parent_ilr_1 0.39 0.27 71 +#> Parameter Estimate SE CV(%) +#> parent_0 omega2.parent_0 6.97 5.72 82 +#> log_k1 omega2.log_k1 1.63 1.06 65 +#> log_k2 omega2.log_k2 3.73 2.39 64 +#> g_qlogis omega2.g_qlogis 0.16 0.27 173 #> ---------------------------------------------------- #> ------ Correlation matrix of random effects ------ #> ---------------------------------------------------- -#> omega2.parent_0 omega2.log_k_parent omega2.log_k_A1 -#> omega2.parent_0 1 0 0 -#> omega2.log_k_parent 0 1 0 -#> omega2.log_k_A1 0 0 1 -#> omega2.f_parent_ilr_1 0 0 0 -#> omega2.f_parent_ilr_1 -#> omega2.parent_0 0 -#> omega2.log_k_parent 0 -#> omega2.log_k_A1 0 -#> omega2.f_parent_ilr_1 1 +#> omega2.parent_0 omega2.log_k1 omega2.log_k2 omega2.g_qlogis +#> omega2.parent_0 1 0 0 0 +#> omega2.log_k1 0 1 0 0 +#> omega2.log_k2 0 0 1 0 +#> omega2.g_qlogis 0 0 0 1 #> ---------------------------------------------------- #> --------------- Statistical criteria ------------- #> ---------------------------------------------------- #> Likelihood computed by linearisation -#> -2LL= 1064.35 -#> AIC = 1082.35 -#> BIC = 1078.835 +#> -2LL= 485.4627 +#> AIC = 503.4627 +#> BIC = 499.9477 #> #> Likelihood computed by importance sampling -#> -2LL= 1063.475 -#> AIC = 1081.475 -#> BIC = 1077.96 -#> ----------------------------------------------------</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_saemix</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span> -</div><div class='output co'>#> Plotting convergence plots</div><div class='img'><img src='saemix-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> -<span class='co'># Synthetic data with two-component error</span> -<span class='va'>sampling_times</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='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> -<span class='va'>dt50_sfo_in</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='fl'>80</span>, <span class='fl'>90</span>, <span class='fl'>100</span>, <span class='fl'>111.111</span>, <span class='fl'>125</span><span class='op'>)</span> -<span class='va'>k_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span> <span class='op'>/</span> <span class='va'>dt50_sfo_in</span> - -<span class='va'>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'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> - -<span class='va'>pred_sfo</span> <span class='op'><-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>k</span><span class='op'>)</span> <span class='op'>{</span> - <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='va'>k</span><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>, <span class='va'>sampling_times</span><span class='op'>)</span> -<span class='op'>}</span> - -<span class='va'>ds_sfo_mean</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'>k_in</span>, <span class='va'>pred_sfo</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>123456L</span><span class='op'>)</span> -<span class='va'>ds_sfo_syn</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'>ds_sfo_mean</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>{</span> - <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>ds</span>, sdfunc <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='fl'>0.07</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span>, - n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span> - <span class='op'>}</span><span class='op'>)</span> -<span class='co'># \dontrun{</span> -<span class='va'>f_mmkin_syn</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>ds_sfo_syn</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='co'># plot(f_mmkin_syn)</span> -<span class='va'>m_saemix_tc</span> <span class='op'><-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin_syn</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> +#> -2LL= 473.563 +#> AIC = 491.563 +#> BIC = 488.048 +#> ----------------------------------------------------</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_saemix_sfo</span>, <span class='va'>f_saemix_fomc</span>, <span class='va'>f_saemix_dfop</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 +#> 1 624.4911 622.5382 +#> 2 467.7499 465.0160 +#> 3 491.5630 488.0480</div><div class='input'><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'>m_saemix_fomc_tc</span> <span class='op'><-</span> <span class='fu'>saemix_model</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'>#> +#> +#> The following SaemixModel object was successfully created: +#> +#> Nonlinear mixed-effects model +#> Model function: Mixed model generated from mmkin object Model type: structural +#> function (psi, id, xidep) +#> { +#> psi[id, 1]/(xidep[, "time"]/exp(psi[id, 3]) + 1)^exp(psi[id, +#> 2]) +#> } +#> <bytecode: 0x55555998dc50> +#> <environment: 0x555559a957f8> +#> Nb of parameters: 3 +#> parameter names: parent_0 log_alpha log_beta +#> distribution: +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_alpha normal Estimated +#> [3,] log_beta normal Estimated +#> Variance-covariance matrix: +#> parent_0 log_alpha log_beta +#> parent_0 1 0 0 +#> log_alpha 0 1 0 +#> log_beta 0 0 1 +#> Error model: combined , initial values: a.1=1.10728182011691 b.1=0.024889924291374 +#> No covariate in the model. +#> Initial values +#> parent_0 log_alpha log_beta +#> Pop.CondInit 93.13042 -0.1215336 2.230815</div><div class='input'><span class='va'>f_saemix_fomc_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_fomc_tc</span>, <span class='va'>d_saemix_parent</span>, <span class='va'>saemix_options</span><span class='op'>)</span> +</div><div class='output co'>#> Running main SAEM algorithm +#> [1] "Thu Nov 5 23:53:38 2020" +#> .. +#> Minimisation finished +#> [1] "Thu Nov 5 23:53:42 2020"</div><div class='img'><img src='saemix-5.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm +#> ----------------------------------- +#> ---- Data ---- +#> ----------------------------------- +#> Object of class SaemixData +#> longitudinal data for use with the SAEM algorithm +#> Dataset ds_saemix +#> Structured data: value ~ time + name | ds +#> X variable for graphs: time () +#> Dataset characteristics: +#> number of subjects: 5 +#> number of observations: 90 +#> average/min/max nb obs: 18.00 / 16 / 20 +#> First 10 lines of data: +#> ds time name value mdv cens occ ytype +#> 1 Dataset 6 0 parent 97.2 0 0 1 1 +#> 2 Dataset 6 0 parent 96.4 0 0 1 1 +#> 3 Dataset 6 3 parent 71.1 0 0 1 1 +#> 4 Dataset 6 3 parent 69.2 0 0 1 1 +#> 5 Dataset 6 6 parent 58.1 0 0 1 1 +#> 6 Dataset 6 6 parent 56.6 0 0 1 1 +#> 7 Dataset 6 10 parent 44.4 0 0 1 1 +#> 8 Dataset 6 10 parent 43.4 0 0 1 1 +#> 9 Dataset 6 20 parent 33.3 0 0 1 1 +#> 10 Dataset 6 20 parent 29.2 0 0 1 1 +#> ----------------------------------- +#> ---- Model ---- +#> ----------------------------------- +#> Nonlinear mixed-effects model +#> Model function: Mixed model generated from mmkin object Model type: structural +#> function (psi, id, xidep) +#> { +#> psi[id, 1]/(xidep[, "time"]/exp(psi[id, 3]) + 1)^exp(psi[id, +#> 2]) +#> } +#> <bytecode: 0x55555998dc50> +#> <environment: 0x555559a957f8> +#> Nb of parameters: 3 +#> parameter names: parent_0 log_alpha log_beta +#> distribution: +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_alpha normal Estimated +#> [3,] log_beta normal Estimated +#> Variance-covariance matrix: +#> parent_0 log_alpha log_beta +#> parent_0 1 0 0 +#> log_alpha 0 1 0 +#> log_beta 0 0 1 +#> Error model: combined , initial values: a.1=1.10728182011691 b.1=0.024889924291374 +#> No covariate in the model. +#> Initial values +#> parent_0 log_alpha log_beta +#> Pop.CondInit 93.13042 -0.1215336 2.230815 +#> ----------------------------------- +#> ---- Key algorithm options ---- +#> ----------------------------------- +#> Estimation of individual parameters (MAP) +#> Estimation of standard errors and linearised log-likelihood +#> Estimation of log-likelihood by importance sampling +#> Number of iterations: K1=200, K2=80 +#> Number of chains: 10 +#> Seed: 123456 +#> Number of MCMC iterations for IS: 5000 +#> Simulations: +#> nb of simulated datasets used for npde: 1000 +#> nb of simulated datasets used for VPC: 100 +#> Input/output +#> save the results to a file: FALSE +#> save the graphs to files: FALSE +#> ---------------------------------------------------- +#> ---- Results ---- +#> ---------------------------------------------------- +#> ----------------- Fixed effects ------------------ +#> ---------------------------------------------------- +#> Parameter Estimate SE CV(%) +#> parent_0 94.4481 1.2052 1.3 +#> log_alpha -0.2088 0.3059 146.5 +#> log_beta 2.0668 0.2182 10.6 +#> a a.1 2.4273 0.3178 13.1 +#> b b.1 -0.0037 0.0062 168.3 +#> ---------------------------------------------------- +#> ----------- Variance of random effects ----------- +#> ---------------------------------------------------- +#> Parameter Estimate SE CV(%) +#> parent_0 omega2.parent_0 5.34 4.58 86 +#> log_alpha omega2.log_alpha 0.46 0.29 65 +#> log_beta omega2.log_beta 0.20 0.15 74 +#> ---------------------------------------------------- +#> ------ Correlation matrix of random effects ------ +#> ---------------------------------------------------- +#> omega2.parent_0 omega2.log_alpha omega2.log_beta +#> omega2.parent_0 1 0 0 +#> omega2.log_alpha 0 1 0 +#> omega2.log_beta 0 0 1 +#> ---------------------------------------------------- +#> --------------- Statistical criteria ------------- +#> ---------------------------------------------------- +#> Likelihood computed by linearisation +#> -2LL= 453.7703 +#> AIC = 469.7703 +#> BIC = 466.6458 +#> +#> Likelihood computed by importance sampling +#> -2LL= 453.6186 +#> AIC = 469.6186 +#> BIC = 466.4942 +#> ----------------------------------------------------</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_saemix_fomc</span>, <span class='va'>f_saemix_fomc_tc</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 +#> 1 467.7499 465.0160 +#> 2 469.6186 466.4942</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='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'>"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='va'>m_saemix</span> <span class='op'><-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span> </div><div class='output co'>#> #> #> The following SaemixModel object was successfully created: @@ -468,7 +956,7 @@ variances of the deviations of the parameters from these mean values.</p> #> transform_fractions = object[[1]]$transform_fractions) #> odeparms <- c(odeparms_optim, odeparms_fixed) #> xidep_i <- subset(xidep, id == i) -#> if (analytical) { +#> if (solution_type == "analytical") { #> out_values <- mkin_model$deg_func(xidep_i, odeini, #> odeparms) #> } @@ -476,7 +964,7 @@ variances of the deviations of the parameters from these mean values.</p> #> i_time <- xidep_i$time #> i_name <- xidep_i$name #> out_wide <- mkinpredict(mkin_model, odeparms = odeparms, -#> odeini = odeini, solution_type = object[[1]]$solution_type, +#> odeini = odeini, solution_type = solution_type, #> outtimes = sort(unique(i_time))) #> out_index <- cbind(as.character(i_time), as.character(i_name)) #> out_values <- out_wide[out_index] @@ -486,23 +974,31 @@ variances of the deviations of the parameters from these mean values.</p> #> res <- unlist(res_list) #> return(res) #> } -#> <bytecode: 0x55555d62aeb8> -#> <environment: 0x55555cd8e028> -#> Nb of parameters: 2 -#> parameter names: parent_0 log_k_parent +#> <bytecode: 0x55555998cba0> +#> <environment: 0x55555bd1fee8> +#> Nb of parameters: 6 +#> parameter names: parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis #> distribution: -#> Parameter Distribution Estimated -#> [1,] parent_0 normal Estimated -#> [2,] log_k_parent normal Estimated +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_k_A1 normal Estimated +#> [3,] f_parent_qlogis normal Estimated +#> [4,] log_k1 normal Estimated +#> [5,] log_k2 normal Estimated +#> [6,] g_qlogis normal Estimated #> Variance-covariance matrix: -#> parent_0 log_k_parent -#> parent_0 1 0 -#> log_k_parent 0 1 -#> Error model: combined , initial values: a.1=1.05209877924905 b.1=0.0586479225303944 +#> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis +#> parent_0 1 0 0 0 0 0 +#> log_k_A1 0 1 0 0 0 0 +#> f_parent_qlogis 0 0 1 0 0 0 +#> log_k1 0 0 0 1 0 0 +#> log_k2 0 0 0 0 1 0 +#> g_qlogis 0 0 0 0 0 1 +#> Error model: constant , initial values: a.1=1.64723790168612 #> No covariate in the model. #> Initial values -#> parent_0 log_k_parent -#> Pop.CondInit 100.315 -4.962075</div><div class='input'><span class='va'>d_saemix_tc</span> <span class='op'><-</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>f_mmkin_syn</span><span class='op'>)</span> +#> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis +#> Pop.CondInit 93.81015 -9.764746 -0.9711148 -1.879937 -4.270814 0.1356441</div><div class='input'><span class='va'>d_saemix</span> <span class='op'><-</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span> </div><div class='output co'>#> #> #> The following SaemixData object was successfully created: @@ -511,12 +1007,12 @@ variances of the deviations of the parameters from these mean values.</p> #> longitudinal data for use with the SAEM algorithm #> Dataset ds_saemix #> Structured data: value ~ time + name | ds -#> X variable for graphs: time () </div><div class='input'><span class='va'>f_saemix_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_tc</span>, <span class='va'>d_saemix_tc</span>, <span class='va'>saemix_options</span><span class='op'>)</span> +#> X variable for graphs: time () </div><div class='input'><span class='va'>f_saemix</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix</span>, <span class='va'>d_saemix</span>, <span class='va'>saemix_options</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Thu Nov 5 08:28:50 2020" +#> [1] "Thu Nov 5 23:53:43 2020" #> .. #> Minimisation finished -#> [1] "Thu Nov 5 08:29:41 2020"</div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm +#> [1] "Thu Nov 5 23:56:33 2020"</div><div class='img'><img src='saemix-6.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm #> ----------------------------------- #> ---- Data ---- #> ----------------------------------- @@ -527,20 +1023,20 @@ variances of the deviations of the parameters from these mean values.</p> #> X variable for graphs: time () #> Dataset characteristics: #> number of subjects: 5 -#> number of observations: 90 -#> average/min/max nb obs: 18.00 / 18 / 18 +#> number of observations: 170 +#> average/min/max nb obs: 34.00 / 30 / 38 #> First 10 lines of data: -#> ds time name value mdv cens occ ytype -#> 1 1 0 parent 105.9 0 0 1 1 -#> 2 1 0 parent 98.0 0 0 1 1 -#> 3 1 1 parent 96.6 0 0 1 1 -#> 4 1 1 parent 99.8 0 0 1 1 -#> 5 1 3 parent 113.0 0 0 1 1 -#> 6 1 3 parent 103.2 0 0 1 1 -#> 7 1 7 parent 102.9 0 0 1 1 -#> 8 1 7 parent 110.8 0 0 1 1 -#> 9 1 14 parent 95.9 0 0 1 1 -#> 10 1 14 parent 85.9 0 0 1 1 +#> ds time name value mdv cens occ ytype +#> 1 Dataset 6 0 parent 97.2 0 0 1 1 +#> 2 Dataset 6 0 parent 96.4 0 0 1 1 +#> 3 Dataset 6 3 parent 71.1 0 0 1 1 +#> 4 Dataset 6 3 parent 69.2 0 0 1 1 +#> 5 Dataset 6 6 parent 58.1 0 0 1 1 +#> 6 Dataset 6 6 parent 56.6 0 0 1 1 +#> 7 Dataset 6 10 parent 44.4 0 0 1 1 +#> 8 Dataset 6 10 parent 43.4 0 0 1 1 +#> 9 Dataset 6 20 parent 33.3 0 0 1 1 +#> 10 Dataset 6 20 parent 29.2 0 0 1 1 #> ----------------------------------- #> ---- Model ---- #> ----------------------------------- @@ -562,7 +1058,7 @@ variances of the deviations of the parameters from these mean values.</p> #> transform_fractions = object[[1]]$transform_fractions) #> odeparms <- c(odeparms_optim, odeparms_fixed) #> xidep_i <- subset(xidep, id == i) -#> if (analytical) { +#> if (solution_type == "analytical") { #> out_values <- mkin_model$deg_func(xidep_i, odeini, #> odeparms) #> } @@ -570,7 +1066,7 @@ variances of the deviations of the parameters from these mean values.</p> #> i_time <- xidep_i$time #> i_name <- xidep_i$name #> out_wide <- mkinpredict(mkin_model, odeparms = odeparms, -#> odeini = odeini, solution_type = object[[1]]$solution_type, +#> odeini = odeini, solution_type = solution_type, #> outtimes = sort(unique(i_time))) #> out_index <- cbind(as.character(i_time), as.character(i_name)) #> out_values <- out_wide[out_index] @@ -580,23 +1076,31 @@ variances of the deviations of the parameters from these mean values.</p> #> res <- unlist(res_list) #> return(res) #> } -#> <bytecode: 0x55555d62aeb8> -#> <environment: 0x55555cd8e028> -#> Nb of parameters: 2 -#> parameter names: parent_0 log_k_parent +#> <bytecode: 0x55555998cba0> +#> <environment: 0x55555bd1fee8> +#> Nb of parameters: 6 +#> parameter names: parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis #> distribution: -#> Parameter Distribution Estimated -#> [1,] parent_0 normal Estimated -#> [2,] log_k_parent normal Estimated +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_k_A1 normal Estimated +#> [3,] f_parent_qlogis normal Estimated +#> [4,] log_k1 normal Estimated +#> [5,] log_k2 normal Estimated +#> [6,] g_qlogis normal Estimated #> Variance-covariance matrix: -#> parent_0 log_k_parent -#> parent_0 1 0 -#> log_k_parent 0 1 -#> Error model: combined , initial values: a.1=1.05209877924905 b.1=0.0586479225303944 +#> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis +#> parent_0 1 0 0 0 0 0 +#> log_k_A1 0 1 0 0 0 0 +#> f_parent_qlogis 0 0 1 0 0 0 +#> log_k1 0 0 0 1 0 0 +#> log_k2 0 0 0 0 1 0 +#> g_qlogis 0 0 0 0 0 1 +#> Error model: constant , initial values: a.1=1.64723790168612 #> No covariate in the model. #> Initial values -#> parent_0 log_k_parent -#> Pop.CondInit 100.315 -4.962075 +#> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis +#> Pop.CondInit 93.81015 -9.764746 -0.9711148 -1.879937 -4.270814 0.1356441 #> ----------------------------------- #> ---- Key algorithm options ---- #> ----------------------------------- @@ -618,37 +1122,55 @@ variances of the deviations of the parameters from these mean values.</p> #> ---------------------------------------------------- #> ----------------- Fixed effects ------------------ #> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> parent_0 100.232 1.266 1.3 -#> log_k_parent -4.961 0.089 1.8 -#> a a.1 -0.106 1.211 1142.0 -#> b b.1 0.071 0.017 24.2 +#> Parameter Estimate SE CV(%) +#> parent_0 93.78 1.35 1.4 +#> log_k_A1 -6.05 1.12 18.5 +#> f_parent_qlogis -0.97 0.20 21.1 +#> log_k1 -2.46 0.51 20.7 +#> log_k2 -3.63 0.95 26.3 +#> g_qlogis -0.08 0.36 447.7 +#> a a.1 1.88 0.11 5.9 #> ---------------------------------------------------- #> ----------- Variance of random effects ----------- #> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> parent_0 omega2.parent_0 3.334 5.024 151 -#> log_k_parent omega2.log_k_parent 0.036 0.024 68 +#> Parameter Estimate SE CV(%) +#> parent_0 omega2.parent_0 7.85 5.76 73 +#> log_k_A1 omega2.log_k_A1 4.27 3.44 80 +#> f_parent_qlogis omega2.f_parent_qlogis 0.20 0.13 65 +#> log_k1 omega2.log_k1 1.08 0.77 72 +#> log_k2 omega2.log_k2 4.24 2.83 67 +#> g_qlogis omega2.g_qlogis 0.21 0.26 123 #> ---------------------------------------------------- #> ------ Correlation matrix of random effects ------ #> ---------------------------------------------------- -#> omega2.parent_0 omega2.log_k_parent -#> omega2.parent_0 1 0 -#> omega2.log_k_parent 0 1 +#> omega2.parent_0 omega2.log_k_A1 omega2.f_parent_qlogis +#> omega2.parent_0 1 0 0 +#> omega2.log_k_A1 0 1 0 +#> omega2.f_parent_qlogis 0 0 1 +#> omega2.log_k1 0 0 0 +#> omega2.log_k2 0 0 0 +#> omega2.g_qlogis 0 0 0 +#> omega2.log_k1 omega2.log_k2 omega2.g_qlogis +#> omega2.parent_0 0 0 0 +#> omega2.log_k_A1 0 0 0 +#> omega2.f_parent_qlogis 0 0 0 +#> omega2.log_k1 1 0 0 +#> omega2.log_k2 0 1 0 +#> omega2.g_qlogis 0 0 1 #> ---------------------------------------------------- #> --------------- Statistical criteria ------------- #> ---------------------------------------------------- #> Likelihood computed by linearisation -#> -2LL= 575.5586 -#> AIC = 587.5586 -#> BIC = 585.2153 +#> -2LL= 879.7721 +#> AIC = 905.7721 +#> BIC = 900.6948 #> #> Likelihood computed by importance sampling -#> -2LL= 575.7797 -#> AIC = 587.7797 -#> BIC = 585.4364 -#> ----------------------------------------------------</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_saemix_tc</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span> -</div><div class='img'><img src='saemix-3.png' alt='' width='700' height='433' /></div><div class='output co'>#> Plotting convergence plots</div><div class='img'><img src='saemix-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> +#> -2LL= 816.8276 +#> AIC = 842.8276 +#> BIC = 837.7503 +#> ----------------------------------------------------</div><div class='input'> +<span class='co'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> diff --git a/docs/dev/reference/transform_odeparms.html b/docs/dev/reference/transform_odeparms.html index 58a1e9a1..6b849d3f 100644 --- a/docs/dev/reference/transform_odeparms.html +++ b/docs/dev/reference/transform_odeparms.html @@ -77,7 +77,7 @@ the ilr transformation is used." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> @@ -125,7 +125,7 @@ the ilr transformation is used." /> </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="http://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/"> <span class="fab fa fab fa-github fa-lg"></span> </a> @@ -144,7 +144,7 @@ the ilr transformation is used." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Functions to transform and backtransform kinetic parameters for fitting</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/transform_odeparms.R'><code>R/transform_odeparms.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/transform_odeparms.R'><code>R/transform_odeparms.R</code></a></small> <div class="hidden name"><code>transform_odeparms.Rd</code></div> </div> @@ -154,22 +154,22 @@ restricted values to the full scale of real numbers. For kinetic rate constants and other parameters that can only take on positive values, a simple log transformation is used. For compositional parameters, such as the formations fractions that should always sum up to 1 and can not be negative, -the <code><a href='ilr.html'>ilr</a></code> transformation is used.</p> +the <a href='ilr.html'>ilr</a> transformation is used.</p> </div> - <pre class="usage"><span class='fu'>transform_odeparms</span>( - <span class='no'>parms</span>, - <span class='no'>mkinmod</span>, - <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span> -) + <pre class="usage"><span class='fu'>transform_odeparms</span><span class='op'>(</span> + <span class='va'>parms</span>, + <span class='va'>mkinmod</span>, + transform_rates <span class='op'>=</span> <span class='cn'>TRUE</span>, + transform_fractions <span class='op'>=</span> <span class='cn'>TRUE</span> +<span class='op'>)</span> -<span class='fu'>backtransform_odeparms</span>( - <span class='no'>transparms</span>, - <span class='no'>mkinmod</span>, - <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span> -)</pre> +<span class='fu'>backtransform_odeparms</span><span class='op'>(</span> + <span class='va'>transparms</span>, + <span class='va'>mkinmod</span>, + transform_rates <span class='op'>=</span> <span class='cn'>TRUE</span>, + transform_fractions <span class='op'>=</span> <span class='cn'>TRUE</span> +<span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -181,9 +181,9 @@ equations.</p></td> </tr> <tr> <th>mkinmod</th> - <td><p>The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing + <td><p>The kinetic model of class <a href='mkinmod.html'>mkinmod</a>, containing the names of the model variables that are needed for grouping the -formation fractions before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter +formation fractions before <a href='ilr.html'>ilr</a> transformation, the parameter names and the information if the pathway to sink is included in the model.</p></td> </tr> <tr> @@ -200,10 +200,13 @@ models and the break point tb of the HS model.</p></td> <td><p>Boolean specifying if formation fractions constants should be transformed in the model specification used in the fitting for better compliance with the assumption of normal distribution -of the estimator. The default (TRUE) is to do transformations. The g -parameter of the DFOP and HS models are also transformed, as they can also -be seen as compositional data. The transformation used for these -transformations is the <code><a href='ilr.html'>ilr</a></code> transformation.</p></td> +of the estimator. The default (TRUE) is to do transformations. +The g parameter of the DFOP model is also seen as a fraction. +If a single fraction is transformed (g parameter of DFOP or only a single +target variable e.g. a single metabolite plus a pathway to sink), a +logistic transformation is used <code><a href='https://rdrr.io/r/stats/Logistic.html'>stats::qlogis()</a></code>. In other cases, i.e. if +two or more formation fractions need to be transformed whose sum cannot +exceed one, the <a href='ilr.html'>ilr</a> transformation is used.</p></td> </tr> <tr> <th>transparms</th> @@ -219,74 +222,96 @@ fitting procedure.</p></td> <p>The transformation of sets of formation fractions is fragile, as it supposes the same ordering of the components in forward and backward transformation. -This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit</a></code>.</p> +This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</p> + <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + + <p>Johannes Ranke</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> -<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( - <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</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'># Fit the model to the FOCUS example dataset D using defaults</span> -<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><span class='no'>fit.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>) +<span class='va'>SFO_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='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, + m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <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'># Fit the model to the FOCUS example dataset D using defaults</span> +<span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> <span class='co'># Transformed and backtransformed parameters</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.598 1.5702 96.4038 102.793 -#> log_k_parent -2.316 0.0409 -2.3988 -2.233 -#> log_k_m1 -5.248 0.1332 -5.5184 -4.977 -#> f_parent_ilr_1 0.041 0.0631 -0.0875 0.169 -#> sigma 3.126 0.3585 2.3961 3.855</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931 +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> Estimate Std. Error Lower Upper +#> parent_0 99.5985 1.5702 96.404 102.79 +#> log_k_parent -2.3157 0.0409 -2.399 -2.23 +#> log_k_m1 -5.2475 0.1332 -5.518 -4.98 +#> f_parent_qlogis 0.0579 0.0893 -0.124 0.24 +#> sigma 3.1255 0.3585 2.396 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40383 102.7931 #> k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073 #> k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 #> f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596 #> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'> <span class='co'># \dontrun{</span> <span class='co'># Compare to the version without transforming rate parameters</span> -<span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='error'>Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", signif(cost.current, 6), "\n", sep = "")}: missing value where TRUE/FALSE needed</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0.002 0 0.003</span></div><div class='input'><span class='no'>fit.2.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</span>)</div><div class='output co'>#> <span class='error'>Error in summary(fit.2): object 'fit.2' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in print(fit.2.s$par, 3): object 'fit.2.s' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in print(fit.2.s$bpar, 3): object 'fit.2.s' not found</span></div><div class='input'><span class='co'># }</span> - -<span class='no'>initials</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>initials</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>fit</span>$<span class='no'>start</span>) -<span class='no'>transformed</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>transformed</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>fit</span>$<span class='no'>start_transformed</span>) -<span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 -#> 100.750000 -2.302585 -2.301586 0.000000 </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 +<span class='va'>fit.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, transform_rates <span class='op'>=</span> <span class='cn'>FALSE</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='error'>Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", signif(cost.current, 6), "\n", sep = "")}: missing value where TRUE/FALSE needed</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0.003 0 0.002</span></div><div class='input'><span class='va'>fit.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'summary': object 'fit.2' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'fit.2.s' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'fit.2.s' not found</span></div><div class='input'><span class='co'># }</span> + +<span class='va'>initials</span> <span class='op'><-</span> <span class='va'>fit</span><span class='op'>$</span><span class='va'>start</span><span class='op'>$</span><span class='va'>value</span> +<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>initials</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>start</span><span class='op'>)</span> +<span class='va'>transformed</span> <span class='op'><-</span> <span class='va'>fit</span><span class='op'>$</span><span class='va'>start_transformed</span><span class='op'>$</span><span class='va'>value</span> +<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>transformed</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>start_transformed</span><span class='op'>)</span> +<span class='fu'>transform_odeparms</span><span class='op'>(</span><span class='va'>initials</span>, <span class='va'>SFO_SFO</span><span class='op'>)</span> +</div><div class='output co'>#> parent_0 log_k_parent log_k_m1 f_parent_qlogis +#> 100.750000 -2.302585 -2.301586 0.000000 </div><div class='input'><span class='fu'>backtransform_odeparms</span><span class='op'>(</span><span class='va'>transformed</span>, <span class='va'>SFO_SFO</span><span class='op'>)</span> +</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 #> 100.7500 0.1000 0.1001 0.5000 </div><div class='input'> <span class='co'># \dontrun{</span> <span class='co'># The case of formation fractions</span> -<span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( - <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), - <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><span class='no'>fit.ff.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.ff</span>) -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.ff.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.598 1.5702 96.4038 102.793 -#> log_k_parent -2.316 0.0409 -2.3988 -2.233 -#> log_k_m1 -5.248 0.1332 -5.5184 -4.977 -#> f_parent_ilr_1 0.041 0.0631 -0.0875 0.169 -#> sigma 3.126 0.3585 2.3961 3.855</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.ff.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931 +<span class='va'>SFO_SFO.ff</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='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, + m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, + use_of_ff <span class='op'>=</span> <span class='st'>"max"</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='va'>fit.ff</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.ff.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> Estimate Std. Error Lower Upper +#> parent_0 99.5985 1.5702 96.404 102.79 +#> log_k_parent -2.3157 0.0409 -2.399 -2.23 +#> log_k_m1 -5.2475 0.1332 -5.518 -4.98 +#> f_parent_qlogis 0.0579 0.0893 -0.124 0.24 +#> sigma 3.1255 0.3585 2.396 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40383 102.7931 #> k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073 #> k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 #> f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'><span class='no'>initials</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) -<span class='no'>transformed</span> <span class='kw'><-</span> <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO.ff</span>) -<span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO.ff</span>)</div><div class='output co'>#> f_parent_to_m1 +#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'><span class='va'>initials</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'>"f_parent_to_m1"</span> <span class='op'>=</span> <span class='fl'>0.5</span><span class='op'>)</span> +<span class='va'>transformed</span> <span class='op'><-</span> <span class='fu'>transform_odeparms</span><span class='op'>(</span><span class='va'>initials</span>, <span class='va'>SFO_SFO.ff</span><span class='op'>)</span> +<span class='fu'>backtransform_odeparms</span><span class='op'>(</span><span class='va'>transformed</span>, <span class='va'>SFO_SFO.ff</span><span class='op'>)</span> +</div><div class='output co'>#> f_parent_to_m1 #> 0.5 </div><div class='input'> <span class='co'># And without sink</span> -<span class='no'>SFO_SFO.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( - <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), - <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>fit.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0242</span></div><div class='input'><span class='no'>fit.ff.2.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.ff.2</span>) -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.ff.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper +<span class='va'>SFO_SFO.ff.2</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='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, + m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, + use_of_ff <span class='op'>=</span> <span class='st'>"max"</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='va'>fit.ff.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff.2</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.ff.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff.2</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> Estimate Std. Error Lower Upper #> parent_0 84.79 3.012 78.67 90.91 #> log_k_parent -2.76 0.082 -2.92 -2.59 #> log_k_m1 -4.21 0.123 -4.46 -3.96 -#> sigma 8.22 0.943 6.31 10.14</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.ff.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> sigma 8.22 0.943 6.31 10.14</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper #> parent_0 84.7916 3.01203 28.15 1.92e-25 78.6704 90.913 #> k_parent 0.0635 0.00521 12.19 2.91e-14 0.0538 0.075 #> k_m1 0.0148 0.00182 8.13 8.81e-10 0.0115 0.019 -#> sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140</div><div class='input'># } +#> sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140</div><div class='input'><span class='co'># }</span> </div></pre> </div> @@ -304,7 +329,7 @@ This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit< </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> |
