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Diffstat (limited to 'docs/dev/reference/dimethenamid_2018.html')
| -rw-r--r-- | docs/dev/reference/dimethenamid_2018.html | 26 |
1 files changed, 13 insertions, 13 deletions
diff --git a/docs/dev/reference/dimethenamid_2018.html b/docs/dev/reference/dimethenamid_2018.html index c893da63..a77cf0f4 100644 --- a/docs/dev/reference/dimethenamid_2018.html +++ b/docs/dev/reference/dimethenamid_2018.html @@ -295,7 +295,7 @@ specific pieces of information in the comments.</p> #> M31 ~ add(sigma_low_M31) + prop(rsd_high_M31) #> }) #> } -#> <environment: 0x555559bfc940></div><div class='input'><span class='co'># The focei fit takes about four minutes on my system</span> +#> <environment: 0x555559ac3820></div><div class='input'><span class='co'># The focei fit takes about four minutes on my system</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'>f_dmta_nlmixr_focei</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_dmta_mkin_tc</span>, est <span class='op'>=</span> <span class='st'>"focei"</span>, control <span class='op'>=</span> <span class='fu'>nlmixr</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/foceiControl.html'>foceiControl</a></span><span class='op'>(</span>print <span class='op'>=</span> <span class='fl'>500</span><span class='op'>)</span><span class='op'>)</span> @@ -303,7 +303,7 @@ specific pieces of information in the comments.</p> </div><div class='output co'>#> <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#> <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#> <span class='message'>→ creating full model...</span></div><div class='output co'>#> <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#> <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#> <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#> <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#> <span class='message'>→ creating full model...</span></div><div class='output co'>#> <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#> <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#> <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#> <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#> <span class='message'>→ calculate jacobian</span></div><div class='output co'>#> [====|====|====|====|====|====|====|====|====|====] 0:00:02 #> </div><div class='output co'>#> <span class='message'>→ calculate sensitivities</span></div><div class='output co'>#> [====|====|====|====|====|====|====|====|====|====] 0:00:04 #> </div><div class='output co'>#> <span class='message'>→ calculate ∂(f)/∂(η)</span></div><div class='output co'>#> [====|====|====|====|====|====|====|====|====|====] 0:00:01 -#> </div><div class='output co'>#> <span class='message'>→ calculate ∂(R²)/∂(η)</span></div><div class='output co'>#> [====|====|====|====|====|====|====|====|====|====] 0:00:09 +#> </div><div class='output co'>#> <span class='message'>→ calculate ∂(R²)/∂(η)</span></div><div class='output co'>#> [====|====|====|====|====|====|====|====|====|====] 0:00:08 #> </div><div class='output co'>#> <span class='message'>→ finding duplicate expressions in inner model...</span></div><div class='output co'>#> [====|====|====|====|====|====|====|====|====|====] 0:00:07 #> </div><div class='output co'>#> <span class='message'>→ optimizing duplicate expressions in inner model...</span></div><div class='output co'>#> [====|====|====|====|====|====|====|====|====|====] 0:00:07 #> </div><div class='output co'>#> <span class='message'>→ finding duplicate expressions in EBE model...</span></div><div class='output co'>#> [====|====|====|====|====|====|====|====|====|====] 0:00:00 @@ -324,12 +324,12 @@ specific pieces of information in the comments.</p> #> <span style='text-decoration: underline;'>|.....................| o9 | o10 |...........|...........|</span> #> calculating covariance matrix #> done</div><div class='output co'>#> <span class='message'>Calculating residuals/tables</span></div><div class='output co'>#> <span class='message'>done</span></div><div class='output co'>#> <span class='warning'>Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))</span></div><div class='output co'>#> <span class='warning'>Warning: last objective function was not at minimum, possible problems in optimization</span></div><div class='output co'>#> <span class='warning'>Warning: S matrix non-positive definite</span></div><div class='output co'>#> <span class='warning'>Warning: using R matrix to calculate covariance</span></div><div class='output co'>#> <span class='warning'>Warning: gradient problems with initial estimate and covariance; see $scaleInfo</span></div><div class='output co'>#> user system elapsed -#> 227.223 8.444 235.624 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>f_dmta_nlmixr_focei</span><span class='op'>)</span> +#> 232.621 14.126 246.850 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>f_dmta_nlmixr_focei</span><span class='op'>)</span> </div><div class='output co'>#> nlmixr version used for fitting: 2.0.4 #> mkin version used for pre-fitting: 1.0.5 #> R version used for fitting: 4.1.0 -#> Date of fit: Thu Jul 29 11:45:46 2021 -#> Date of summary: Thu Jul 29 11:45:46 2021 +#> Date of fit: Wed Aug 4 15:53:54 2021 +#> Date of summary: Wed Aug 4 15:53:54 2021 #> #> Equations: #> d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -350,7 +350,7 @@ specific pieces of information in the comments.</p> #> #> Degradation model predictions using RxODE #> -#> Fitted in 235.457 s +#> Fitted in 246.669 s #> #> Variance model: Two-component variance function #> @@ -489,11 +489,11 @@ specific pieces of information in the comments.</p> <span class='va'>f_dmta_saemix</span> <span class='op'><-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_dmta_mkin_tc</span>, test_log_parms <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Thu Jul 29 11:45:47 2021" +#> [1] "Wed Aug 4 15:53:55 2021" #> .... #> Minimisation finished -#> [1] "Thu Jul 29 12:04:25 2021"</div><div class='output co'>#> user system elapsed -#> 1185.594 0.028 1185.687 </div><div class='input'> +#> [1] "Wed Aug 4 16:12:40 2021"</div><div class='output co'>#> user system elapsed +#> 1192.021 0.064 1192.182 </div><div class='input'> <span class='co'># nlmixr with est = "saem" is pretty fast with default iteration numbers, most</span> <span class='co'># of the time (about 2.5 minutes) is spent for calculating the log likelihood at the end</span> <span class='co'># The likelihood calculated for the nlmixr fit is much lower than that found by saemix</span> @@ -506,13 +506,13 @@ specific pieces of information in the comments.</p> <span class='op'>)</span> </div><div class='output co'>#> <span class='message'>With est = 'saem', a different error model is required for each observed variableChanging the error model to 'obs_tc' (Two-component error for each observed variable)</span></div><div class='output co'>#> <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#> <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#> <span class='message'> </span></div><div class='output co'>#> <span class='message'>→ generate SAEM model</span></div><div class='output co'>#> <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#> 1: 98.3427 -3.5148 -3.3187 -3.7728 -2.1163 -2.8457 0.9482 -2.8064 -2.7412 -2.8745 2.7912 0.6805 0.8213 0.8055 0.8578 1.4980 2.9309 0.2850 0.2854 0.2850 4.0990 0.3821 3.5349 0.6537 5.4143 0.0002 4.5093 0.1905 #> 500: 97.8277 -4.3506 -4.0318 -4.1520 -3.0553 -3.5843 1.1326 -2.0873 -2.0421 -2.0751 0.2960 1.2515 0.2531 0.3807 0.7928 0.8863 6.5211 0.1433 0.1082 0.3353 0.8960 0.0470 0.7501 0.0475 0.9527 0.0281 0.7321 0.0594</div><div class='output co'>#> <span class='message'>Calculating covariance matrix</span></div><div class='output co'>#> </div><div class='output co'>#> <span class='message'>Calculating -2LL by Gaussian quadrature (nnodes=3,nsd=1.6)</span></div><div class='output co'>#> </div><div class='output co'>#> <span class='message'>→ creating full model...</span></div><div class='output co'>#> <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#> <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#> <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#> <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#> <span class='message'>→ compiling EBE model...</span></div><div class='output co'>#> <span class='message'> </span></div><div class='output co'>#> <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#> <span class='message'>Needed Covariates:</span></div><div class='output co'>#> [1] "CMT"</div><div class='output co'>#> <span class='message'>Calculating residuals/tables</span></div><div class='output co'>#> <span class='message'>done</span></div><div class='output co'>#> user system elapsed -#> 809.956 4.286 156.438 </div><div class='input'><span class='fu'>traceplot</span><span class='op'>(</span><span class='va'>f_dmta_nlmixr_saem</span><span class='op'>$</span><span class='va'>nm</span><span class='op'>)</span> +#> 813.299 3.736 151.935 </div><div class='input'><span class='fu'>traceplot</span><span class='op'>(</span><span class='va'>f_dmta_nlmixr_saem</span><span class='op'>$</span><span class='va'>nm</span><span class='op'>)</span> </div><div class='output co'>#> <span class='error'>Error in traceplot(f_dmta_nlmixr_saem$nm): could not find function "traceplot"</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>f_dmta_nlmixr_saem</span><span class='op'>)</span> </div><div class='output co'>#> nlmixr version used for fitting: 2.0.4 #> mkin version used for pre-fitting: 1.0.5 #> R version used for fitting: 4.1.0 -#> Date of fit: Thu Jul 29 12:08:09 2021 -#> Date of summary: Thu Jul 29 12:08:09 2021 +#> Date of fit: Wed Aug 4 16:16:18 2021 +#> Date of summary: Wed Aug 4 16:16:18 2021 #> #> Equations: #> d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -533,7 +533,7 @@ specific pieces of information in the comments.</p> #> #> Degradation model predictions using RxODE #> -#> Fitted in 156.17 s +#> Fitted in 151.67 s #> #> Variance model: Two-component variance function #> |