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Diffstat (limited to 'docs/dev/articles/prebuilt')
| -rw-r--r-- | docs/dev/articles/prebuilt/2022_cyan_pathway.html | 263 | ||||
| -rw-r--r-- | docs/dev/articles/prebuilt/2022_dmta_parent.html | 140 | ||||
| -rw-r--r-- | docs/dev/articles/prebuilt/2022_dmta_pathway.html | 51 |
3 files changed, 231 insertions, 223 deletions
diff --git a/docs/dev/articles/prebuilt/2022_cyan_pathway.html b/docs/dev/articles/prebuilt/2022_cyan_pathway.html index 7bb0fa5b..2359969e 100644 --- a/docs/dev/articles/prebuilt/2022_cyan_pathway.html +++ b/docs/dev/articles/prebuilt/2022_cyan_pathway.html @@ -34,7 +34,7 @@ </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">1.2.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -136,7 +136,7 @@ residue data on cyantraniliprole</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change on 20 April 2023, -last compiled on 20 April 2023</h4> +last compiled on 19 Mai 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> @@ -156,7 +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 1.2.4 which is currently under +<p>The mkin package is used in version 1.2.5 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 @@ -2220,10 +2220,10 @@ Hierarchical SFO path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:33:05 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:42:02 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2236,7 +2236,7 @@ Data: Model predictions using solution type deSolve -Fitted in 438.011 s +Fitted in 443.997 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2348,10 +2348,10 @@ Hierarchical SFO path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:32:55 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:42:01 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2364,7 +2364,7 @@ Data: Model predictions using solution type deSolve -Fitted in 427.249 s +Fitted in 442.545 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -2478,10 +2478,10 @@ Hierarchical FOMC path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:33:49 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:42:38 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2496,7 +2496,7 @@ Data: Model predictions using solution type deSolve -Fitted in 481.497 s +Fitted in 479.463 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2623,10 +2623,10 @@ Hierarchical FOMC path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:33:59 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:42:53 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2641,7 +2641,7 @@ Data: Model predictions using solution type deSolve -Fitted in 491.071 s +Fitted in 494.121 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -2761,10 +2761,10 @@ Hierarchical DFOP path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:34:33 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:43:22 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2783,7 +2783,7 @@ Data: Model predictions using solution type deSolve -Fitted in 525.551 s +Fitted in 523.691 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2907,10 +2907,10 @@ Hierarchical DFOP path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:37:03 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:46:08 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2929,7 +2929,7 @@ Data: Model predictions using solution type deSolve -Fitted in 675.804 s +Fitted in 689.217 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3053,10 +3053,10 @@ Hierarchical SFORB path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:34:43 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:43:37 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3074,7 +3074,7 @@ Data: Model predictions using solution type deSolve -Fitted in 535.818 s +Fitted in 538.025 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3218,10 +3218,10 @@ Hierarchical SFORB path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:37:02 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:45:51 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3239,7 +3239,7 @@ Data: Model predictions using solution type deSolve -Fitted in 674.859 s +Fitted in 672.309 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3383,10 +3383,10 @@ Hierarchical HS path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:34:41 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:43:26 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan @@ -3401,7 +3401,7 @@ Data: Model predictions using solution type deSolve -Fitted in 533.787 s +Fitted in 526.974 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3525,10 +3525,10 @@ Hierarchical HS path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:34:39 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:43:29 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan @@ -3543,7 +3543,7 @@ Data: Model predictions using solution type deSolve -Fitted in 531.084 s +Fitted in 529.515 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3673,10 +3673,10 @@ Hierarchical FOMC path 2 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:45:51 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:54:58 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -3691,7 +3691,7 @@ Data: Model predictions using solution type deSolve -Fitted in 517.002 s +Fitted in 519.639 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3837,10 +3837,10 @@ Hierarchical FOMC path 2 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:45:39 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:54:41 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -3855,7 +3855,7 @@ Data: Model predictions using solution type deSolve -Fitted in 505.619 s +Fitted in 503.222 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3983,10 +3983,10 @@ Hierarchical DFOP path 2 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:46:46 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:55:53 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4006,7 +4006,7 @@ Data: Model predictions using solution type deSolve -Fitted in 572.382 s +Fitted in 574.8 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -4174,10 +4174,10 @@ Hierarchical DFOP path 2 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:49:18 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:58:32 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4197,7 +4197,7 @@ Data: Model predictions using solution type deSolve -Fitted in 724.515 s +Fitted in 733.398 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4365,10 +4365,10 @@ Hierarchical SFORB path 2 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:46:33 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:55:51 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4386,7 +4386,7 @@ Data: Model predictions using solution type deSolve -Fitted in 559.097 s +Fitted in 572.747 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -4561,10 +4561,10 @@ Hierarchical SFORB path 2 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:49:20 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:58:21 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4582,7 +4582,7 @@ Data: Model predictions using solution type deSolve -Fitted in 726.293 s +Fitted in 722.847 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4762,10 +4762,10 @@ error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 21:02:39 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:12:10 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -4780,7 +4780,7 @@ Data: Model predictions using solution type deSolve -Fitted in 796.615 s +Fitted in 816.454 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4905,10 +4905,10 @@ variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 21:04:15 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:13:38 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4928,7 +4928,7 @@ Data: Model predictions using solution type deSolve -Fitted in 893.328 s +Fitted in 904.25 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -5071,10 +5071,10 @@ error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 21:04:33 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:00 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -5094,7 +5094,7 @@ Data: Model predictions using solution type deSolve -Fitted in 910.788 s +Fitted in 926.094 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -5237,10 +5237,10 @@ variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 21:04:09 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:13:34 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -5258,7 +5258,7 @@ Data: Model predictions using solution type deSolve -Fitted in 887.369 s +Fitted in 900.859 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -5408,10 +5408,10 @@ error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 21:04:32 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:13:37 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -5429,7 +5429,7 @@ Data: Model predictions using solution type deSolve -Fitted in 910.017 s +Fitted in 903.326 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -5578,13 +5578,13 @@ JSE76 26.89 89.33 NA NA NA <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.2.3 (2023-03-15) +<pre><code>R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so +BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 +LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so; LAPACK version 3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -5594,37 +5594,40 @@ locale: [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C +time zone: Europe/Berlin +tzcode source: system (glibc) + attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.4 +[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.5 loaded via a namespace (and not attached): - [1] deSolve_1.35 zoo_1.8-12 tidyselect_1.2.0 xfun_0.38 - [5] bslib_0.4.2 purrr_1.0.1 lattice_0.21-8 colorspace_2.1-0 - [9] vctrs_0.6.1 generics_0.1.3 htmltools_0.5.5 yaml_2.3.7 -[13] utf8_1.2.3 rlang_1.1.0 pkgbuild_1.4.0 pkgdown_2.0.7 -[17] jquerylib_0.1.4 pillar_1.9.0 glue_1.6.2 DBI_1.1.3 -[21] readxl_1.4.2 lifecycle_1.0.3 stringr_1.5.0 munsell_0.5.0 -[25] gtable_0.3.3 cellranger_1.1.0 ragg_1.2.5 codetools_0.2-19 -[29] memoise_2.0.1 evaluate_0.20 inline_0.3.19 callr_3.7.3 -[33] fastmap_1.1.1 ps_1.7.4 lmtest_0.9-40 fansi_1.0.4 -[37] highr_0.10 scales_1.2.1 cachem_1.0.7 desc_1.4.2 -[41] jsonlite_1.8.4 systemfonts_1.0.4 fs_1.6.1 textshaping_0.3.6 -[45] gridExtra_2.3 ggplot2_3.4.2 digest_0.6.31 stringi_1.7.12 -[49] processx_3.8.0 dplyr_1.1.1 grid_4.2.3 rprojroot_2.0.3 -[53] cli_3.6.1 tools_4.2.3 magrittr_2.0.3 sass_0.4.5 -[57] tibble_3.2.1 crayon_1.5.2 pkgconfig_2.0.3 prettyunits_1.1.1 -[61] rmarkdown_2.21 R6_2.5.1 mclust_6.0.0 nlme_3.1-162 -[65] compiler_4.2.3 </code></pre> + [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 + [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 + [9] grid_4.3.0 fastmap_1.1.1 cellranger_1.1.0 rprojroot_2.0.3 +[13] jsonlite_1.8.4 processx_3.8.1 pkgbuild_1.4.0 deSolve_1.35 +[17] DBI_1.1.3 mclust_6.0.0 ps_1.7.5 gridExtra_2.3 +[21] purrr_1.0.1 fansi_1.0.4 scales_1.2.1 codetools_0.2-19 +[25] textshaping_0.3.6 jquerylib_0.1.4 cli_3.6.1 crayon_1.5.2 +[29] rlang_1.1.1 munsell_0.5.0 cachem_1.0.8 yaml_2.3.7 +[33] inline_0.3.19 tools_4.3.0 memoise_2.0.1 dplyr_1.1.2 +[37] colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1 +[41] zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2 +[45] ragg_1.2.5 callr_3.7.3 pkgconfig_2.0.3 desc_1.4.2 +[49] pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 gtable_0.3.3 +[53] glue_1.6.2 systemfonts_1.0.4 highr_0.10 xfun_0.39 +[57] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 +[61] nlme_3.1-162 rmarkdown_2.21 compiler_4.3.0 prettyunits_1.1.1 +[65] readxl_1.4.2 </code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> <pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64936316 kB</code></pre> +<pre><code>MemTotal: 64925476 kB</code></pre> </div> </div> </div> diff --git a/docs/dev/articles/prebuilt/2022_dmta_parent.html b/docs/dev/articles/prebuilt/2022_dmta_parent.html index 92259add..45a925b3 100644 --- a/docs/dev/articles/prebuilt/2022_dmta_parent.html +++ b/docs/dev/articles/prebuilt/2022_dmta_parent.html @@ -34,7 +34,7 @@ </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">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -136,7 +136,7 @@ with residue data on dimethenamid and dimethenamid-P</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change on 5 January -2023, last compiled on 16 April 2023</h4> +2023, last compiled on 19 Mai 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_dmta_parent.rmd" class="external-link"><code>vignettes/prebuilt/2022_dmta_parent.rmd</code></a></small> <div class="hidden name"><code>2022_dmta_parent.rmd</code></div> @@ -155,7 +155,7 @@ FOMC, DFOP and HS can 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 1.2.3. It contains the test data +<p>The mkin package is used in version 1.2.5. It contains the test data and the functions used in the evaluations. The <code>saemix</code> package is used as a backend for fitting the NLHM, but is also loaded to make the convergence plot function available.</p> @@ -1287,10 +1287,10 @@ Plot of the final NLHM DFOP fit <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_tc_no_ranef_k2</span><span class="op">)</span></span></code></pre></div> <pre><code>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 11:22:51 2023 -Date of summary: Sat Jan 28 11:22:52 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:27 2023 +Date of summary: Fri May 19 18:14:28 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1302,7 +1302,7 @@ Data: Model predictions using solution type analytical -Fitted in 3.74 s +Fitted in 4.477 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1463,10 +1463,10 @@ Hierarchical mkin fit of the SFO model with error model const </caption> <pre><code> 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 11:22:44 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:19 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - k_DMTA * DMTA @@ -1476,7 +1476,7 @@ Data: Model predictions using solution type analytical -Fitted in 0.982 s +Fitted in 1.091 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1535,10 +1535,10 @@ Hierarchical mkin fit of the SFO model with error model tc </caption> <pre><code> 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 11:22:46 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:21 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - k_DMTA * DMTA @@ -1548,7 +1548,7 @@ Data: Model predictions using solution type analytical -Fitted in 2.39 s +Fitted in 2.517 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1609,10 +1609,10 @@ Hierarchical mkin fit of the FOMC model with error model const </caption> <pre><code> 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 11:22:45 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:20 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA @@ -1622,7 +1622,7 @@ Data: Model predictions using solution type analytical -Fitted in 1.552 s +Fitted in 1.25 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1686,10 +1686,10 @@ Hierarchical mkin fit of the FOMC model with error model tc </caption> <pre><code> 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 11:22:46 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:21 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA @@ -1699,7 +1699,7 @@ Data: Model predictions using solution type analytical -Fitted in 2.764 s +Fitted in 2.666 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1765,10 +1765,10 @@ Hierarchical mkin fit of the DFOP model with error model const </caption> <pre><code> 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 11:22:45 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:20 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1780,7 +1780,7 @@ Data: Model predictions using solution type analytical -Fitted in 1.649 s +Fitted in 1.639 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1849,10 +1849,10 @@ Hierarchical mkin fit of the DFOP model with error model tc </caption> <pre><code> 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 11:22:46 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:22 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1864,7 +1864,7 @@ Data: Model predictions using solution type analytical -Fitted in 3.288 s +Fitted in 3.435 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1935,10 +1935,10 @@ Hierarchical mkin fit of the HS model with error model const </caption> <pre><code> 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 11:22:45 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:20 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - ifelse(time <= tb, k1, k2) * DMTA @@ -1948,7 +1948,7 @@ Data: Model predictions using solution type analytical -Fitted in 2.006 s +Fitted in 1.946 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -2017,10 +2017,10 @@ Hierarchical mkin fit of the HS model with error model tc </caption> <pre><code> 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 11:22:46 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:22 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - ifelse(time <= tb, k1, k2) * DMTA @@ -2030,7 +2030,7 @@ Data: Model predictions using solution type analytical -Fitted in 3.267 s +Fitted in 3.626 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -2144,13 +2144,13 @@ Convergence plot for the NLHM HS fit with two-component error <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.2.2 Patched (2022-11-10 r83330) +<pre><code>R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) -Running under: Debian GNU/Linux bookworm/sid +Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so +BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 +LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so; LAPACK version 3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -2160,35 +2160,37 @@ locale: [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C +time zone: Europe/Berlin +tzcode source: system (glibc) + attached base packages: [1] parallel stats graphics grDevices utils datasets methods [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_1.42 mkin_1.2.5 loaded via a namespace (and not attached): - [1] deSolve_1.34 zoo_1.8-11 tidyselect_1.2.0 xfun_0.35 - [5] bslib_0.4.2 purrr_1.0.0 lattice_0.20-45 colorspace_2.0-3 - [9] vctrs_0.5.1 generics_0.1.3 htmltools_0.5.4 yaml_2.3.6 -[13] utf8_1.2.2 rlang_1.0.6 pkgdown_2.0.7 jquerylib_0.1.4 -[17] pillar_1.8.1 glue_1.6.2 DBI_1.1.3 lifecycle_1.0.3 -[21] stringr_1.5.0 munsell_0.5.0 gtable_0.3.1 ragg_1.2.4 -[25] codetools_0.2-18 memoise_2.0.1 evaluate_0.19 fastmap_1.1.0 -[29] lmtest_0.9-40 fansi_1.0.3 highr_0.9 scales_1.2.1 -[33] cachem_1.0.6 desc_1.4.2 jsonlite_1.8.4 systemfonts_1.0.4 -[37] fs_1.5.2 textshaping_0.3.6 gridExtra_2.3 ggplot2_3.4.0 -[41] digest_0.6.31 stringi_1.7.8 dplyr_1.0.10 grid_4.2.2 -[45] rprojroot_2.0.3 cli_3.5.0 tools_4.2.2 magrittr_2.0.3 -[49] sass_0.4.4 tibble_3.1.8 pkgconfig_2.0.3 assertthat_0.2.1 -[53] rmarkdown_2.19 R6_2.5.1 mclust_6.0.0 nlme_3.1-161 -[57] compiler_4.2.2 </code></pre> + [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 + [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 + [9] grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4 +[13] DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 purrr_1.0.1 +[17] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 +[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 munsell_0.5.0 +[25] cachem_1.0.8 yaml_2.3.7 tools_4.3.0 memoise_2.0.1 +[29] dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2 +[33] R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 +[37] fs_1.6.2 ragg_1.2.5 pkgconfig_2.0.3 desc_1.4.2 +[41] pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 gtable_0.3.3 +[45] glue_1.6.2 systemfonts_1.0.4 highr_0.10 xfun_0.39 +[49] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 +[53] nlme_3.1-162 rmarkdown_2.21 compiler_4.3.0 </code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> <pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64940452 kB</code></pre> +<pre><code>MemTotal: 64925476 kB</code></pre> </div> </div> </div> diff --git a/docs/dev/articles/prebuilt/2022_dmta_pathway.html b/docs/dev/articles/prebuilt/2022_dmta_pathway.html index 959f3429..1861db06 100644 --- a/docs/dev/articles/prebuilt/2022_dmta_pathway.html +++ b/docs/dev/articles/prebuilt/2022_dmta_pathway.html @@ -34,7 +34,7 @@ </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">1.2.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -136,7 +136,7 @@ residue data on dimethenamid and dimethenamid-P</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change on 20 April 2023, -last compiled on 20 April 2023</h4> +last compiled on 19 Mai 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_dmta_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_dmta_pathway.rmd</code></a></small> <div class="hidden name"><code>2022_dmta_pathway.rmd</code></div> @@ -156,7 +156,7 @@ can 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 1.2.4, which is currently under +<p>The mkin package is used in version 1.2.5, which is currently under development. It contains the test data, and the functions used in the evaluations. The <code>saemix</code> package is used as a backend for fitting the NLHM, but is also loaded to make the convergence plot @@ -1972,13 +1972,13 @@ error<a class="anchor" aria-label="anchor" href="#improved-fit-of-the-sforb-path <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.2.3 (2023-03-15) +<pre><code>R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so +BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 +LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so; LAPACK version 3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -1988,36 +1988,39 @@ locale: [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C +time zone: Europe/Berlin +tzcode source: system (glibc) + attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.4 +[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.5 loaded via a namespace (and not attached): - [1] deSolve_1.35 zoo_1.8-12 tidyselect_1.2.0 xfun_0.38 - [5] bslib_0.4.2 purrr_1.0.1 lattice_0.21-8 colorspace_2.1-0 - [9] vctrs_0.6.1 generics_0.1.3 htmltools_0.5.5 yaml_2.3.7 -[13] utf8_1.2.3 rlang_1.1.0 pkgbuild_1.4.0 pkgdown_2.0.7 -[17] jquerylib_0.1.4 pillar_1.9.0 glue_1.6.2 DBI_1.1.3 -[21] lifecycle_1.0.3 stringr_1.5.0 munsell_0.5.0 gtable_0.3.3 -[25] ragg_1.2.5 codetools_0.2-19 memoise_2.0.1 evaluate_0.20 -[29] inline_0.3.19 callr_3.7.3 fastmap_1.1.1 ps_1.7.4 -[33] lmtest_0.9-40 fansi_1.0.4 highr_0.10 scales_1.2.1 -[37] cachem_1.0.7 desc_1.4.2 jsonlite_1.8.4 systemfonts_1.0.4 -[41] fs_1.6.1 textshaping_0.3.6 gridExtra_2.3 ggplot2_3.4.2 -[45] digest_0.6.31 stringi_1.7.12 processx_3.8.0 dplyr_1.1.1 -[49] grid_4.2.3 rprojroot_2.0.3 cli_3.6.1 tools_4.2.3 -[53] magrittr_2.0.3 sass_0.4.5 tibble_3.2.1 crayon_1.5.2 -[57] pkgconfig_2.0.3 prettyunits_1.1.1 rmarkdown_2.21 R6_2.5.1 -[61] mclust_6.0.0 nlme_3.1-162 compiler_4.2.3 </code></pre> + [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 + [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 + [9] grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4 +[13] processx_3.8.1 pkgbuild_1.4.0 deSolve_1.35 DBI_1.1.3 +[17] mclust_6.0.0 ps_1.7.5 gridExtra_2.3 purrr_1.0.1 +[21] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 +[25] jquerylib_0.1.4 cli_3.6.1 crayon_1.5.2 rlang_1.1.1 +[29] munsell_0.5.0 cachem_1.0.8 yaml_2.3.7 inline_0.3.19 +[33] tools_4.3.0 memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0 +[37] ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1 zoo_1.8-12 +[41] lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2 ragg_1.2.5 +[45] callr_3.7.3 pkgconfig_2.0.3 desc_1.4.2 pkgdown_2.0.7 +[49] bslib_0.4.2 pillar_1.9.0 gtable_0.3.3 glue_1.6.2 +[53] systemfonts_1.0.4 highr_0.10 xfun_0.39 tibble_3.2.1 +[57] lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 nlme_3.1-162 +[61] rmarkdown_2.21 compiler_4.3.0 prettyunits_1.1.1</code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> <pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64936316 kB</code></pre> +<pre><code>MemTotal: 64925476 kB</code></pre> </div> </div> </div> |