diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2023-05-19 17:08:43 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2023-05-19 17:10:16 +0200 |
| commit | cf54ccca37d27480dbf8d59eb027300518f7ad75 (patch) | |
| tree | 81a9d5955f716a74822ecb65dc83daeeb7efbba6 /docs/reference/dimethenamid_2018.html | |
| parent | c931057ce8f05d3a0dfefea72b73903efb82e900 (diff) | |
Prepare release of v1.2.4v1.2.4
- Update DESCRIPTION
- Update Makefile to document how to use R-patched
- Remove markup from two URLs to avoid CRAN NOTE
- Switch two vignettes from html_document to html_vignette to save space
in the docs directory, also avoiding a CRAN NOTE
- Complete rebuild of pkgdown docs for release
Diffstat (limited to 'docs/reference/dimethenamid_2018.html')
| -rw-r--r-- | docs/reference/dimethenamid_2018.html | 118 |
1 files changed, 59 insertions, 59 deletions
diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index 0581830c..a1c800e8 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -22,7 +22,7 @@ constrained by data protection regulations."><!-- mathjax --><script src="https: </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -132,7 +132,7 @@ constrained by data protection regulations.</p> <p>Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria (2018) Renewal Assessment Report Dimethenamid-P Volume 3 - B.8 Environmental fate and behaviour Rev. 2 - November 2017 -<a href="https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716" class="external-link">https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716</a></p> +https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716</p> </div> <div id="details"> <h2>Details</h2> @@ -222,10 +222,10 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co">#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")</span></span></span> <span class="r-in"><span><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> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Apr 20 07:32:09 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Apr 20 07:32:09 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.4 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:15:21 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:15:21 2023 </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> @@ -238,7 +238,7 @@ 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 301.026 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 282.941 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> @@ -284,75 +284,75 @@ 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 88.3192 83.8656 92.7729</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0530 -3.5686 -2.5373</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0620 -4.9202 -3.2038</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8633 -4.2668 -3.4598</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9731 -4.4763 -3.4699</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1346 -0.2150 0.4841</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1449 -0.2593 0.5491</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3882 -1.7011 -1.0753</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.9156 0.8217 1.0095</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1216 0.1550</span> -<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.7280 -0.6949 8.1508</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0096 0.3782 1.6409</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4583 0.1541 0.7625</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5738 0.1942 0.9533</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4119 0.1528 0.6709</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1806 0.7754</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3657 0.1383 0.5931</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.4862 84.1127 92.8598</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0512 -3.5674 -2.5351</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0576 -4.9013 -3.2139</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8584 -4.2572 -3.4595</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9779 -4.4844 -3.4714</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1264 -0.2186 0.4714</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1509 -0.2547 0.5565</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3891 -1.6962 -1.0819</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9196 0.8231 1.0161</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1377 0.1203 0.1551</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.5956 -0.8154 8.0066</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6437 0.2784 1.0091</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 0.9929 0.3719 1.6139</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4530 0.1522 0.7537</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5773 0.1952 0.9595</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4063 0.1505 0.6621</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4800 0.1817 0.7783</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3582 0.1350 0.5814</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 0.0303 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0229 -0.0032 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0372 -0.0049 0.0041 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0245 -0.0032 0.0022 0.0815 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0046 -0.0006 0.0415 -0.0433 0.0324 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0008 -0.0002 0.0214 -0.0267 -0.0893 -0.0361 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1755 -0.0135 0.0423 0.0775 0.0377 -0.0066 0.0060 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0306 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0234 -0.0032 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0380 -0.0049 0.0041 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0247 -0.0031 0.0022 0.0817 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0046 -0.0006 0.0425 -0.0438 0.0319 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0008 -0.0002 0.0216 -0.0267 -0.0890 -0.0349 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1805 -0.0136 0.0434 0.0791 0.0390 -0.0061 0.0053 </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 3.7280 -0.6949 8.1508</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0096 0.3782 1.6409</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4583 0.1541 0.7625</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5738 0.1942 0.9533</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4119 0.1528 0.6709</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1806 0.7754</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3657 0.1383 0.5931</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.5956 -0.8154 8.0066</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6437 0.2784 1.0091</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 0.9929 0.3719 1.6139</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4530 0.1522 0.7537</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5773 0.1952 0.9595</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4063 0.1505 0.6621</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4800 0.1817 0.7783</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3582 0.1350 0.5814</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 0.9156 0.8217 1.009</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1216 0.155</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 0.9196 0.8231 1.0161</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1377 0.1203 0.1551</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 88.31924 83.865625 92.77286</span> -<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04722 0.028196 0.07908</span> -<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01721 0.007298 0.04061</span> -<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02100 0.014027 0.03144</span> -<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01882 0.011375 0.03112</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14608 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12077 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11123 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.48621 84.112654 92.85977</span> +<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04730 0.028230 0.07926</span> +<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01729 0.007437 0.04020</span> +<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02110 0.014162 0.03144</span> +<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01872 0.011283 0.03107</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14551 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12169 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11062 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 0.1461</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1208</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1112</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6219</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M23 0.1455</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1217</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1106</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6222</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 14.68 48.76</span> -<span class="r-out co"><span class="r-pr">#></span> M23 40.27 133.76</span> -<span class="r-out co"><span class="r-pr">#></span> M27 33.01 109.65</span> -<span class="r-out co"><span class="r-pr">#></span> M31 36.84 122.38</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA 14.65 48.68</span> +<span class="r-out co"><span class="r-pr">#></span> M23 40.09 133.17</span> +<span class="r-out co"><span class="r-pr">#></span> M27 32.85 109.11</span> +<span class="r-out co"><span class="r-pr">#></span> M31 37.02 122.97</span> <span class="r-in"><span><span class="co"># As the confidence interval for the random effects of DMTA_0</span></span></span> <span class="r-in"><span><span class="co"># includes zero, we could try an alternative model without</span></span></span> <span class="r-in"><span><span class="co"># such random effects</span></span></span> |