From 91c5db736a4d3f2290a0cc5698fb4e35ae7bda59 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 May 2022 21:26:17 +0200 Subject: Remove outdated comment in FOCUS L vignette, update docs This also adds the first benchmark results obtained on my laptop system --- docs/reference/dimethenamid_2018.html | 92 +++++++++++++++++------------------ 1 file changed, 46 insertions(+), 46 deletions(-) (limited to 'docs/reference/dimethenamid_2018.html') diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index d2ed8647..a3cfc271 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -202,9 +202,9 @@ specific pieces of information in the comments.

summary(f_dmta_saem_tc) #> saemix version used for fitting: 3.0 #> mkin version used for pre-fitting: 1.1.0 -#> R version used for fitting: 4.1.3 -#> Date of fit: Sat Apr 9 18:03:34 2022 -#> Date of summary: Sat Apr 9 18:03:34 2022 +#> R version used for fitting: 4.2.0 +#> Date of fit: Wed May 18 20:37:14 2022 +#> Date of summary: Wed May 18 20:37:14 2022 #> #> Equations: #> d_DMTA/dt = - k_DMTA * DMTA @@ -217,7 +217,7 @@ specific pieces of information in the comments.

#> #> Model predictions using solution type deSolve #> -#> Fitted in 787.836 s +#> Fitted in 1660.941 s #> Using 300, 100 iterations and 9 chains #> #> Variance model: Two-component variance function @@ -239,65 +239,65 @@ specific pieces of information in the comments.

#> #> Optimised parameters: #> est. lower upper -#> DMTA_0 88.5943 84.3961 92.7925 -#> log_k_DMTA -3.0466 -3.5609 -2.5322 -#> log_k_M23 -4.0684 -4.9340 -3.2029 -#> log_k_M27 -3.8628 -4.2627 -3.4628 -#> log_k_M31 -3.9803 -4.4804 -3.4801 -#> f_DMTA_ilr_1 0.1304 -0.2186 0.4795 -#> f_DMTA_ilr_2 0.1490 -0.2559 0.5540 -#> f_DMTA_ilr_3 -1.3970 -1.6976 -1.0964 +#> DMTA_0 88.3098 84.1383 92.4813 +#> log_k_DMTA -3.0510 -3.5659 -2.5361 +#> log_k_M23 -4.0567 -4.9178 -3.1955 +#> log_k_M27 -3.8592 -4.2571 -3.4614 +#> log_k_M31 -3.9685 -4.4683 -3.4686 +#> f_DMTA_ilr_1 0.1382 -0.2120 0.4885 +#> f_DMTA_ilr_2 0.1429 -0.2616 0.5473 +#> f_DMTA_ilr_3 -1.3889 -1.6943 -1.0836 #> #> Correlation: #> DMTA_0 l__DMTA lg__M23 lg__M27 lg__M31 f_DMTA__1 f_DMTA__2 -#> log_k_DMTA 0.0309 -#> log_k_M23 -0.0231 -0.0031 -#> log_k_M27 -0.0381 -0.0048 0.0039 -#> log_k_M31 -0.0251 -0.0031 0.0021 0.0830 -#> f_DMTA_ilr_1 -0.0046 -0.0006 0.0417 -0.0437 0.0328 -#> f_DMTA_ilr_2 -0.0008 -0.0002 0.0214 -0.0270 -0.0909 -0.0361 -#> f_DMTA_ilr_3 -0.1832 -0.0135 0.0434 0.0804 0.0395 -0.0070 0.0059 +#> log_k_DMTA 0.0315 +#> log_k_M23 -0.0237 -0.0031 +#> log_k_M27 -0.0392 -0.0048 0.0040 +#> log_k_M31 -0.0257 -0.0032 0.0022 0.0821 +#> f_DMTA_ilr_1 -0.0048 -0.0007 0.0415 -0.0435 0.0333 +#> f_DMTA_ilr_2 -0.0007 -0.0002 0.0214 -0.0270 -0.0900 -0.0372 +#> f_DMTA_ilr_3 -0.1861 -0.0136 0.0431 0.0797 0.0382 -0.0072 0.0066 #> #> Random effects: #> est. lower upper -#> SD.DMTA_0 3.3651 -0.9655 7.6956 -#> SD.log_k_DMTA 0.6415 0.2774 1.0055 -#> SD.log_k_M23 1.0176 0.3809 1.6543 -#> SD.log_k_M27 0.4538 0.1522 0.7554 -#> SD.log_k_M31 0.5684 0.1905 0.9464 -#> SD.f_DMTA_ilr_1 0.4111 0.1524 0.6699 -#> SD.f_DMTA_ilr_2 0.4788 0.1808 0.7768 -#> SD.f_DMTA_ilr_3 0.3501 0.1316 0.5685 +#> SD.DMTA_0 3.2733 -1.1098 7.6564 +#> SD.log_k_DMTA 0.6422 0.2777 1.0066 +#> SD.log_k_M23 1.0131 0.3797 1.6465 +#> SD.log_k_M27 0.4511 0.1510 0.7513 +#> SD.log_k_M31 0.5695 0.1923 0.9466 +#> SD.f_DMTA_ilr_1 0.4123 0.1526 0.6720 +#> SD.f_DMTA_ilr_2 0.4780 0.1804 0.7757 +#> SD.f_DMTA_ilr_3 0.3559 0.1344 0.5775 #> #> Variance model: #> est. lower upper -#> a.1 0.9349 0.8395 1.0302 -#> b.1 0.1344 0.1176 0.1512 +#> a.1 0.9255 0.8288 1.0221 +#> b.1 0.1365 0.1191 0.1538 #> #> Backtransformed parameters: #> est. lower upper -#> DMTA_0 88.59431 84.396147 92.79246 -#> k_DMTA 0.04752 0.028413 0.07948 -#> k_M23 0.01710 0.007198 0.04064 -#> k_M27 0.02101 0.014084 0.03134 -#> k_M31 0.01868 0.011329 0.03080 -#> f_DMTA_to_M23 0.14498 NA NA -#> f_DMTA_to_M27 0.12056 NA NA -#> f_DMTA_to_M31 0.11015 NA NA +#> DMTA_0 88.30980 84.138334 92.48126 +#> k_DMTA 0.04731 0.028272 0.07918 +#> k_M23 0.01731 0.007315 0.04095 +#> k_M27 0.02108 0.014164 0.03139 +#> k_M31 0.01890 0.011467 0.03116 +#> f_DMTA_to_M23 0.14626 NA NA +#> f_DMTA_to_M27 0.12029 NA NA +#> f_DMTA_to_M31 0.11135 NA NA #> #> Resulting formation fractions: #> ff -#> DMTA_M23 0.1450 -#> DMTA_M27 0.1206 -#> DMTA_M31 0.1101 -#> DMTA_sink 0.6243 +#> DMTA_M23 0.1463 +#> DMTA_M27 0.1203 +#> DMTA_M31 0.1113 +#> DMTA_sink 0.6221 #> #> Estimated disappearance times: #> DT50 DT90 -#> DMTA 14.59 48.45 -#> M23 40.52 134.62 -#> M27 32.99 109.60 -#> M31 37.11 123.26 +#> DMTA 14.65 48.67 +#> M23 40.05 133.05 +#> M27 32.88 109.21 +#> M31 36.67 121.81 # As the confidence interval for the random effects of DMTA_0 # includes zero, we could try an alternative model without # such random effects @@ -321,7 +321,7 @@ specific pieces of information in the comments.

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