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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> diff --git a/docs/dev/articles/prebuilt/2023_mesotrione_parent.html b/docs/dev/articles/prebuilt/2023_mesotrione_parent.html new file mode 100644 index 00000000..e3f2794f --- /dev/null +++ b/docs/dev/articles/prebuilt/2023_mesotrione_parent.html @@ -0,0 +1,2564 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; 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class="page-header toc-ignore"> + <h1 data-toc-skip>Testing covariate modelling in hierarchical +parent degradation kinetics with residue data on mesotrione</h1> + <h4 data-toc-skip class="author">Johannes +Ranke</h4> + + <h4 data-toc-skip class="date">Last change on 4 August 2023, +last compiled on 10 August 2023</h4> + + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2023_mesotrione_parent.rmd" class="external-link"><code>vignettes/prebuilt/2023_mesotrione_parent.rmd</code></a></small> + <div class="hidden name"><code>2023_mesotrione_parent.rmd</code></div> + + </div> + + + +<div class="section level2"> +<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> +</h2> +<p>The purpose of this document is to test demonstrate how nonlinear +hierarchical models (NLHM) based on the parent degradation models SFO, +FOMC, DFOP and HS can be fitted with the mkin package, also considering +the influence of covariates like soil pH on different degradation +parameters. Because in some other case studies, the SFORB +parameterisation of biexponential decline has shown some advantages over +the DFOP parameterisation, SFORB was included in the list of tested +models as well.</p> +<p>The mkin package is used in version 1.2.6, which is contains the +functions that were used for 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> +<p>This document is processed with the <code>knitr</code> package, which +also provides the <code>kable</code> function that is used to improve +the display of tabular data in R markdown documents. For parallel +processing, the <code>parallel</code> package is used.</p> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span> +<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://yihui.org/knitr/" class="external-link">knitr</a></span><span class="op">)</span></span> +<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span> +<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">parallel</span><span class="op">)</span></span> +<span><span class="va">n_cores</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span></span> +<span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="va">cl</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makePSOCKcluster</a></span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span></span> +<span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span> +<span> <span class="va">cl</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makeForkCluster</a></span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span></span> +<span><span class="op">}</span></span></code></pre></div> +<div class="section level3"> +<h3 id="test-data">Test data<a class="anchor" aria-label="anchor" href="#test-data"></a> +</h3> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">data_file</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span></span> +<span> <span class="st">"testdata"</span>, <span class="st">"mesotrione_soil_efsa_2016.xlsx"</span>, package <span class="op">=</span> <span class="st">"mkin"</span><span class="op">)</span></span> +<span><span class="va">meso_ds</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/read_spreadsheet.html">read_spreadsheet</a></span><span class="op">(</span><span class="va">data_file</span>, parent_only <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<p>The following tables show the covariate data and the 18 datasets that +were read in from the spreadsheet file.</p> +<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">pH</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/attr.html" class="external-link">attr</a></span><span class="op">(</span><span class="va">meso_ds</span>, <span class="st">"covariates"</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="va">pH</span>, caption <span class="op">=</span> <span class="st">"Covariate data"</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<caption>Covariate data</caption> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">pH</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">Richmond</td> +<td align="right">6.2</td> +</tr> +<tr class="even"> +<td align="left">Richmond 2</td> +<td align="right">6.2</td> +</tr> +<tr class="odd"> +<td align="left">ERTC</td> +<td align="right">6.4</td> +</tr> +<tr class="even"> +<td align="left">Toulouse</td> +<td align="right">7.7</td> +</tr> +<tr class="odd"> +<td align="left">Picket Piece</td> +<td align="right">7.1</td> +</tr> +<tr class="even"> +<td align="left">721</td> +<td align="right">5.6</td> +</tr> +<tr class="odd"> +<td align="left">722</td> +<td align="right">5.7</td> +</tr> +<tr class="even"> +<td align="left">723</td> +<td align="right">5.4</td> +</tr> +<tr class="odd"> +<td align="left">724</td> +<td align="right">4.8</td> +</tr> +<tr class="even"> +<td align="left">725</td> +<td align="right">5.8</td> +</tr> +<tr class="odd"> +<td align="left">727</td> +<td align="right">5.1</td> +</tr> +<tr class="even"> +<td align="left">728</td> +<td align="right">5.9</td> +</tr> +<tr class="odd"> +<td align="left">729</td> +<td align="right">5.6</td> +</tr> +<tr class="even"> +<td align="left">730</td> +<td align="right">5.3</td> +</tr> +<tr class="odd"> +<td align="left">731</td> +<td align="right">6.1</td> +</tr> +<tr class="even"> +<td align="left">732</td> +<td align="right">5.0</td> +</tr> +<tr class="odd"> +<td align="left">741</td> +<td align="right">5.7</td> +</tr> +<tr class="even"> +<td align="left">742</td> +<td align="right">7.2</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw">for</span> <span class="op">(</span><span class="va">ds_name</span> <span class="kw">in</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">meso_ds</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span></span> +<span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mkin_long_to_wide.html">mkin_long_to_wide</a></span><span class="op">(</span><span class="va">meso_ds</span><span class="op">[[</span><span class="va">ds_name</span><span class="op">]</span><span class="op">]</span><span class="op">)</span>,</span> +<span> caption <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="va">ds_name</span><span class="op">)</span>,</span> +<span> booktabs <span class="op">=</span> <span class="cn">TRUE</span>, row.names <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="op">}</span></span></code></pre></div> +<table class="table"> +<caption>Dataset Richmond</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.000000</td> +<td align="right">91.00</td> +</tr> +<tr class="even"> +<td align="right">1.179050</td> +<td align="right">86.70</td> +</tr> +<tr class="odd"> +<td align="right">3.537149</td> +<td align="right">73.60</td> +</tr> +<tr class="even"> +<td align="right">7.074299</td> +<td align="right">61.50</td> +</tr> +<tr class="odd"> +<td align="right">10.611448</td> +<td align="right">55.70</td> +</tr> +<tr class="even"> +<td align="right">15.327647</td> +<td align="right">47.70</td> +</tr> +<tr class="odd"> +<td align="right">17.685747</td> +<td align="right">39.50</td> +</tr> +<tr class="even"> +<td align="right">24.760046</td> +<td align="right">29.80</td> +</tr> +<tr class="odd"> +<td align="right">35.371494</td> +<td align="right">19.60</td> +</tr> +<tr class="even"> +<td align="right">68.384889</td> +<td align="right">5.67</td> +</tr> +<tr class="odd"> +<td align="right">0.000000</td> +<td align="right">97.90</td> +</tr> +<tr class="even"> +<td align="right">1.179050</td> +<td align="right">96.40</td> +</tr> +<tr class="odd"> +<td align="right">3.537149</td> +<td align="right">89.10</td> +</tr> +<tr class="even"> +<td align="right">7.074299</td> +<td align="right">74.40</td> +</tr> +<tr class="odd"> +<td align="right">10.611448</td> +<td align="right">57.40</td> +</tr> +<tr class="even"> +<td align="right">15.327647</td> +<td align="right">46.30</td> +</tr> +<tr class="odd"> +<td align="right">18.864797</td> +<td align="right">35.50</td> +</tr> +<tr class="even"> +<td align="right">27.118146</td> +<td align="right">27.20</td> +</tr> +<tr class="odd"> +<td align="right">35.371494</td> +<td align="right">19.10</td> +</tr> +<tr class="even"> +<td align="right">74.280138</td> +<td align="right">6.50</td> +</tr> +<tr class="odd"> +<td align="right">108.472582</td> +<td align="right">3.40</td> +</tr> +<tr class="even"> +<td align="right">142.665027</td> +<td align="right">2.20</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset Richmond 2</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.000000</td> +<td align="right">96.0</td> +</tr> +<tr class="even"> +<td align="right">2.422004</td> +<td align="right">82.4</td> +</tr> +<tr class="odd"> +<td align="right">5.651343</td> +<td align="right">71.2</td> +</tr> +<tr class="even"> +<td align="right">8.073348</td> +<td align="right">53.1</td> +</tr> +<tr class="odd"> +<td align="right">11.302687</td> +<td align="right">48.5</td> +</tr> +<tr class="even"> +<td align="right">16.954030</td> +<td align="right">33.4</td> +</tr> +<tr class="odd"> +<td align="right">22.605373</td> +<td align="right">24.2</td> +</tr> +<tr class="even"> +<td align="right">45.210746</td> +<td align="right">11.9</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset ERTC</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.000000</td> +<td align="right">99.9</td> +</tr> +<tr class="even"> +<td align="right">2.755193</td> +<td align="right">80.0</td> +</tr> +<tr class="odd"> +<td align="right">6.428782</td> +<td align="right">42.1</td> +</tr> +<tr class="even"> +<td align="right">9.183975</td> +<td align="right">50.1</td> +</tr> +<tr class="odd"> +<td align="right">12.857565</td> +<td align="right">28.4</td> +</tr> +<tr class="even"> +<td align="right">19.286347</td> +<td align="right">39.8</td> +</tr> +<tr class="odd"> +<td align="right">25.715130</td> +<td align="right">29.9</td> +</tr> +<tr class="even"> +<td align="right">51.430259</td> +<td align="right">2.5</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset Toulouse</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.000000</td> +<td align="right">96.8</td> +</tr> +<tr class="even"> +<td align="right">2.897983</td> +<td align="right">63.3</td> +</tr> +<tr class="odd"> +<td align="right">6.761960</td> +<td align="right">22.3</td> +</tr> +<tr class="even"> +<td align="right">9.659942</td> +<td align="right">16.6</td> +</tr> +<tr class="odd"> +<td align="right">13.523919</td> +<td align="right">16.1</td> +</tr> +<tr class="even"> +<td align="right">20.285879</td> +<td align="right">17.2</td> +</tr> +<tr class="odd"> +<td align="right">27.047838</td> +<td align="right">1.8</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset Picket Piece</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.000000</td> +<td align="right">102.0</td> +</tr> +<tr class="even"> +<td align="right">2.841195</td> +<td align="right">73.7</td> +</tr> +<tr class="odd"> +<td align="right">6.629454</td> +<td align="right">35.5</td> +</tr> +<tr class="even"> +<td align="right">9.470649</td> +<td align="right">31.8</td> +</tr> +<tr class="odd"> +<td align="right">13.258909</td> +<td align="right">18.0</td> +</tr> +<tr class="even"> +<td align="right">19.888364</td> +<td align="right">3.7</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 721</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">86.4</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">61.4</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">49.8</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">41.0</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">35.1</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 722</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">90.3</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">52.1</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">37.4</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">21.2</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">14.3</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 723</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">89.3</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">70.8</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">51.1</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">42.7</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">26.7</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 724</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.000000</td> +<td align="right">89.4</td> +</tr> +<tr class="even"> +<td align="right">9.008208</td> +<td align="right">65.2</td> +</tr> +<tr class="odd"> +<td align="right">18.016415</td> +<td align="right">55.8</td> +</tr> +<tr class="even"> +<td align="right">27.024623</td> +<td align="right">46.0</td> +</tr> +<tr class="odd"> +<td align="right">36.032831</td> +<td align="right">41.7</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 725</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">89.0</td> +</tr> +<tr class="even"> +<td align="right">10.99058</td> +<td align="right">35.4</td> +</tr> +<tr class="odd"> +<td align="right">21.98116</td> +<td align="right">18.6</td> +</tr> +<tr class="even"> +<td align="right">32.97174</td> +<td align="right">11.6</td> +</tr> +<tr class="odd"> +<td align="right">43.96232</td> +<td align="right">7.6</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 727</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">91.3</td> +</tr> +<tr class="even"> +<td align="right">10.96104</td> +<td align="right">63.2</td> +</tr> +<tr class="odd"> +<td align="right">21.92209</td> +<td align="right">51.1</td> +</tr> +<tr class="even"> +<td align="right">32.88313</td> +<td align="right">42.0</td> +</tr> +<tr class="odd"> +<td align="right">43.84417</td> +<td align="right">40.8</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 728</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">91.8</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">43.6</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">22.0</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">15.9</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">8.8</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 729</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">91.6</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">60.5</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">43.5</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">28.4</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">20.5</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 730</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">92.7</td> +</tr> +<tr class="even"> +<td align="right">11.07446</td> +<td align="right">58.9</td> +</tr> +<tr class="odd"> +<td align="right">22.14893</td> +<td align="right">44.0</td> +</tr> +<tr class="even"> +<td align="right">33.22339</td> +<td align="right">46.0</td> +</tr> +<tr class="odd"> +<td align="right">44.29785</td> +<td align="right">29.3</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 731</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">92.1</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">64.4</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">45.3</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">33.6</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">23.5</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 732</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">90.3</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">58.2</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">40.1</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">33.1</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">25.8</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 741</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">90.3</td> +</tr> +<tr class="even"> +<td align="right">10.84712</td> +<td align="right">68.7</td> +</tr> +<tr class="odd"> +<td align="right">21.69424</td> +<td align="right">58.0</td> +</tr> +<tr class="even"> +<td align="right">32.54136</td> +<td align="right">52.2</td> +</tr> +<tr class="odd"> +<td align="right">43.38848</td> +<td align="right">48.0</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 742</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">92.0</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">60.9</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">36.2</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">18.3</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">8.7</td> +</tr> +</tbody> +</table> +</div> +</div> +<div class="section level2"> +<h2 id="separate-evaluations">Separate evaluations<a class="anchor" aria-label="anchor" href="#separate-evaluations"></a> +</h2> +<p>In order to obtain suitable starting parameters for the NLHM fits, +separate fits of the five models to the data for each soil are generated +using the <code>mmkin</code> function from the mkin package. In a first +step, constant variance is assumed. Convergence is checked with the +<code>status</code> function.</p> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">deg_mods</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"SFORB"</span>, <span class="st">"HS"</span><span class="op">)</span></span> +<span><span class="va">f_sep_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span></span> +<span> <span class="va">deg_mods</span>,</span> +<span> <span class="va">meso_ds</span>,</span> +<span> error_model <span class="op">=</span> <span class="st">"const"</span>,</span> +<span> cluster <span class="op">=</span> <span class="va">cl</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/status.html">status</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">]</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">Richmond</th> +<th align="left">Richmond 2</th> +<th align="left">ERTC</th> +<th align="left">Toulouse</th> +<th align="left">Picket Piece</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/status.html">status</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">18</span><span class="op">]</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<colgroup> +<col width="10%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +</colgroup> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">721</th> +<th align="left">722</th> +<th align="left">723</th> +<th align="left">724</th> +<th align="left">725</th> +<th align="left">727</th> +<th align="left">728</th> +<th align="left">729</th> +<th align="left">730</th> +<th align="left">731</th> +<th align="left">732</th> +<th align="left">741</th> +<th align="left">742</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +</tbody> +</table> +<p>In the tables above, OK indicates convergence and C indicates failure +to converge. Most separate fits with constant variance converged, with +the exception of two FOMC fits, one SFORB fit and one HS fit.</p> +<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_sep_const</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/status.html">status</a></span><span class="op">(</span><span class="va">f_sep_tc</span><span class="op">[</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">]</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">Richmond</th> +<th align="left">Richmond 2</th> +<th align="left">ERTC</th> +<th align="left">Toulouse</th> +<th align="left">Picket Piece</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/status.html">status</a></span><span class="op">(</span><span class="va">f_sep_tc</span><span class="op">[</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">18</span><span class="op">]</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<colgroup> +<col width="10%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +</colgroup> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">721</th> +<th align="left">722</th> +<th align="left">723</th> +<th align="left">724</th> +<th align="left">725</th> +<th align="left">727</th> +<th align="left">728</th> +<th align="left">729</th> +<th align="left">730</th> +<th align="left">731</th> +<th align="left">732</th> +<th align="left">741</th> +<th align="left">742</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +</tbody> +</table> +<p>With the two-component error model, the set of fits that did not +converge is larger, with convergence problems appearing for a number of +non-SFO fits.</p> +</div> +<div class="section level2"> +<h2 id="hierarchical-model-fits-without-covariate-effect">Hierarchical model fits without covariate effect<a class="anchor" aria-label="anchor" href="#hierarchical-model-fits-without-covariate-effect"></a> +</h2> +<p>The following code fits hierarchical kinetic models for the ten +combinations of the five different degradation models with the two +different error models in parallel.</p> +<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_saem_1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mhmkin.html">mhmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">f_sep_const</span>, <span class="va">f_sep_tc</span><span class="op">)</span>, cluster <span class="op">=</span> <span class="va">cl</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/status.html">status</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">const</th> +<th align="left">tc</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +</tbody> +</table> +<p>All fits terminate without errors (status OK).</p> +<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">npar</th> +<th align="right">AIC</th> +<th align="right">BIC</th> +<th align="right">Lik</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO const</td> +<td align="right">5</td> +<td align="right">800.0</td> +<td align="right">804.5</td> +<td align="right">-395.0</td> +</tr> +<tr class="even"> +<td align="left">SFO tc</td> +<td align="right">6</td> +<td align="right">801.9</td> +<td align="right">807.2</td> +<td align="right">-394.9</td> +</tr> +<tr class="odd"> +<td align="left">FOMC const</td> +<td align="right">7</td> +<td align="right">787.4</td> +<td align="right">793.6</td> +<td align="right">-386.7</td> +</tr> +<tr class="even"> +<td align="left">FOMC tc</td> +<td align="right">8</td> +<td align="right">788.9</td> +<td align="right">796.1</td> +<td align="right">-386.5</td> +</tr> +<tr class="odd"> +<td align="left">DFOP const</td> +<td align="right">9</td> +<td align="right">787.6</td> +<td align="right">795.6</td> +<td align="right">-384.8</td> +</tr> +<tr class="even"> +<td align="left">SFORB const</td> +<td align="right">9</td> +<td align="right">787.4</td> +<td align="right">795.4</td> +<td align="right">-384.7</td> +</tr> +<tr class="odd"> +<td align="left">HS const</td> +<td align="right">9</td> +<td align="right">781.9</td> +<td align="right">789.9</td> +<td align="right">-382.0</td> +</tr> +<tr class="even"> +<td align="left">DFOP tc</td> +<td align="right">10</td> +<td align="right">787.4</td> +<td align="right">796.3</td> +<td align="right">-383.7</td> +</tr> +<tr class="odd"> +<td align="left">SFORB tc</td> +<td align="right">10</td> +<td align="right">795.8</td> +<td align="right">804.7</td> +<td align="right">-387.9</td> +</tr> +<tr class="even"> +<td align="left">HS tc</td> +<td align="right">10</td> +<td align="right">783.7</td> +<td align="right">792.7</td> +<td align="right">-381.9</td> +</tr> +</tbody> +</table> +<p>The model comparisons show that the fits with constant variance are +consistently preferable to the corresponding fits with two-component +error for these data. This is confirmed by the fact that the parameter +<code>b.1</code> (the relative standard deviation in the fits obtained +with the saemix package), is ill-defined in all fits.</p> +<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<colgroup> +<col width="6%"> +<col width="44%"> +<col width="49%"> +</colgroup> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">const</th> +<th align="left">tc</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left">sd(meso_0)</td> +<td align="left">sd(meso_0), b.1</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left">sd(meso_0), sd(log_beta)</td> +<td align="left">sd(meso_0), sd(log_beta), b.1</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left">sd(meso_0), sd(log_k1)</td> +<td align="left">sd(meso_0), sd(g_qlogis), b.1</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left">sd(meso_free_0), sd(log_k_meso_free_bound)</td> +<td align="left">sd(meso_free_0), sd(log_k_meso_free_bound), b.1</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left">sd(meso_0)</td> +<td align="left">sd(meso_0), b.1</td> +</tr> +</tbody> +</table> +<p>For obtaining fits with only well-defined random effects, we update +the set of fits, excluding random effects that were ill-defined +according to the <code>illparms</code> function.</p> +<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_saem_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_1</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/status.html">status</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">const</th> +<th align="left">tc</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +</tbody> +</table> +<p>The updated fits terminate without errors.</p> +<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">const</th> +<th align="left">tc</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left"></td> +<td align="left">b.1</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left"></td> +<td align="left">b.1</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left"></td> +<td align="left">b.1</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left"></td> +<td align="left">b.1</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left"></td> +<td align="left"></td> +</tr> +</tbody> +</table> +<p>No ill-defined errors remain in the fits with constant variance.</p> +</div> +<div class="section level2"> +<h2 id="hierarchical-model-fits-with-covariate-effect">Hierarchical model fits with covariate effect<a class="anchor" aria-label="anchor" href="#hierarchical-model-fits-with-covariate-effect"></a> +</h2> +<p>In the following sections, hierarchical fits including a model for +the influence of pH on selected degradation parameters are shown for all +parent models. Constant variance is selected as the error model based on +the fits without covariate effects. Random effects that were ill-defined +in the fits without pH influence are excluded. A potential influence of +the soil pH is only included for parameters with a well-defined random +effect, because experience has shown that only for such parameters a +significant pH effect could be found.</p> +<div class="section level3"> +<h3 id="sfo">SFO<a class="anchor" aria-label="anchor" href="#sfo"></a> +</h3> +<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">sfo_pH</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, no_random_effect <span class="op">=</span> <span class="st">"meso_0"</span>, covariates <span class="op">=</span> <span class="va">pH</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_k_meso</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb17"><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">sfo_pH</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_0</td> +<td align="right">91.35</td> +<td align="right">89.27</td> +<td align="right">93.43</td> +</tr> +<tr class="even"> +<td align="left">log_k_meso</td> +<td align="right">-6.66</td> +<td align="right">-7.97</td> +<td align="right">-5.35</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_k_meso)</td> +<td align="right">0.59</td> +<td align="right">0.37</td> +<td align="right">0.81</td> +</tr> +<tr class="even"> +<td align="left">a.1</td> +<td align="right">5.48</td> +<td align="right">4.71</td> +<td align="right">6.24</td> +</tr> +<tr class="odd"> +<td align="left">SD.log_k_meso</td> +<td align="right">0.35</td> +<td align="right">0.23</td> +<td align="right">0.47</td> +</tr> +</tbody> +</table> +<p>The parameter showing the pH influence in the above table is +<code>beta_pH(log_k_meso)</code>. Its confidence interval does not +include zero, indicating that the influence of soil pH on the log of the +degradation rate constant is significantly greater than zero.</p> +<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="st">"const"</span><span class="op">]</span><span class="op">]</span>, <span class="va">sfo_pH</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code>Data: 116 observations of 1 variable(s) grouped in 18 datasets + + npar AIC BIC Lik Chisq Df Pr(>Chisq) +f_saem_2[["SFO", "const"]] 4 797.56 801.12 -394.78 +sfo_pH 5 783.09 787.54 -386.54 16.473 1 4.934e-05 *** +--- +Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code></pre> +<p>The comparison with the SFO fit without covariate effect confirms +that considering the soil pH improves the model, both by comparison of +AIC and BIC and by the likelihood ratio test.</p> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sfo_pH</span><span class="op">)</span></span></code></pre></div> +<p><img src="2023_mesotrione_parent_files/figure-html/unnamed-chunk-8-1.png" width="700" style="display: block; margin: auto;"></p> +<p>Endpoints for a model with covariates are by default calculated for +the median of the covariate values. This quantile can be adapted, or a +specific covariate value can be given as shown below.</p> +<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">sfo_pH</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +50% 5.75 + +$distimes + DT50 DT90 +meso 18.52069 61.52441</code></pre> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">sfo_pH</span>, covariate_quantile <span class="op">=</span> <span class="fl">0.9</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +90% 7.13 + +$distimes + DT50 DT90 +meso 8.237019 27.36278</code></pre> +<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">sfo_pH</span>, covariates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>pH <span class="op">=</span> <span class="fl">7.0</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +User 7 + +$distimes + DT50 DT90 +meso 8.89035 29.5331</code></pre> +</div> +<div class="section level3"> +<h3 id="fomc">FOMC<a class="anchor" aria-label="anchor" href="#fomc"></a> +</h3> +<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">fomc_pH</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, no_random_effect <span class="op">=</span> <span class="st">"meso_0"</span>, covariates <span class="op">=</span> <span class="va">pH</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_alpha</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fomc_pH</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_0</td> +<td align="right">92.84</td> +<td align="right">90.75</td> +<td align="right">94.93</td> +</tr> +<tr class="even"> +<td align="left">log_alpha</td> +<td align="right">-2.21</td> +<td align="right">-3.49</td> +<td align="right">-0.92</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_alpha)</td> +<td align="right">0.58</td> +<td align="right">0.37</td> +<td align="right">0.79</td> +</tr> +<tr class="even"> +<td align="left">log_beta</td> +<td align="right">4.21</td> +<td align="right">3.44</td> +<td align="right">4.99</td> +</tr> +<tr class="odd"> +<td align="left">a.1</td> +<td align="right">5.03</td> +<td align="right">4.32</td> +<td align="right">5.73</td> +</tr> +<tr class="even"> +<td align="left">SD.log_alpha</td> +<td align="right">0.00</td> +<td align="right">-23.77</td> +<td align="right">23.78</td> +</tr> +<tr class="odd"> +<td align="left">SD.log_beta</td> +<td align="right">0.37</td> +<td align="right">0.01</td> +<td align="right">0.74</td> +</tr> +</tbody> +</table> +<p>As in the case of SFO, the confidence interval of the slope parameter +(here <code>beta_pH(log_alpha)</code>) quantifying the influence of soil +pH does not include zero, and the model comparison clearly indicates +that the model with covariate influence is preferable. However, the +random effect for <code>alpha</code> is not well-defined any more after +inclusion of the covariate effect (the confidence interval of +<code>SD.log_alpha</code> includes zero).</p> +<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">fomc_pH</span><span class="op">)</span></span></code></pre></div> +<pre><code>[1] "sd(log_alpha)"</code></pre> +<p>Therefore, the model is updated without this random effect, and no +ill-defined parameters remain.</p> +<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">fomc_pH_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">fomc_pH</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_0"</span>, <span class="st">"log_alpha"</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">fomc_pH_2</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="st">"const"</span><span class="op">]</span><span class="op">]</span>, <span class="va">fomc_pH</span>, <span class="va">fomc_pH_2</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code>Data: 116 observations of 1 variable(s) grouped in 18 datasets + + npar AIC BIC Lik Chisq Df Pr(>Chisq) +f_saem_2[["FOMC", "const"]] 5 783.25 787.71 -386.63 +fomc_pH_2 6 767.49 772.83 -377.75 17.762 1 2.503e-05 *** +fomc_pH 7 770.07 776.30 -378.04 0.000 1 1 +--- +Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code></pre> +<p>Model comparison indicates that including pH dependence significantly +improves the fit, and that the reduced model with covariate influence +results in the most preferable FOMC fit.</p> +<div class="sourceCode" id="cb34"><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">fomc_pH_2</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_0</td> +<td align="right">93.05</td> +<td align="right">90.98</td> +<td align="right">95.13</td> +</tr> +<tr class="even"> +<td align="left">log_alpha</td> +<td align="right">-2.91</td> +<td align="right">-4.18</td> +<td align="right">-1.63</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_alpha)</td> +<td align="right">0.66</td> +<td align="right">0.44</td> +<td align="right">0.87</td> +</tr> +<tr class="even"> +<td align="left">log_beta</td> +<td align="right">3.95</td> +<td align="right">3.29</td> +<td align="right">4.62</td> +</tr> +<tr class="odd"> +<td align="left">a.1</td> +<td align="right">4.98</td> +<td align="right">4.28</td> +<td align="right">5.68</td> +</tr> +<tr class="even"> +<td align="left">SD.log_beta</td> +<td align="right">0.40</td> +<td align="right">0.26</td> +<td align="right">0.54</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fomc_pH_2</span><span class="op">)</span></span></code></pre></div> +<p><img src="2023_mesotrione_parent_files/figure-html/unnamed-chunk-14-1.png" width="700" style="display: block; margin: auto;"></p> +<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fomc_pH_2</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +50% 5.75 + +$distimes + DT50 DT90 DT50back +meso 17.30248 82.91343 24.95943</code></pre> +<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fomc_pH_2</span>, covariates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>pH <span class="op">=</span> <span class="fl">7</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +User 7 + +$distimes + DT50 DT90 DT50back +meso 6.986239 27.02927 8.136621</code></pre> +</div> +<div class="section level3"> +<h3 id="dfop">DFOP<a class="anchor" aria-label="anchor" href="#dfop"></a> +</h3> +<p>In the DFOP fits without covariate effects, random effects for two +degradation parameters (<code>k2</code> and <code>g</code>) were +identifiable.</p> +<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="st">"const"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_0</td> +<td align="right">93.61</td> +<td align="right">91.58</td> +<td align="right">95.63</td> +</tr> +<tr class="even"> +<td align="left">log_k1</td> +<td align="right">-1.53</td> +<td align="right">-2.27</td> +<td align="right">-0.79</td> +</tr> +<tr class="odd"> +<td align="left">log_k2</td> +<td align="right">-3.42</td> +<td align="right">-3.73</td> +<td align="right">-3.11</td> +</tr> +<tr class="even"> +<td align="left">g_qlogis</td> +<td align="right">-1.67</td> +<td align="right">-2.57</td> +<td align="right">-0.77</td> +</tr> +<tr class="odd"> +<td align="left">a.1</td> +<td align="right">4.74</td> +<td align="right">4.02</td> +<td align="right">5.45</td> +</tr> +<tr class="even"> +<td align="left">SD.log_k2</td> +<td align="right">0.60</td> +<td align="right">0.38</td> +<td align="right">0.81</td> +</tr> +<tr class="odd"> +<td align="left">SD.g_qlogis</td> +<td align="right">0.94</td> +<td align="right">0.33</td> +<td align="right">1.54</td> +</tr> +</tbody> +</table> +<p>A fit with pH dependent degradation parameters was obtained by +excluding the same random effects as in the refined DFOP fit without +covariate influence, and including covariate models for the two +identifiable parameters <code>k2</code> and <code>g</code>.</p> +<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">dfop_pH</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_0"</span>, <span class="st">"log_k1"</span><span class="op">)</span>,</span> +<span> covariates <span class="op">=</span> <span class="va">pH</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_k2</span> <span class="op">~</span> <span class="va">pH</span>, <span class="va">g_qlogis</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<p>The corresponding parameters for the influence of soil pH are +<code>beta_pH(log_k2)</code> for the influence of soil pH on +<code>k2</code>, and <code>beta_pH(g_qlogis)</code> for its influence on +<code>g</code>.</p> +<div class="sourceCode" id="cb42"><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">dfop_pH</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_0</td> +<td align="right">92.84</td> +<td align="right">90.85</td> +<td align="right">94.84</td> +</tr> +<tr class="even"> +<td align="left">log_k1</td> +<td align="right">-2.82</td> +<td align="right">-3.09</td> +<td align="right">-2.54</td> +</tr> +<tr class="odd"> +<td align="left">log_k2</td> +<td align="right">-11.48</td> +<td align="right">-15.32</td> +<td align="right">-7.64</td> +</tr> +<tr class="even"> +<td align="left">beta_pH(log_k2)</td> +<td align="right">1.31</td> +<td align="right">0.69</td> +<td align="right">1.92</td> +</tr> +<tr class="odd"> +<td align="left">g_qlogis</td> +<td align="right">3.13</td> +<td align="right">0.47</td> +<td align="right">5.80</td> +</tr> +<tr class="even"> +<td align="left">beta_pH(g_qlogis)</td> +<td align="right">-0.57</td> +<td align="right">-1.04</td> +<td align="right">-0.09</td> +</tr> +<tr class="odd"> +<td align="left">a.1</td> +<td align="right">4.96</td> +<td align="right">4.26</td> +<td align="right">5.65</td> +</tr> +<tr class="even"> +<td align="left">SD.log_k2</td> +<td align="right">0.76</td> +<td align="right">0.47</td> +<td align="right">1.05</td> +</tr> +<tr class="odd"> +<td align="left">SD.g_qlogis</td> +<td align="right">0.01</td> +<td align="right">-9.96</td> +<td align="right">9.97</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">dfop_pH</span><span class="op">)</span></span></code></pre></div> +<pre><code>[1] "sd(g_qlogis)"</code></pre> +<p>Confidence intervals for neither of them include zero, indicating a +significant difference from zero. However, the random effect for +<code>g</code> is now ill-defined. The fit is updated without this +ill-defined random effect.</p> +<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">dfop_pH_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">dfop_pH</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_0"</span>, <span class="st">"log_k1"</span>, <span class="st">"g_qlogis"</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">dfop_pH_2</span><span class="op">)</span></span></code></pre></div> +<pre><code>[1] "beta_pH(g_qlogis)"</code></pre> +<p>Now, the slope parameter for the pH effect on <code>g</code> is +ill-defined. Therefore, another attempt is made without the +corresponding covariate model.</p> +<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">dfop_pH_3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_0"</span>, <span class="st">"log_k1"</span><span class="op">)</span>,</span> +<span> covariates <span class="op">=</span> <span class="va">pH</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_k2</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">dfop_pH_3</span><span class="op">)</span></span></code></pre></div> +<pre><code>[1] "sd(g_qlogis)"</code></pre> +<p>As the random effect for <code>g</code> is again ill-defined, the fit +is repeated without it.</p> +<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">dfop_pH_4</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">dfop_pH_3</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_0"</span>, <span class="st">"log_k1"</span>, <span class="st">"g_qlogis"</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">dfop_pH_4</span><span class="op">)</span></span></code></pre></div> +<p>While no ill-defined parameters remain, model comparison suggests +that the previous model <code>dfop_pH_2</code> with two pH dependent +parameters is preferable, based on information criteria as well as based +on the likelihood ratio test.</p> +<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="st">"const"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dfop_pH</span>, <span class="va">dfop_pH_2</span>, <span class="va">dfop_pH_3</span>, <span class="va">dfop_pH_4</span><span class="op">)</span></span></code></pre></div> +<pre><code>Data: 116 observations of 1 variable(s) grouped in 18 datasets + + npar AIC BIC Lik +f_saem_2[["DFOP", "const"]] 7 782.94 789.18 -384.47 +dfop_pH_4 7 767.35 773.58 -376.68 +dfop_pH_2 8 765.14 772.26 -374.57 +dfop_pH_3 8 769.00 776.12 -376.50 +dfop_pH 9 769.10 777.11 -375.55</code></pre> +<div class="sourceCode" id="cb52"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">dfop_pH_2</span>, <span class="va">dfop_pH_4</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code>Data: 116 observations of 1 variable(s) grouped in 18 datasets + + npar AIC BIC Lik Chisq Df Pr(>Chisq) +dfop_pH_4 7 767.35 773.58 -376.68 +dfop_pH_2 8 765.14 772.26 -374.57 4.2153 1 0.04006 * +--- +Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code></pre> +<p>When focussing on parameter identifiability using the test if the +confidence interval includes zero, <code>dfop_pH_4</code> would still be +the preferred model. However, it should be kept in mind that parameter +confidence intervals are constructed using a simple linearisation of the +likelihood. As the confidence interval of the random effect for +<code>g</code> only marginally includes zero, it is suggested that this +is acceptable, and that <code>dfop_pH_2</code> can be considered the +most preferable model.</p> +<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">dfop_pH_2</span><span class="op">)</span></span></code></pre></div> +<p><img src="2023_mesotrione_parent_files/figure-html/unnamed-chunk-19-1.png" width="700" style="display: block; margin: auto;"></p> +<div class="sourceCode" id="cb55"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">dfop_pH_2</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +50% 5.75 + +$distimes + DT50 DT90 DT50back DT50_k1 DT50_k2 +meso 18.36876 73.51841 22.13125 4.191901 23.98672</code></pre> +<div class="sourceCode" id="cb57"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">dfop_pH_2</span>, covariates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>pH <span class="op">=</span> <span class="fl">7</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +User 7 + +$distimes + DT50 DT90 DT50back DT50_k1 DT50_k2 +meso 8.346428 28.34437 8.532507 4.191901 8.753618</code></pre> +</div> +<div class="section level3"> +<h3 id="sforb">SFORB<a class="anchor" aria-label="anchor" href="#sforb"></a> +</h3> +<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">sforb_pH</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span><span class="st">"SFORB"</span>, <span class="op">]</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_free_0"</span>, <span class="st">"log_k_meso_free_bound"</span><span class="op">)</span>,</span> +<span> covariates <span class="op">=</span> <span class="va">pH</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_k_meso_free</span> <span class="op">~</span> <span class="va">pH</span>, <span class="va">log_k_meso_bound_free</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">sforb_pH</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_free_0</td> +<td align="right">93.42</td> +<td align="right">91.32</td> +<td align="right">95.52</td> +</tr> +<tr class="even"> +<td align="left">log_k_meso_free</td> +<td align="right">-5.37</td> +<td align="right">-6.94</td> +<td align="right">-3.81</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_k_meso_free)</td> +<td align="right">0.42</td> +<td align="right">0.18</td> +<td align="right">0.67</td> +</tr> +<tr class="even"> +<td align="left">log_k_meso_free_bound</td> +<td align="right">-3.49</td> +<td align="right">-4.92</td> +<td align="right">-2.05</td> +</tr> +<tr class="odd"> +<td align="left">log_k_meso_bound_free</td> +<td align="right">-9.98</td> +<td align="right">-19.22</td> +<td align="right">-0.74</td> +</tr> +<tr class="even"> +<td align="left">beta_pH(log_k_meso_bound_free)</td> +<td align="right">1.23</td> +<td align="right">-0.21</td> +<td align="right">2.67</td> +</tr> +<tr class="odd"> +<td align="left">a.1</td> +<td align="right">4.90</td> +<td align="right">4.18</td> +<td align="right">5.63</td> +</tr> +<tr class="even"> +<td align="left">SD.log_k_meso_free</td> +<td align="right">0.35</td> +<td align="right">0.23</td> +<td align="right">0.47</td> +</tr> +<tr class="odd"> +<td align="left">SD.log_k_meso_bound_free</td> +<td align="right">0.13</td> +<td align="right">-1.95</td> +<td align="right">2.20</td> +</tr> +</tbody> +</table> +<p>The confidence interval of +<code>beta_pH(log_k_meso_bound_free)</code> includes zero, indicating +that the influence of soil pH on <code>k_meso_bound_free</code> cannot +reliably be quantified. Also, the confidence interval for the random +effect on this parameter (<code>SD.log_k_meso_bound_free</code>) +includes zero.</p> +<p>Using the <code>illparms</code> function, these ill-defined +parameters can be found more conveniently.</p> +<div class="sourceCode" id="cb61"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_pH</span><span class="op">)</span></span></code></pre></div> +<pre><code>[1] "sd(log_k_meso_bound_free)" "beta_pH(log_k_meso_bound_free)"</code></pre> +<p>To remove the ill-defined parameters, a second variant of the SFORB +model with pH influence is fitted. No ill-defined parameters remain.</p> +<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">sforb_pH_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">sforb_pH</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_free_0"</span>, <span class="st">"log_k_meso_free_bound"</span>, <span class="st">"log_k_meso_bound_free"</span><span class="op">)</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_k_meso_free</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_pH_2</span><span class="op">)</span></span></code></pre></div> +<p>The model comparison of the SFORB fits includes the refined model +without covariate effect, and both versions of the SFORB fit with +covariate effect.</p> +<div class="sourceCode" id="cb64"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"SFORB"</span>, <span class="st">"const"</span><span class="op">]</span><span class="op">]</span>, <span class="va">sforb_pH</span>, <span class="va">sforb_pH_2</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code>Data: 116 observations of 1 variable(s) grouped in 18 datasets + + npar AIC BIC Lik Chisq Df Pr(>Chisq) +f_saem_2[["SFORB", "const"]] 7 783.40 789.63 -384.70 +sforb_pH_2 7 770.94 777.17 -378.47 12.4616 0 +sforb_pH 9 768.81 776.83 -375.41 6.1258 2 0.04675 * +--- +Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code></pre> +<p>The first model including pH influence is preferable based on +information criteria and the likelihood ratio test. However, as it is +not fully identifiable, the second model is selected.</p> +<div class="sourceCode" id="cb66"><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">sforb_pH_2</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_free_0</td> +<td align="right">93.32</td> +<td align="right">91.16</td> +<td align="right">95.48</td> +</tr> +<tr class="even"> +<td align="left">log_k_meso_free</td> +<td align="right">-6.15</td> +<td align="right">-7.43</td> +<td align="right">-4.86</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_k_meso_free)</td> +<td align="right">0.54</td> +<td align="right">0.33</td> +<td align="right">0.75</td> +</tr> +<tr class="even"> +<td align="left">log_k_meso_free_bound</td> +<td align="right">-3.80</td> +<td align="right">-5.20</td> +<td align="right">-2.40</td> +</tr> +<tr class="odd"> +<td align="left">log_k_meso_bound_free</td> +<td align="right">-2.95</td> +<td align="right">-4.26</td> +<td align="right">-1.64</td> +</tr> +<tr class="even"> +<td align="left">a.1</td> +<td align="right">5.08</td> +<td align="right">4.38</td> +<td align="right">5.79</td> +</tr> +<tr class="odd"> +<td align="left">SD.log_k_meso_free</td> +<td align="right">0.33</td> +<td align="right">0.22</td> +<td align="right">0.45</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb67"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sforb_pH_2</span><span class="op">)</span></span></code></pre></div> +<p><img src="2023_mesotrione_parent_files/figure-html/unnamed-chunk-25-1.png" width="700" style="display: block; margin: auto;"></p> +<div class="sourceCode" id="cb68"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">sforb_pH_2</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +50% 5.75 + +$ff +meso_free + 1 + +$SFORB + meso_b1 meso_b2 meso_g +0.09735824 0.02631699 0.31602120 + +$distimes + DT50 DT90 DT50back DT50_meso_b1 DT50_meso_b2 +meso 16.86549 73.15824 22.02282 7.119554 26.33839</code></pre> +<div class="sourceCode" id="cb70"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">sforb_pH_2</span>, covariates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>pH <span class="op">=</span> <span class="fl">7</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +User 7 + +$ff +meso_free + 1 + +$SFORB + meso_b1 meso_b2 meso_g +0.13315233 0.03795988 0.61186191 + +$distimes + DT50 DT90 DT50back DT50_meso_b1 DT50_meso_b2 +meso 7.932495 36.93311 11.11797 5.205671 18.26</code></pre> +</div> +<div class="section level3"> +<h3 id="hs">HS<a class="anchor" aria-label="anchor" href="#hs"></a> +</h3> +<div class="sourceCode" id="cb72"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">hs_pH</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span><span class="st">"HS"</span>, <span class="op">]</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_0"</span><span class="op">)</span>,</span> +<span> covariates <span class="op">=</span> <span class="va">pH</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_k1</span> <span class="op">~</span> <span class="va">pH</span>, <span class="va">log_k2</span> <span class="op">~</span> <span class="va">pH</span>, <span class="va">log_tb</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">hs_pH</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_0</td> +<td align="right">93.33</td> +<td align="right">91.47</td> +<td align="right">95.19</td> +</tr> +<tr class="even"> +<td align="left">log_k1</td> +<td align="right">-5.81</td> +<td align="right">-7.27</td> +<td align="right">-4.36</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_k1)</td> +<td align="right">0.47</td> +<td align="right">0.23</td> +<td align="right">0.72</td> +</tr> +<tr class="even"> +<td align="left">log_k2</td> +<td align="right">-6.80</td> +<td align="right">-8.76</td> +<td align="right">-4.83</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_k2)</td> +<td align="right">0.54</td> +<td align="right">0.21</td> +<td align="right">0.87</td> +</tr> +<tr class="even"> +<td align="left">log_tb</td> +<td align="right">3.25</td> +<td align="right">1.25</td> +<td align="right">5.25</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_tb)</td> +<td align="right">-0.10</td> +<td align="right">-0.43</td> +<td align="right">0.23</td> +</tr> +<tr class="even"> +<td align="left">a.1</td> +<td align="right">4.49</td> +<td align="right">3.78</td> +<td align="right">5.21</td> +</tr> +<tr class="odd"> +<td align="left">SD.log_k1</td> +<td align="right">0.37</td> +<td align="right">0.24</td> +<td align="right">0.51</td> +</tr> +<tr class="even"> +<td align="left">SD.log_k2</td> +<td align="right">0.29</td> +<td align="right">0.10</td> +<td align="right">0.48</td> +</tr> +<tr class="odd"> +<td align="left">SD.log_tb</td> +<td align="right">0.25</td> +<td align="right">-0.07</td> +<td align="right">0.57</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb74"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">hs_pH</span><span class="op">)</span></span></code></pre></div> +<pre><code>[1] "sd(log_tb)" "beta_pH(log_tb)"</code></pre> +<p>According to the output of the <code>illparms</code> function, the +random effect on the break time <code>tb</code> cannot reliably be +quantified, neither can the influence of soil pH on <code>tb</code>. The +fit is repeated without the corresponding covariate model, and no +ill-defined parameters remain.</p> +<div class="sourceCode" id="cb76"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">hs_pH_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">hs_pH</span>, covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_k1</span> <span class="op">~</span> <span class="va">pH</span>, <span class="va">log_k2</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">hs_pH_2</span><span class="op">)</span></span></code></pre></div> +<p>Model comparison confirms that this model is preferable to the fit +without covariate influence, and also to the first version with +covariate influence.</p> +<div class="sourceCode" id="cb77"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"HS"</span>, <span class="st">"const"</span><span class="op">]</span><span class="op">]</span>, <span class="va">hs_pH</span>, <span class="va">hs_pH_2</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code>Data: 116 observations of 1 variable(s) grouped in 18 datasets + + npar AIC BIC Lik Chisq Df Pr(>Chisq) +f_saem_2[["HS", "const"]] 8 780.08 787.20 -382.04 +hs_pH_2 10 766.47 775.37 -373.23 17.606 2 0.0001503 *** +hs_pH 11 769.80 779.59 -373.90 0.000 1 1.0000000 +--- +Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code></pre> +<div class="sourceCode" id="cb79"><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">hs_pH_2</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_0</td> +<td align="right">93.33</td> +<td align="right">91.50</td> +<td align="right">95.15</td> +</tr> +<tr class="even"> +<td align="left">log_k1</td> +<td align="right">-5.68</td> +<td align="right">-7.09</td> +<td align="right">-4.27</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_k1)</td> +<td align="right">0.46</td> +<td align="right">0.22</td> +<td align="right">0.69</td> +</tr> +<tr class="even"> +<td align="left">log_k2</td> +<td align="right">-6.61</td> +<td align="right">-8.34</td> +<td align="right">-4.88</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_k2)</td> +<td align="right">0.50</td> +<td align="right">0.21</td> +<td align="right">0.79</td> +</tr> +<tr class="even"> +<td align="left">log_tb</td> +<td align="right">2.70</td> +<td align="right">2.33</td> +<td align="right">3.08</td> +</tr> +<tr class="odd"> +<td align="left">a.1</td> +<td align="right">4.45</td> +<td align="right">3.74</td> +<td align="right">5.16</td> +</tr> +<tr class="even"> +<td align="left">SD.log_k1</td> +<td align="right">0.36</td> +<td align="right">0.22</td> +<td align="right">0.49</td> +</tr> +<tr class="odd"> +<td align="left">SD.log_k2</td> +<td align="right">0.23</td> +<td align="right">0.02</td> +<td align="right">0.43</td> +</tr> +<tr class="even"> +<td align="left">SD.log_tb</td> +<td align="right">0.55</td> +<td align="right">0.25</td> +<td align="right">0.85</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb80"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">hs_pH_2</span><span class="op">)</span></span></code></pre></div> +<p><img src="2023_mesotrione_parent_files/figure-html/unnamed-chunk-30-1.png" width="700" style="display: block; margin: auto;"></p> +<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">hs_pH_2</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +50% 5.75 + +$distimes + DT50 DT90 DT50back DT50_k1 DT50_k2 +meso 14.68725 82.45287 24.82079 14.68725 29.29299</code></pre> +<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">hs_pH_2</span>, covariates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>pH <span class="op">=</span> <span class="fl">7</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +User 7 + +$distimes + DT50 DT90 DT50back DT50_k1 DT50_k2 +meso 8.298536 38.85371 11.69613 8.298536 15.71561</code></pre> +</div> +<div class="section level3"> +<h3 id="comparison-across-parent-models">Comparison across parent models<a class="anchor" aria-label="anchor" href="#comparison-across-parent-models"></a> +</h3> +<p>After model reduction for all models with pH influence, they are +compared with each other.</p> +<div class="sourceCode" id="cb85"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">sfo_pH</span>, <span class="va">fomc_pH_2</span>, <span class="va">dfop_pH_2</span>, <span class="va">dfop_pH_4</span>, <span class="va">sforb_pH_2</span>, <span class="va">hs_pH_2</span><span class="op">)</span></span></code></pre></div> +<pre><code>Data: 116 observations of 1 variable(s) grouped in 18 datasets + + npar AIC BIC Lik +sfo_pH 5 783.09 787.54 -386.54 +fomc_pH_2 6 767.49 772.83 -377.75 +dfop_pH_4 7 767.35 773.58 -376.68 +sforb_pH_2 7 770.94 777.17 -378.47 +dfop_pH_2 8 765.14 772.26 -374.57 +hs_pH_2 10 766.47 775.37 -373.23</code></pre> +<p>The DFOP model with pH influence on <code>k2</code> and +<code>g</code> and a random effect only on <code>k2</code> is finally +selected as the best fit.</p> +<p>The endpoints resulting from this model are listed below. Please +refer to the Appendix for a detailed listing.</p> +<div class="sourceCode" id="cb87"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">dfop_pH_2</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +50% 5.75 + +$distimes + DT50 DT90 DT50back DT50_k1 DT50_k2 +meso 18.36876 73.51841 22.13125 4.191901 23.98672</code></pre> +<div class="sourceCode" id="cb89"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">dfop_pH_2</span>, covariates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>pH <span class="op">=</span> <span class="fl">7</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +User 7 + +$distimes + DT50 DT90 DT50back DT50_k1 DT50_k2 +meso 8.346428 28.34437 8.532507 4.191901 8.753618</code></pre> +</div> +</div> +<div class="section level2"> +<h2 id="conclusions">Conclusions<a class="anchor" aria-label="anchor" href="#conclusions"></a> +</h2> +<p>These evaluations demonstrate that covariate effects can be included +for all types of parent degradation models. These models can then be +further refined to make them fully identifiable.</p> +</div> +<div class="section level2"> +<h2 id="appendix">Appendix<a class="anchor" aria-label="anchor" href="#appendix"></a> +</h2> +<div class="section level3"> +<h3 id="hierarchical-fit-listings">Hierarchical fit listings<a class="anchor" aria-label="anchor" href="#hierarchical-fit-listings"></a> +</h3> +<div class="section level4"> +<h4 id="fits-without-covariate-effects">Fits without covariate effects<a class="anchor" aria-label="anchor" href="#fits-without-covariate-effects"></a> +</h4> + +</div> +<div class="section level4"> +<h4 id="fits-with-covariate-effects">Fits with covariate effects<a class="anchor" aria-label="anchor" href="#fits-with-covariate-effects"></a> +</h4> + +</div> +</div> +<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 4.3.1 (2023-06-16) +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/blas/libblas.so.3.11.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 + +locale: + [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C + [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 + [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 + [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C + [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_1.43 mkin_1.2.6 + +loaded via a namespace (and not attached): + [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 + [5] lattice_0.20-45 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 + [9] grid_4.3.1 fastmap_1.1.1 cellranger_1.1.0 rprojroot_2.0.3 +[13] jsonlite_1.8.5 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_4.3.1 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_2.22 compiler_4.3.1 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: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</code></pre> +<pre><code>MemTotal: 12165632 kB</code></pre> +</div> +</div> + </div> + + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + + <nav id="toc" 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