diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-05-18 21:26:17 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-05-18 21:26:17 +0200 |
| commit | 91c5db736a4d3f2290a0cc5698fb4e35ae7bda59 (patch) | |
| tree | 8e9e34d18f055936172329c1248e6e2ff136bff9 /docs/reference/dimethenamid_2018.html | |
| parent | ea57db98cef3fb882f7bd9656b44f270e7bded38 (diff) | |
Remove outdated comment in FOCUS L vignette, update docs
This also adds the first benchmark results obtained on my laptop system
Diffstat (limited to 'docs/reference/dimethenamid_2018.html')
| -rw-r--r-- | docs/reference/dimethenamid_2018.html | 92 |
1 files changed, 46 insertions, 46 deletions
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.</p> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_dmta_saem_tc</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.0 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sat Apr 9 18:03:34 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sat Apr 9 18:03:34 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed May 18 20:37:14 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed May 18 20:37:14 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_DMTA/dt = - k_DMTA * DMTA</span> @@ -217,7 +217,7 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 787.836 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 1660.941 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 9 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> @@ -239,65 +239,65 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.5943 84.3961 92.7925</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0466 -3.5609 -2.5322</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0684 -4.9340 -3.2029</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8628 -4.2627 -3.4628</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9803 -4.4804 -3.4801</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1304 -0.2186 0.4795</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1490 -0.2559 0.5540</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3970 -1.6976 -1.0964</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.3098 84.1383 92.4813</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0510 -3.5659 -2.5361</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0567 -4.9178 -3.1955</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8592 -4.2571 -3.4614</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9685 -4.4683 -3.4686</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1382 -0.2120 0.4885</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1429 -0.2616 0.5473</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3889 -1.6943 -1.0836</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> DMTA_0 l__DMTA lg__M23 lg__M27 lg__M31 f_DMTA__1 f_DMTA__2</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0309 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0231 -0.0031 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0381 -0.0048 0.0039 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0251 -0.0031 0.0021 0.0830 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0046 -0.0006 0.0417 -0.0437 0.0328 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0008 -0.0002 0.0214 -0.0270 -0.0909 -0.0361 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1832 -0.0135 0.0434 0.0804 0.0395 -0.0070 0.0059 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0315 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0237 -0.0031 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0392 -0.0048 0.0040 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0257 -0.0032 0.0022 0.0821 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0048 -0.0007 0.0415 -0.0435 0.0333 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0007 -0.0002 0.0214 -0.0270 -0.0900 -0.0372 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1861 -0.0136 0.0431 0.0797 0.0382 -0.0072 0.0066 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.3651 -0.9655 7.6956</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6415 0.2774 1.0055</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0176 0.3809 1.6543</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4538 0.1522 0.7554</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5684 0.1905 0.9464</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4111 0.1524 0.6699</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4788 0.1808 0.7768</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3501 0.1316 0.5685</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.2733 -1.1098 7.6564</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6422 0.2777 1.0066</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0131 0.3797 1.6465</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4511 0.1510 0.7513</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5695 0.1923 0.9466</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4123 0.1526 0.6720</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1804 0.7757</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3559 0.1344 0.5775</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.9349 0.8395 1.0302</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.1344 0.1176 0.1512</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9255 0.8288 1.0221</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1365 0.1191 0.1538</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.59431 84.396147 92.79246</span> -<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04752 0.028413 0.07948</span> -<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01710 0.007198 0.04064</span> -<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02101 0.014084 0.03134</span> -<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01868 0.011329 0.03080</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14498 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12056 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11015 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.30980 84.138334 92.48126</span> +<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04731 0.028272 0.07918</span> +<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01731 0.007315 0.04095</span> +<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02108 0.014164 0.03139</span> +<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01890 0.011467 0.03116</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14626 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12029 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11135 NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> <span class="r-out co"><span class="r-pr">#></span> ff</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M23 0.1450</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1206</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1101</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6243</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M23 0.1463</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1203</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1113</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6221</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA 14.59 48.45</span> -<span class="r-out co"><span class="r-pr">#></span> M23 40.52 134.62</span> -<span class="r-out co"><span class="r-pr">#></span> M27 32.99 109.60</span> -<span class="r-out co"><span class="r-pr">#></span> M31 37.11 123.26</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA 14.65 48.67</span> +<span class="r-out co"><span class="r-pr">#></span> M23 40.05 133.05</span> +<span class="r-out co"><span class="r-pr">#></span> M27 32.88 109.21</span> +<span class="r-out co"><span class="r-pr">#></span> M31 36.67 121.81</span> <span class="r-in"><span class="co"># As the confidence interval for the random effects of DMTA_0</span></span> <span class="r-in"><span class="co"># includes zero, we could try an alternative model without</span></span> <span class="r-in"><span class="co"># such random effects</span></span> @@ -321,7 +321,7 @@ specific pieces of information in the comments.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> |