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Diffstat (limited to 'docs/dev/articles/prebuilt/2022_cyan_pathway.html')
| -rw-r--r-- | docs/dev/articles/prebuilt/2022_cyan_pathway.html | 116 |
1 files changed, 67 insertions, 49 deletions
diff --git a/docs/dev/articles/prebuilt/2022_cyan_pathway.html b/docs/dev/articles/prebuilt/2022_cyan_pathway.html index 87d4ca4a..1095dd28 100644 --- a/docs/dev/articles/prebuilt/2022_cyan_pathway.html +++ b/docs/dev/articles/prebuilt/2022_cyan_pathway.html @@ -34,14 +34,14 @@ </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">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../../reference/index.html">Functions and data</a> + <a href="../../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -53,6 +53,9 @@ <li> <a href="../../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -60,22 +63,31 @@ <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li class="divider"> </li> +<li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + </li> +<li class="dropdown-header">Performance</li> + <li> + <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -83,6 +95,15 @@ <li> <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul> </li> <li> @@ -115,7 +136,7 @@ residue data on cyantraniliprole</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change on 6 January -2023, last compiled on 28 Januar 2023</h4> +2023, last compiled on 17 Februar 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_cyan_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_cyan_pathway.rmd</code></a></small> <div class="hidden name"><code>2022_cyan_pathway.rmd</code></div> @@ -135,7 +156,7 @@ be fitted with the mkin package.</p> 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data) of the German Environment Agency carried out in 2022 and 2023.</p> -<p>The mkin package is used in version 1.2.2 which is currently under +<p>The mkin package is used in version 1.2.3 which is currently under development. The newly introduced functionality that is used here is a simplification of excluding random effects for a set of fits based on a related set of fits with a reduced model, and the documentation of the @@ -2185,7 +2206,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:07:38 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2313,7 +2334,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:08:17 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2443,7 +2464,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:09:12 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2588,7 +2609,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:09:18 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2726,7 +2747,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:10:30 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2872,7 +2893,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:16:28 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -3018,7 +3039,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:10:49 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3183,7 +3204,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:17:00 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3348,7 +3369,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:11:04 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan @@ -3490,7 +3511,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:11:24 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan @@ -3638,7 +3659,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:34:28 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -3802,7 +3823,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:37:36 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -3948,7 +3969,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:38:34 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4139,7 +4160,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:45:32 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4330,7 +4351,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:38:37 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4526,7 +4547,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:46:02 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4727,7 +4748,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 11:18:41 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -4870,7 +4891,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 11:16:32 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -5036,7 +5057,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 11:22:28 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -5202,7 +5223,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 11:17:37 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -5373,7 +5394,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 11:21:01 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -5561,26 +5582,23 @@ attached base packages: [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.41 mkin_1.2.2 +[1] saemix_3.2 npde_3.3 knitr_1.41 mkin_1.2.3 loaded via a namespace (and not attached): - [1] mclust_6.0.0 lattice_0.20-45 prettyunits_1.1.1 ps_1.7.2 - [5] zoo_1.8-11 assertthat_0.2.1 rprojroot_2.0.3 digest_0.6.31 - [9] lmtest_0.9-40 utf8_1.2.2 R6_2.5.1 cellranger_1.1.0 -[13] evaluate_0.19 ggplot2_3.4.0 highr_0.9 pillar_1.8.1 -[17] rlang_1.0.6 readxl_1.4.1 callr_3.7.3 jquerylib_0.1.4 -[21] rmarkdown_2.19 pkgdown_2.0.7 textshaping_0.3.6 desc_1.4.2 -[25] stringr_1.5.0 munsell_0.5.0 compiler_4.2.2 xfun_0.35 -[29] pkgconfig_2.0.3 systemfonts_1.0.4 pkgbuild_1.4.0 htmltools_0.5.4 -[33] tidyselect_1.2.0 tibble_3.1.8 gridExtra_2.3 codetools_0.2-18 -[37] fansi_1.0.3 crayon_1.5.2 dplyr_1.0.10 grid_4.2.2 -[41] nlme_3.1-161 jsonlite_1.8.4 gtable_0.3.1 lifecycle_1.0.3 -[45] DBI_1.1.3 magrittr_2.0.3 scales_1.2.1 cli_3.5.0 -[49] stringi_1.7.8 cachem_1.0.6 fs_1.5.2 bslib_0.4.2 -[53] ragg_1.2.4 generics_0.1.3 vctrs_0.5.1 deSolve_1.34 -[57] tools_4.2.2 glue_1.6.2 purrr_1.0.0 processx_3.8.0 -[61] fastmap_1.1.0 yaml_2.3.6 inline_0.3.19 colorspace_2.0-3 -[65] memoise_2.0.1 sass_0.4.4 </code></pre> + [1] pillar_1.8.1 bslib_0.4.2 compiler_4.2.2 jquerylib_0.1.4 + [5] tools_4.2.2 mclust_6.0.0 digest_0.6.31 tibble_3.1.8 + [9] jsonlite_1.8.4 evaluate_0.19 memoise_2.0.1 lifecycle_1.0.3 +[13] nlme_3.1-162 gtable_0.3.1 lattice_0.20-45 pkgconfig_2.0.3 +[17] rlang_1.0.6 DBI_1.1.3 cli_3.5.0 yaml_2.3.6 +[21] pkgdown_2.0.7 xfun_0.35 fastmap_1.1.0 gridExtra_2.3 +[25] dplyr_1.0.10 stringr_1.5.0 generics_0.1.3 desc_1.4.2 +[29] fs_1.5.2 vctrs_0.5.1 sass_0.4.4 systemfonts_1.0.4 +[33] tidyselect_1.2.0 rprojroot_2.0.3 lmtest_0.9-40 grid_4.2.2 +[37] inline_0.3.19 glue_1.6.2 R6_2.5.1 textshaping_0.3.6 +[41] fansi_1.0.3 rmarkdown_2.19 purrr_1.0.0 ggplot2_3.4.0 +[45] magrittr_2.0.3 scales_1.2.1 htmltools_0.5.4 assertthat_0.2.1 +[49] colorspace_2.0-3 ragg_1.2.4 utf8_1.2.2 stringi_1.7.8 +[53] munsell_0.5.0 cachem_1.0.6 zoo_1.8-11 </code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> |