diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2023-02-17 22:48:18 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2023-02-17 22:48:18 +0100 |
| commit | bcd98a1fa3cd2fb4b7105b7ec6c129ca18f872e8 (patch) | |
| tree | 80ce30d68fb33fe92a0939e1f5be9790263909c1 | |
| parent | 5811ab93d856bb339a35eef2d23266fcb781cbe7 (diff) | |
Update online docs, fix bug that surfaced
42 files changed, 750 insertions, 294 deletions
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index cafccae9..9606507a 100644 --- a/R/plot.mkinfit.R +++ b/R/plot.mkinfit.R @@ -140,15 +140,16 @@ plot.mkinfit <- function(x, fit = x, rownames(subset(fit$fixed, type == "deparm"))) odeparms <- parms.all[odenames] + + if (solution_type == "deSolve" & !is.null(fit$mkinmod$cf)) { + fit$mkinmod[["symbols"]] <- deSolve::checkDLL(dllname = fit$mkinmod$dll_info[["name"]], + func = "diffs", initfunc = "initpar", + jacfunc = NULL, nout = 0, outnames = NULL) + } out <- try(mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, atol = fit$atol, rtol = fit$rtol), silent = TRUE) - if (inherits(out, "try-error")) { - out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, - solution_type = solution_type, atol = fit$atol, rtol = fit$rtol, - use_compiled = FALSE) - } out <- as.data.frame(out) names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index b9571a60..2aacc53a 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -17,7 +17,7 @@ </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">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> diff --git a/docs/dev/articles/prebuilt/2022_cyan_pathway.html b/docs/dev/articles/prebuilt/2022_cyan_pathway.html index 87d4ca4a..1095dd28 100644 --- a/docs/dev/articles/prebuilt/2022_cyan_pathway.html +++ b/docs/dev/articles/prebuilt/2022_cyan_pathway.html @@ -34,14 +34,14 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../../reference/index.html">Functions and data</a> + <a href="../../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -53,6 +53,9 @@ <li> <a href="../../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -60,22 +63,31 @@ <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li class="divider"> </li> +<li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + </li> +<li class="dropdown-header">Performance</li> + <li> + <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -83,6 +95,15 @@ <li> <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul> </li> <li> @@ -115,7 +136,7 @@ residue data on cyantraniliprole</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change on 6 January -2023, last compiled on 28 Januar 2023</h4> +2023, last compiled on 17 Februar 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_cyan_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_cyan_pathway.rmd</code></a></small> <div class="hidden name"><code>2022_cyan_pathway.rmd</code></div> @@ -135,7 +156,7 @@ be fitted with the mkin package.</p> 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data) of the German Environment Agency carried out in 2022 and 2023.</p> -<p>The mkin package is used in version 1.2.2 which is currently under +<p>The mkin package is used in version 1.2.3 which is currently under development. The newly introduced functionality that is used here is a simplification of excluding random effects for a set of fits based on a related set of fits with a reduced model, and the documentation of the @@ -2185,7 +2206,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:07:38 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2313,7 +2334,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:08:17 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2443,7 +2464,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:09:12 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2588,7 +2609,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:09:18 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2726,7 +2747,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:10:30 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2872,7 +2893,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:16:28 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -3018,7 +3039,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:10:49 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3183,7 +3204,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:17:00 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3348,7 +3369,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:11:04 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan @@ -3490,7 +3511,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:11:24 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan @@ -3638,7 +3659,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:34:28 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -3802,7 +3823,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:37:36 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -3948,7 +3969,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:38:34 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4139,7 +4160,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:45:32 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4330,7 +4351,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:38:37 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4526,7 +4547,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 10:46:02 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4727,7 +4748,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 11:18:41 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -4870,7 +4891,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 11:16:32 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -5036,7 +5057,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 11:22:28 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -5202,7 +5223,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 11:17:37 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -5373,7 +5394,7 @@ saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.2 R version used for fitting: 4.2.2 Date of fit: Sat Jan 28 11:21:01 2023 -Date of summary: Sat Jan 28 11:22:29 2023 +Date of summary: Fri Feb 17 22:24:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -5561,26 +5582,23 @@ attached base packages: [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.41 mkin_1.2.2 +[1] saemix_3.2 npde_3.3 knitr_1.41 mkin_1.2.3 loaded via a namespace (and not attached): - [1] mclust_6.0.0 lattice_0.20-45 prettyunits_1.1.1 ps_1.7.2 - [5] zoo_1.8-11 assertthat_0.2.1 rprojroot_2.0.3 digest_0.6.31 - [9] lmtest_0.9-40 utf8_1.2.2 R6_2.5.1 cellranger_1.1.0 -[13] evaluate_0.19 ggplot2_3.4.0 highr_0.9 pillar_1.8.1 -[17] rlang_1.0.6 readxl_1.4.1 callr_3.7.3 jquerylib_0.1.4 -[21] rmarkdown_2.19 pkgdown_2.0.7 textshaping_0.3.6 desc_1.4.2 -[25] stringr_1.5.0 munsell_0.5.0 compiler_4.2.2 xfun_0.35 -[29] pkgconfig_2.0.3 systemfonts_1.0.4 pkgbuild_1.4.0 htmltools_0.5.4 -[33] tidyselect_1.2.0 tibble_3.1.8 gridExtra_2.3 codetools_0.2-18 -[37] fansi_1.0.3 crayon_1.5.2 dplyr_1.0.10 grid_4.2.2 -[41] nlme_3.1-161 jsonlite_1.8.4 gtable_0.3.1 lifecycle_1.0.3 -[45] DBI_1.1.3 magrittr_2.0.3 scales_1.2.1 cli_3.5.0 -[49] stringi_1.7.8 cachem_1.0.6 fs_1.5.2 bslib_0.4.2 -[53] ragg_1.2.4 generics_0.1.3 vctrs_0.5.1 deSolve_1.34 -[57] tools_4.2.2 glue_1.6.2 purrr_1.0.0 processx_3.8.0 -[61] fastmap_1.1.0 yaml_2.3.6 inline_0.3.19 colorspace_2.0-3 -[65] memoise_2.0.1 sass_0.4.4 </code></pre> + [1] pillar_1.8.1 bslib_0.4.2 compiler_4.2.2 jquerylib_0.1.4 + [5] tools_4.2.2 mclust_6.0.0 digest_0.6.31 tibble_3.1.8 + [9] jsonlite_1.8.4 evaluate_0.19 memoise_2.0.1 lifecycle_1.0.3 +[13] nlme_3.1-162 gtable_0.3.1 lattice_0.20-45 pkgconfig_2.0.3 +[17] rlang_1.0.6 DBI_1.1.3 cli_3.5.0 yaml_2.3.6 +[21] pkgdown_2.0.7 xfun_0.35 fastmap_1.1.0 gridExtra_2.3 +[25] dplyr_1.0.10 stringr_1.5.0 generics_0.1.3 desc_1.4.2 +[29] fs_1.5.2 vctrs_0.5.1 sass_0.4.4 systemfonts_1.0.4 +[33] tidyselect_1.2.0 rprojroot_2.0.3 lmtest_0.9-40 grid_4.2.2 +[37] inline_0.3.19 glue_1.6.2 R6_2.5.1 textshaping_0.3.6 +[41] fansi_1.0.3 rmarkdown_2.19 purrr_1.0.0 ggplot2_3.4.0 +[45] magrittr_2.0.3 scales_1.2.1 htmltools_0.5.4 assertthat_0.2.1 +[49] colorspace_2.0-3 ragg_1.2.4 utf8_1.2.2 stringi_1.7.8 +[53] munsell_0.5.0 cachem_1.0.6 zoo_1.8-11 </code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> diff --git a/docs/dev/articles/prebuilt/2022_dmta_parent.html b/docs/dev/articles/prebuilt/2022_dmta_parent.html index 89c9bfd8..2ff966b4 100644 --- a/docs/dev/articles/prebuilt/2022_dmta_parent.html +++ b/docs/dev/articles/prebuilt/2022_dmta_parent.html @@ -34,14 +34,14 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../../reference/index.html">Functions and data</a> + <a href="../../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -53,6 +53,9 @@ <li> <a href="../../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -60,22 +63,31 @@ <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li class="divider"> </li> +<li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + </li> +<li class="dropdown-header">Performance</li> + <li> + <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -83,6 +95,15 @@ <li> <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul> </li> <li> @@ -115,7 +136,7 @@ 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 28 Januar 2023</h4> +2023, last compiled on 17 Februar 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_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> @@ -134,7 +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 1.2.2. It contains the test data +<p>The mkin package is used in version 1.2.3. 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> diff --git a/docs/dev/articles/prebuilt/2022_dmta_pathway.html b/docs/dev/articles/prebuilt/2022_dmta_pathway.html index 2e89fb9d..4a6f224e 100644 --- a/docs/dev/articles/prebuilt/2022_dmta_pathway.html +++ b/docs/dev/articles/prebuilt/2022_dmta_pathway.html @@ -34,14 +34,14 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../../reference/index.html">Functions and data</a> + <a href="../../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -53,6 +53,9 @@ <li> <a href="../../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -60,22 +63,31 @@ <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li class="divider"> </li> +<li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + </li> +<li class="dropdown-header">Performance</li> + <li> + <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -83,6 +95,15 @@ <li> <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul> </li> <li> @@ -115,7 +136,7 @@ residue data on dimethenamid and dimethenamid-P</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change on 8 January -2023, last compiled on 28 Januar 2023</h4> +2023, last compiled on 17 Februar 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_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> @@ -135,7 +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 1.2.2, which is currently under +<p>The mkin package is used in version 1.2.3, 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 diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html index b37ac926..a2d9f7e8 100644 --- a/docs/dev/articles/web_only/benchmarks.html +++ b/docs/dev/articles/web_only/benchmarks.html @@ -34,14 +34,14 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../../reference/index.html">Functions and data</a> + <a href="../../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -53,6 +53,9 @@ <li> <a href="../../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -60,22 +63,31 @@ <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + </li> +<li class="dropdown-header">Performance</li> + <li> + <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -83,6 +95,15 @@ <li> <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul> </li> <li> @@ -106,13 +127,15 @@ - </header><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Benchmark timings for mkin</h1> - <h4 data-toc-skip class="author">Johannes Ranke</h4> + <h4 data-toc-skip class="author">Johannes +Ranke</h4> - <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-11-24)</h4> + <h4 data-toc-skip class="date">Last change 17 February 2023 +(rebuilt 2023-02-17)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small> <div class="hidden name"><code>benchmarks.rmd</code></div> @@ -121,9 +144,15 @@ -<p>Each system is characterized by the operating system type, the CPU type, the mkin version, and, as in June 2022 the current R version lead to worse performance, the R version. A compiler was available, so if no analytical solution was available, compiled ODE models are used.</p> -<p>Every fit is only performed once, so the accuracy of the benchmarks is limited.</p> -<p>The following wrapper function for <code>mmkin</code> is used because the way the error model is specified was changed in mkin version 0.9.49.1.</p> +<p>Each system is characterized by the operating system type, the CPU +type, the mkin version, and, as in June 2022 the current R version lead +to worse performance, the R version. A compiler was available, so if no +analytical solution was available, compiled ODE models are used.</p> +<p>Every fit is only performed once, so the accuracy of the benchmarks +is limited.</p> +<p>The following wrapper function for <code>mmkin</code> is used because +the way the error model is specified was changed in mkin version +0.9.49.1.</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/utils/packageDescription.html" class="external-link">packageVersion</a></span><span class="op">(</span><span class="st">"mkin"</span><span class="op">)</span> <span class="op">></span> <span class="st">"0.9.48.1"</span><span class="op">)</span> <span class="op">{</span></span> <span> <span class="va">mmkin_bench</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, <span class="va">error_model</span> <span class="op">=</span> <span class="st">"const"</span><span class="op">)</span> <span class="op">{</span></span> @@ -195,11 +224,14 @@ <div class="section level2"> <h2 id="results">Results<a class="anchor" aria-label="anchor" href="#results"></a> </h2> -<p>Benchmarks for all available error models are shown. They are intended for improving mkin, not for comparing CPUs or operating systems. All trademarks belong to their respective owners.</p> +<p>Benchmarks for all available error models are shown. They are +intended for improving mkin, not for comparing CPUs or operating +systems. All trademarks belong to their respective owners.</p> <div class="section level3"> <h3 id="parent-only">Parent only<a class="anchor" aria-label="anchor" href="#parent-only"></a> </h3> -<p>Constant variance (t1) and two-component error model (t2) for four models fitted to two datasets, i.e. eight fits for each test.</p> +<p>Constant variance (t1) and two-component error model (t2) for four +models fitted to two datasets, i.e. eight fits for each test.</p> <table class="table"> <thead><tr class="header"> <th align="left">OS</th> @@ -362,13 +394,39 @@ <td align="right">2.187</td> <td align="right">3.851</td> </tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">1.288</td> +<td align="right">1.794</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">1.276</td> +<td align="right">1.804</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.3</td> +<td align="right">1.370</td> +<td align="right">1.883</td> +</tr> </tbody> </table> </div> <div class="section level3"> <h3 id="one-metabolite">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite"></a> </h3> -<p>Constant variance (t3), two-component error model (t4), and variance by variable (t5) for three models fitted to one dataset, i.e. three fits for each test.</p> +<p>Constant variance (t3), two-component error model (t4), and variance +by variable (t5) for three models fitted to one dataset, i.e. three fits +for each test.</p> <table class="table"> <thead><tr class="header"> <th align="left">OS</th> @@ -551,14 +609,55 @@ <td align="right">6.335</td> <td align="right">3.003</td> </tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">0.792</td> +<td align="right">2.378</td> +<td align="right">1.245</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">0.784</td> +<td align="right">2.355</td> +<td align="right">1.233</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.3</td> +<td align="right">0.770</td> +<td align="right">2.011</td> +<td align="right">1.123</td> +</tr> </tbody> </table> </div> <div class="section level3"> <h3 id="two-metabolites">Two metabolites<a class="anchor" aria-label="anchor" href="#two-metabolites"></a> </h3> -<p>Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.</p> +<p>Constant variance (t6 and t7), two-component error model (t8 and t9), +and variance by variable (t10 and t11) for one model fitted to one +dataset, i.e. one fit for each test.</p> <table class="table"> +<colgroup> +<col width="8%"> +<col width="19%"> +<col width="8%"> +<col width="12%"> +<col width="8%"> +<col width="8%"> +<col width="8%"> +<col width="9%"> +<col width="8%"> +<col width="9%"> +</colgroup> <thead><tr class="header"> <th align="left">OS</th> <th align="left">CPU</th> @@ -800,6 +899,42 @@ <td align="right">1.976</td> <td align="right">3.013</td> </tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">0.445</td> +<td align="right">0.591</td> +<td align="right">0.660</td> +<td align="right">1.190</td> +<td align="right">0.814</td> +<td align="right">1.100</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">0.443</td> +<td align="right">0.586</td> +<td align="right">0.661</td> +<td align="right">1.176</td> +<td align="right">0.803</td> +<td align="right">1.097</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.3</td> +<td align="right">0.418</td> +<td align="right">0.530</td> +<td align="right">0.591</td> +<td align="right">1.006</td> +<td align="right">0.716</td> +<td align="right">0.949</td> +</tr> </tbody> </table> </div> @@ -823,7 +958,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer> diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html index 4fe648c6..551b34d4 100644 --- a/docs/dev/articles/web_only/saem_benchmarks.html +++ b/docs/dev/articles/web_only/saem_benchmarks.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">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> @@ -134,8 +134,8 @@ <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 14 November 2022 -(rebuilt 2023-01-28)</h4> + <h4 data-toc-skip class="date">Last change 17 February 2023 +(rebuilt 2023-02-17)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small> <div class="hidden name"><code>saem_benchmarks.rmd</code></div> @@ -191,7 +191,7 @@ explanation of the following preprocessing.</p> <div class="sourceCode" id="cb4"><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> <span> <span class="va">sfo_const</span>, <span class="va">dfop_const</span>, <span class="va">sforb_const</span>, <span class="va">hs_const</span>,</span> -<span> <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_tc</span><span class="op">)</span> <span class="op">|></span> <span class="fu">kable</span><span class="op">(</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> +<span> <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_tc</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> @@ -331,17 +331,7 @@ systems. All trademarks belong to their respective owners.</p> <h3 id="parent-only-1">Parent only<a class="anchor" aria-label="anchor" href="#parent-only-1"></a> </h3> <p>Constant variance for SFO, DFOP, SFORB and HS.</p> -<table style="width:100%;" class="table"> -<colgroup> -<col width="42%"> -<col width="8%"> -<col width="8%"> -<col width="9%"> -<col width="8%"> -<col width="8%"> -<col width="8%"> -<col width="8%"> -</colgroup> +<table class="table"> <thead><tr class="header"> <th align="left">CPU</th> <th align="left">OS</th> @@ -374,29 +364,39 @@ systems. All trademarks belong to their respective owners.</p> <td align="right">4.851</td> </tr> <tr class="odd"> -<td align="left">Ryzen 9 7950X 16-Core Processor</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.1</td> +<td align="left">3.2</td> +<td align="right">1.352</td> +<td align="right">2.813</td> +<td align="right">2.401</td> +<td align="right">2.074</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> <td align="left">Linux</td> <td align="left">1.2.2</td> <td align="left">3.2</td> -<td align="right">1.470</td> -<td align="right">2.263</td> -<td align="right">1.840</td> -<td align="right">2.299</td> +<td align="right">1.328</td> +<td align="right">2.738</td> +<td align="right">2.336</td> +<td align="right">2.023</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.3</td> +<td align="left">3.2</td> +<td align="right">1.118</td> +<td align="right">2.036</td> +<td align="right">2.010</td> +<td align="right">2.088</td> </tr> </tbody> </table> <p>Two-component error fits for SFO, DFOP, SFORB and HS.</p> -<table style="width:100%;" class="table"> -<colgroup> -<col width="42%"> -<col width="8%"> -<col width="8%"> -<col width="9%"> -<col width="8%"> -<col width="8%"> -<col width="8%"> -<col width="8%"> -</colgroup> +<table class="table"> <thead><tr class="header"> <th align="left">CPU</th> <th align="left">OS</th> @@ -429,14 +429,34 @@ systems. All trademarks belong to their respective owners.</p> <td align="right">8.401</td> </tr> <tr class="odd"> -<td align="left">Ryzen 9 7950X 16-Core Processor</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.1</td> +<td align="left">3.2</td> +<td align="right">2.388</td> +<td align="right">3.033</td> +<td align="right">3.532</td> +<td align="right">3.310</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> <td align="left">Linux</td> <td align="left">1.2.2</td> <td align="left">3.2</td> -<td align="right">2.118</td> -<td align="right">3.528</td> -<td align="right">3.295</td> -<td align="right">3.157</td> +<td align="right">2.341</td> +<td align="right">2.968</td> +<td align="right">3.465</td> +<td align="right">3.341</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.3</td> +<td align="left">3.2</td> +<td align="right">2.159</td> +<td align="right">3.584</td> +<td align="right">3.307</td> +<td align="right">3.460</td> </tr> </tbody> </table> @@ -446,14 +466,6 @@ systems. All trademarks belong to their respective owners.</p> </h3> <p>Two-component error for DFOP-SFO and SFORB-SFO.</p> <table class="table"> -<colgroup> -<col width="48%"> -<col width="9%"> -<col width="9%"> -<col width="10%"> -<col width="10%"> -<col width="12%"> -</colgroup> <thead><tr class="header"> <th align="left">CPU</th> <th align="left">OS</th> @@ -480,12 +492,28 @@ systems. All trademarks belong to their respective owners.</p> <td align="right">798.580</td> </tr> <tr class="odd"> -<td align="left">Ryzen 9 7950X 16-Core Processor</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.1</td> +<td align="left">3.2</td> +<td align="right">11.247</td> +<td align="right">285.216</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> <td align="left">Linux</td> <td align="left">1.2.2</td> <td align="left">3.2</td> -<td align="right">12.336</td> -<td align="right">277.666</td> +<td align="right">11.242</td> +<td align="right">284.258</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.3</td> +<td align="left">3.2</td> +<td align="right">11.796</td> +<td align="right">216.012</td> </tr> </tbody> </table> @@ -518,11 +546,25 @@ systems. All trademarks belong to their respective owners.</p> <td align="right">1312.445</td> </tr> <tr class="odd"> -<td align="left">Ryzen 9 7950X 16-Core Processor</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.1</td> +<td align="left">3.2</td> +<td align="right">489.939</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> <td align="left">Linux</td> <td align="left">1.2.2</td> <td align="left">3.2</td> -<td align="right">459.051</td> +<td align="right">482.970</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.3</td> +<td align="left">3.2</td> +<td align="right">392.364</td> </tr> </tbody> </table> diff --git a/docs/dev/authors.html b/docs/dev/authors.html index 4146fdf2..3c95e7e0 100644 --- a/docs/dev/authors.html +++ b/docs/dev/authors.html @@ -17,7 +17,7 @@ </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">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> @@ -132,13 +132,13 @@ <p>Ranke J (2023). <em>mkin: Kinetic Evaluation of Chemical Degradation Data</em>. -R package version 1.2.2, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. +R package version 1.2.3, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. </p> <pre>@Manual{, title = {mkin: Kinetic Evaluation of Chemical Degradation Data}, author = {Johannes Ranke}, year = {2023}, - note = {R package version 1.2.2}, + note = {R package version 1.2.3}, url = {https://pkgdown.jrwb.de/mkin/}, }</pre> diff --git a/docs/dev/index.html b/docs/dev/index.html index 36a005ad..6ed5f55d 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -45,7 +45,7 @@ </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">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index d8fcbfe9..a22f005b 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -17,7 +17,7 @@ </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">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> @@ -105,9 +105,13 @@ </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.2" id="mkin-122">mkin 1.2.2<a class="anchor" aria-label="anchor" href="#mkin-122"></a></h2> +<h2 class="page-header" data-toc-text="1.2.3" id="mkin-123">mkin 1.2.3<a class="anchor" aria-label="anchor" href="#mkin-123"></a></h2> +<ul><li>Depend on upcoming deSolve version with the possibility to avoid resolving symbols in a shared library (compiled models) over and over.</li> +</ul></div> + <div class="section level2"> +<h2 class="page-header" data-toc-text="1.2.2" id="mkin-122-unreleased">mkin 1.2.2 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-122-unreleased"></a></h2> <ul><li><p>‘inst/rmarkdown/templates/hier’: R markdown template to facilitate the application of hierarchical kinetic models.</p></li> -<li><p>‘inst/testdata/lambda-cyhalothrin_soil_efsa_2014.xlsx’: Example spreadsheet for use with ‘read_spreadsheet()’.</p></li> +<li><p>‘inst/testdata/{cyantraniliprole_soil_efsa_2014,lambda-cyhalothrin_soil_efsa_2014}.xlsx’: Example spreadsheets for use with ‘read_spreadsheet()’.</p></li> <li><p>‘R/mhmkin.R’: Allow an ‘illparms.mhmkin’ object or a list with suitable dimensions as value of the argument ‘no_random_effects’, making it possible to exclude random effects that were ill-defined in simpler variants of the set of degradation models. Remove the possibility to exclude random effects based on separate fits, as it did not work well.</p></li> <li><p>‘R/summary.saem.mmkin.R’: List all initial parameter values in the summary, including random effects and error model parameters. Avoid redundant warnings that occurred in the calculation of correlations of the fixed effects in the case that the Fisher information matrix could not be inverted. List correlations of random effects if specified by the user in the covariance model.</p></li> <li><p>‘R/parplot.R’: Possibility to select the top ‘llquant’ fraction of the fits for the parameter plots, and improved legend text.</p></li> diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index c8fdd89a..7ee056e3 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -16,7 +16,7 @@ articles: dimethenamid_2018: web_only/dimethenamid_2018.html multistart: web_only/multistart.html saem_benchmarks: web_only/saem_benchmarks.html -last_built: 2023-01-28T16:59Z +last_built: 2023-02-17T21:22Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png Binary files differindex 27feab09..34efa229 100644 --- a/docs/dev/reference/Rplot002.png +++ b/docs/dev/reference/Rplot002.png diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png Binary files differindex 774715e0..30cf38f3 100644 --- a/docs/dev/reference/Rplot003.png +++ b/docs/dev/reference/Rplot003.png diff --git a/docs/dev/reference/Rplot004.png b/docs/dev/reference/Rplot004.png Binary files differindex 37e0e95e..377229db 100644 --- a/docs/dev/reference/Rplot004.png +++ b/docs/dev/reference/Rplot004.png diff --git a/docs/dev/reference/Rplot005.png b/docs/dev/reference/Rplot005.png Binary files differindex 76f25647..93a5c2dd 100644 --- a/docs/dev/reference/Rplot005.png +++ b/docs/dev/reference/Rplot005.png diff --git a/docs/dev/reference/Rplot006.png b/docs/dev/reference/Rplot006.png Binary files differindex 48f5bbd8..9f8e6868 100644 --- a/docs/dev/reference/Rplot006.png +++ b/docs/dev/reference/Rplot006.png diff --git a/docs/dev/reference/ds_mixed-1.png b/docs/dev/reference/ds_mixed-1.png Binary files differindex a7f5c395..d8505ffd 100644 --- a/docs/dev/reference/ds_mixed-1.png +++ b/docs/dev/reference/ds_mixed-1.png diff --git a/docs/dev/reference/ds_mixed.html b/docs/dev/reference/ds_mixed.html index 09a6cc8c..2d0274ff 100644 --- a/docs/dev/reference/ds_mixed.html +++ b/docs/dev/reference/ds_mixed.html @@ -18,13 +18,13 @@ the 'dataset_generation' directory."><meta name="robots" content="noindex"><!-- </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Functions and data</a> + <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -35,6 +35,8 @@ the 'dataset_generation' directory."><meta name="robots" content="noindex"><!-- <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -42,22 +44,29 @@ the 'dataset_generation' directory."><meta name="robots" content="noindex"><!-- <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + <li class="dropdown-header">Performance</li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -65,6 +74,14 @@ the 'dataset_generation' directory."><meta name="robots" content="noindex"><!-- <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul></li> <li> <a href="../news/index.html">News</a> @@ -226,7 +243,7 @@ the 'dataset_generation' directory.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer></div> diff --git a/docs/dev/reference/hierarchical_kinetics.html b/docs/dev/reference/hierarchical_kinetics.html index bedb8753..2dc2ec6a 100644 --- a/docs/dev/reference/hierarchical_kinetics.html +++ b/docs/dev/reference/hierarchical_kinetics.html @@ -18,13 +18,13 @@ provided with the mkin package."><meta name="robots" content="noindex"><!-- math </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Functions and data</a> + <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -35,6 +35,8 @@ provided with the mkin package."><meta name="robots" content="noindex"><!-- math <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -42,22 +44,29 @@ provided with the mkin package."><meta name="robots" content="noindex"><!-- math <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + <li class="dropdown-header">Performance</li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -65,6 +74,14 @@ provided with the mkin package."><meta name="robots" content="noindex"><!-- math <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul></li> <li> <a href="../news/index.html">News</a> @@ -124,6 +141,7 @@ provided with the mkin package.</p> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><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://github.com/rstudio/rmarkdown" class="external-link">rmarkdown</a></span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://pkgs.rstudio.com/rmarkdown/reference/draft.html" class="external-link">draft</a></span><span class="op">(</span><span class="st">"example_analysis.rmd"</span>, template <span class="op">=</span> <span class="st">"hierarchical_kinetics"</span>, package <span class="op">=</span> <span class="st">"mkin"</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in draft("example_analysis.rmd", template = "hierarchical_kinetics", package = "mkin"):</span> The directory 'example_analysis' already exists.</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> </code></pre></div> diff --git a/docs/dev/reference/illparms.html b/docs/dev/reference/illparms.html index 9c498e1c..7bf6c1fe 100644 --- a/docs/dev/reference/illparms.html +++ b/docs/dev/reference/illparms.html @@ -21,13 +21,13 @@ without parameter transformations is used."><meta name="robots" content="noindex </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Functions and data</a> + <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -38,6 +38,8 @@ without parameter transformations is used."><meta name="robots" content="noindex <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -45,22 +47,29 @@ without parameter transformations is used."><meta name="robots" content="noindex <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + <li class="dropdown-header">Performance</li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -68,6 +77,14 @@ without parameter transformations is used."><meta name="robots" content="noindex <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul></li> <li> <a href="../news/index.html">News</a> @@ -222,7 +239,7 @@ does not output anything in the case no ill-defined parameters are found.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer></div> diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index b6d2db20..1d21cddf 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -17,7 +17,7 @@ </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">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> diff --git a/docs/dev/reference/mhmkin-1.png b/docs/dev/reference/mhmkin-1.png Binary files differindex 2ecb6759..1c99aead 100644 --- a/docs/dev/reference/mhmkin-1.png +++ b/docs/dev/reference/mhmkin-1.png diff --git a/docs/dev/reference/mhmkin-2.png b/docs/dev/reference/mhmkin-2.png Binary files differindex 9bb43d35..ea04ebfd 100644 --- a/docs/dev/reference/mhmkin-2.png +++ b/docs/dev/reference/mhmkin-2.png diff --git a/docs/dev/reference/mhmkin.html b/docs/dev/reference/mhmkin.html index 1328aa48..b41c11df 100644 --- a/docs/dev/reference/mhmkin.html +++ b/docs/dev/reference/mhmkin.html @@ -22,13 +22,13 @@ mixed-effects model fitting functions."><meta name="robots" content="noindex"><! </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Functions and data</a> + <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -39,6 +39,8 @@ mixed-effects model fitting functions."><meta name="robots" content="noindex"><! <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -46,22 +48,29 @@ mixed-effects model fitting functions."><meta name="robots" content="noindex"><! <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + <li class="dropdown-header">Performance</li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -69,6 +78,14 @@ mixed-effects model fitting functions."><meta name="robots" content="noindex"><! <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul></li> <li> <a href="../news/index.html">News</a> @@ -305,7 +322,7 @@ attribute 'mhmkin'.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer></div> diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html index 145dee83..2bade85e 100644 --- a/docs/dev/reference/mkinmod.html +++ b/docs/dev/reference/mkinmod.html @@ -21,13 +21,13 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src=" </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Functions and data</a> + <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -38,6 +38,8 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src=" <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -45,22 +47,29 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src=" <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + <li class="dropdown-header">Performance</li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -68,6 +77,14 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src=" <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul></li> <li> <a href="../news/index.html">News</a> @@ -169,7 +186,9 @@ applicable to give detailed information about the C function being built.</p></d <dd><p>Directory where an DLL object, if generated internally by <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code>, should be saved. The DLL will only be stored in a permanent location for use in future sessions, if 'dll_dir' and 'name' -are specified.</p></dd> +are specified. This is helpful if fit objects are cached e.g. by knitr, +as the cache remains functional across sessions if the DLL is stored in +a user defined location.</p></dd> <dt>unload</dt> @@ -310,7 +329,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpelWAOB/fileb43c31a25a86.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> +<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpQitVfY/file9cd3235ec83e.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> <span class="r-in"><span><span class="co"># Now we can save the model and restore it in a new session</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="co"># Terminate the R session here if you would like to check, and then do</span></span></span> @@ -318,6 +337,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"><span><span class="va">SFO_SFO.3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.3</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in is.loaded(initfunc, PACKAGE = dllname, type = ""):</span> invalid 'PACKAGE' argument</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Show details of creating the C function</span></span></span> <span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> @@ -363,7 +383,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> })</span> <span class="r-out co"><span class="r-pr">#></span> return(predicted)</span> <span class="r-out co"><span class="r-pr">#></span> }</span> -<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55555f013820></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55558875dc90></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># If we have several parallel metabolites</span></span></span> <span class="r-in"><span><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span></span> diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html index 10d2c9a9..f265a234 100644 --- a/docs/dev/reference/mkinpredict.html +++ b/docs/dev/reference/mkinpredict.html @@ -19,13 +19,13 @@ kinetic parameters and initial values for the state variables."><meta name="robo </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Functions and data</a> + <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -36,6 +36,8 @@ kinetic parameters and initial values for the state variables."><meta name="robo <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -43,22 +45,29 @@ kinetic parameters and initial values for the state variables."><meta name="robo <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + <li class="dropdown-header">Performance</li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -66,6 +75,14 @@ kinetic parameters and initial values for the state variables."><meta name="robo <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul></li> <li> <a href="../news/index.html">News</a> @@ -110,7 +127,7 @@ kinetic parameters and initial values for the state variables.</p> <span> method.ode <span class="op">=</span> <span class="st">"lsoda"</span>,</span> <span> atol <span class="op">=</span> <span class="fl">1e-08</span>,</span> <span> rtol <span class="op">=</span> <span class="fl">1e-10</span>,</span> -<span> maxsteps <span class="op">=</span> <span class="fl">20000</span>,</span> +<span> maxsteps <span class="op">=</span> <span class="fl">20000L</span>,</span> <span> map_output <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> na_stop <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> <span class="va">...</span></span> @@ -166,8 +183,9 @@ solver is used.</p></dd> <dd><p>The method that should be used for producing the predictions. This should generally be "analytical" if there is only one observed variable, and usually "deSolve" in the case of several observed -variables. The third possibility "eigen" is faster but not applicable to -some models e.g. using FOMC for the parent compound.</p></dd> +variables. The third possibility "eigen" is fast in comparison to uncompiled +ODE models, but not applicable to some models, e.g. using FOMC for the +parent compound.</p></dd> <dt>use_compiled</dt> @@ -177,22 +195,20 @@ some models e.g. using FOMC for the parent compound.</p></dd> <dt>method.ode</dt> <dd><p>The solution method passed via mkinpredict to ode] in -case the solution type is "deSolve". The default "lsoda" is performant, but -sometimes fails to converge.</p></dd> +case the solution type is "deSolve" and we are not using compiled code. +When using compiled code, only lsoda is supported.</p></dd> <dt>atol</dt> -<dd><p>Absolute error tolerance, passed to ode. Default is 1e-8, -lower than in lsoda.</p></dd> +<dd><p>Absolute error tolerance, passed to the ode solver.</p></dd> <dt>rtol</dt> -<dd><p>Absolute error tolerance, passed to ode. Default is 1e-10, -much lower than in lsoda.</p></dd> +<dd><p>Absolute error tolerance, passed to the ode solver.</p></dd> <dt>maxsteps</dt> -<dd><p>Maximum number of steps, passed to ode.</p></dd> +<dd><p>Maximum number of steps, passed to the ode solver.</p></dd> <dt>map_output</dt> @@ -325,15 +341,15 @@ as these always return mapped output.</p></dd> <span class="r-out co"><span class="r-pr">#></span> time degradinol </span> <span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2478752 </span> <span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</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>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span> -<span class="r-in"><span> method <span class="op">=</span> <span class="st">"lsoda"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span> +<span class="r-in"><span> method <span class="op">=</span> <span class="st">"lsoda"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span> <span class="r-out co"><span class="r-pr">#></span> time degradinol </span> <span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2478752 </span> <span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</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>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span> -<span class="r-in"><span> method <span class="op">=</span> <span class="st">"ode45"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span> +<span class="r-in"><span> method <span class="op">=</span> <span class="st">"ode45"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span> <span class="r-out co"><span class="r-pr">#></span> time degradinol </span> <span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2478752 </span> <span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</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>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span> -<span class="r-in"><span> method <span class="op">=</span> <span class="st">"rk4"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span> +<span class="r-in"><span> method <span class="op">=</span> <span class="st">"rk4"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span> <span class="r-out co"><span class="r-pr">#></span> time degradinol </span> <span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2480043 </span> <span class="r-in"><span><span class="co"># rk4 is not as precise here</span></span></span> @@ -372,11 +388,12 @@ as these always return mapped output.</p></dd> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span> <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.0 0.005</span> -<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.0 0.005</span> -<span class="r-out co"><span class="r-pr">#></span> 1 eigen 4.4 0.022</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 41.0 0.205</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.000 0.007</span> +<span class="r-out co"><span class="r-pr">#></span> 1 eigen 1.143 0.008</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 8.857 0.062</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 8.857 0.062</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span> <span class="co"># Predict from a fitted model</span></span></span> @@ -408,7 +425,7 @@ as these always return mapped output.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer></div> diff --git a/docs/dev/reference/mmkin-1.png b/docs/dev/reference/mmkin-1.png Binary files differindex 8ad9c11d..dae64316 100644 --- a/docs/dev/reference/mmkin-1.png +++ b/docs/dev/reference/mmkin-1.png diff --git a/docs/dev/reference/mmkin-2.png b/docs/dev/reference/mmkin-2.png Binary files differindex da2a48a8..b281cd7e 100644 --- a/docs/dev/reference/mmkin-2.png +++ b/docs/dev/reference/mmkin-2.png diff --git a/docs/dev/reference/mmkin-3.png b/docs/dev/reference/mmkin-3.png Binary files differindex 10d3f35b..23b0725c 100644 --- a/docs/dev/reference/mmkin-3.png +++ b/docs/dev/reference/mmkin-3.png diff --git a/docs/dev/reference/mmkin-4.png b/docs/dev/reference/mmkin-4.png Binary files differindex 132380a8..11eae1f9 100644 --- a/docs/dev/reference/mmkin-4.png +++ b/docs/dev/reference/mmkin-4.png diff --git a/docs/dev/reference/mmkin-5.png b/docs/dev/reference/mmkin-5.png Binary files differindex 4bfcc55e..e88bd59f 100644 --- a/docs/dev/reference/mmkin-5.png +++ b/docs/dev/reference/mmkin-5.png diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html index 5aa259f9..e0afa788 100644 --- a/docs/dev/reference/mmkin.html +++ b/docs/dev/reference/mmkin.html @@ -20,13 +20,13 @@ datasets specified in its first two arguments."><meta name="robots" content="noi </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Functions and data</a> + <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -37,6 +37,8 @@ datasets specified in its first two arguments."><meta name="robots" content="noi <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -44,22 +46,29 @@ datasets specified in its first two arguments."><meta name="robots" content="noi <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + <li class="dropdown-header">Performance</li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -67,6 +76,14 @@ datasets specified in its first two arguments."><meta name="robots" content="noi <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul></li> <li> <a href="../news/index.html">News</a> @@ -189,10 +206,10 @@ plotting.</p></div> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">time_default</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 7.113 0.837 2.580 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.531 0.312 0.595 </span> <span class="r-in"><span><span class="va">time_1</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 5.617 0.008 5.626 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.821 0.000 1.821 </span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="st">"SFO_lin"</span>, <span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> @@ -223,21 +240,25 @@ plotting.</p></div> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="mmkin-5.png" alt="" width="700" height="433"></span> <span class="r-in"><span></span></span> -<span class="r-in"><span><span class="co"># On Windows, we can use multiple cores by making a cluster using the parallel</span></span></span> -<span class="r-in"><span><span class="co"># package, which gets loaded with mkin, and passing it to mmkin, e.g.</span></span></span> -<span class="r-in"><span><span class="va">cl</span> <span class="op"><-</span> <span class="fu">makePSOCKcluster</span><span class="op">(</span><span class="fl">12</span><span class="op">)</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in makePSOCKcluster(12):</span> could not find function "makePSOCKcluster"</span> +<span class="r-in"><span><span class="co"># On Windows, we can use multiple cores by making a cluster first</span></span></span> +<span class="r-in"><span><span class="va">cl</span> <span class="op"><-</span> <span class="fu">parallel</span><span class="fu">::</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="fl">12</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu">mmkin</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="op">)</span>,</span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>A <span class="op">=</span> <span class="va">FOCUS_2006_A</span>, B <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, C <span class="op">=</span> <span class="va">FOCUS_2006_C</span>, D <span class="op">=</span> <span class="va">FOCUS_2006_D</span><span class="op">)</span>,</span></span> <span class="r-in"><span> cluster <span class="op">=</span> <span class="va">cl</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in system.time({ if (is.null(cluster)) { results <- parallel::mclapply(as.list(1:n.fits), fit_function, mc.cores = cores, mc.preschedule = FALSE) } else { results <- parallel::parLapply(cluster, as.list(1:n.fits), fit_function) }}):</span> object 'cl' not found</span> -<span class="r-msg co"><span class="r-pr">#></span> Timing stopped at: 0 0 0.001</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in print(f):</span> object 'f' not found</span> +<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> +<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model A B C D </span> +<span class="r-out co"><span class="r-pr">#></span> SFO OK OK OK OK</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC OK OK OK OK</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP OK OK OK OK</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> <span class="r-in"><span><span class="co"># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span></span></span> <span class="r-in"><span><span class="co"># dataset is really SFO, and the FOMC fit is overparameterised</span></span></span> -<span class="r-in"><span><span class="fu">stopCluster</span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in stopCluster(cl):</span> could not find function "stopCluster"</span> +<span class="r-in"><span><span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> </code></pre></div> @@ -254,7 +275,7 @@ plotting.</p></div> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer></div> diff --git a/docs/dev/reference/parplot.html b/docs/dev/reference/parplot.html index 720c0b2a..ee2ec7b2 100644 --- a/docs/dev/reference/parplot.html +++ b/docs/dev/reference/parplot.html @@ -19,13 +19,13 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><meta n </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Functions and data</a> + <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -36,6 +36,8 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><meta n <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -43,22 +45,29 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><meta n <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + <li class="dropdown-header">Performance</li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -66,6 +75,14 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><meta n <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul></li> <li> <a href="../news/index.html">News</a> @@ -174,7 +191,7 @@ doi: 10.1186/s12859-021-04373-4.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer></div> diff --git a/docs/dev/reference/saem-1.png b/docs/dev/reference/saem-1.png Binary files differindex 9e310252..1fa206c4 100644 --- a/docs/dev/reference/saem-1.png +++ b/docs/dev/reference/saem-1.png diff --git a/docs/dev/reference/saem-2.png b/docs/dev/reference/saem-2.png Binary files differindex de1bcf57..e5c62c35 100644 --- a/docs/dev/reference/saem-2.png +++ b/docs/dev/reference/saem-2.png diff --git a/docs/dev/reference/saem-3.png b/docs/dev/reference/saem-3.png Binary files differindex de569ce0..f191ad3a 100644 --- a/docs/dev/reference/saem-3.png +++ b/docs/dev/reference/saem-3.png diff --git a/docs/dev/reference/saem-4.png b/docs/dev/reference/saem-4.png Binary files differindex 0f2ee3e7..a74e21f8 100644 --- a/docs/dev/reference/saem-4.png +++ b/docs/dev/reference/saem-4.png diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 131b168b..66e5478a 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -19,13 +19,13 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Functions and data</a> + <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -36,6 +36,8 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -43,22 +45,29 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + <li class="dropdown-header">Performance</li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -66,6 +75,14 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul></li> <li> <a href="../news/index.html">News</a> @@ -430,10 +447,10 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span> <span class="r-in"><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_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.3 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Dec 7 16:22:26 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Dec 7 16:22:26 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Feb 17 22:22:33 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Feb 17 22:22:33 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -448,7 +465,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.508 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 4.212 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Constant variance </span> @@ -711,12 +728,31 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 120 12.1 12.79238 -0.69238 1.882 -0.36791</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># The following takes about 6 minutes</span></span></span> -<span class="r-in"><span><span class="co">#f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve",</span></span></span> -<span class="r-in"><span><span class="co"># control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span></span></span> +<span class="r-in"><span><span class="va">f_saem_dfop_sfo_deSolve</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>,</span></span> +<span class="r-in"><span> nbiter.saemix <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="fl">200</span>, <span class="fl">80</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> DINTDY- T (=R1) illegal </span> +<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 70</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> T not in interval TCUR - HU (= R1) to TCUR (=R2) </span> +<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 53.1122, R2 = 56.6407</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> DINTDY- T (=R1) illegal </span> +<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 91</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> T not in interval TCUR - HU (= R1) to TCUR (=R2) </span> +<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 53.1122, R2 = 56.6407</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> DLSODA- Trouble in DINTDY. ITASK = I1, TOUT = R1</span> +<span class="r-out co"><span class="r-pr">#></span> In above message, I1 = 1</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 91</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Error in deSolve::lsoda(y = odeini, times = outtimes, func = x$symbols, : </span> +<span class="r-out co"><span class="r-pr">#></span> illegal input detected before taking any integration steps - see written message</span> <span class="r-in"><span></span></span> -<span class="r-in"><span><span class="co">#saemix::compare.saemix(list(</span></span></span> -<span class="r-in"><span><span class="co"># f_saem_dfop_sfo$so,</span></span></span> -<span class="r-in"><span><span class="co"># f_saem_dfop_sfo_deSolve$so))</span></span></span> +<span class="r-in"><span><span class="co">#anova(</span></span></span> +<span class="r-in"><span><span class="co"># f_saem_dfop_sfo,</span></span></span> +<span class="r-in"><span><span class="co"># f_saem_dfop_sfo_deSolve))</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># If the model supports it, we can also use eigenvalue based solutions, which</span></span></span> <span class="r-in"><span><span class="co"># take a similar amount of time</span></span></span> @@ -737,7 +773,7 @@ using <a href="mmkin.html">mmkin</a>.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer></div> diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index 3b5869f1..aa573589 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -21,13 +21,13 @@ endpoints such as formation fractions and DT50 values. Optionally </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Functions and data</a> + <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -38,6 +38,8 @@ endpoints such as formation fractions and DT50 values. Optionally <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -45,22 +47,29 @@ endpoints such as formation fractions and DT50 values. Optionally <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + <li class="dropdown-header">Performance</li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -68,6 +77,14 @@ endpoints such as formation fractions and DT50 values. Optionally <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul></li> <li> <a href="../news/index.html">News</a> @@ -102,7 +119,7 @@ endpoints such as formation fractions and DT50 values. Optionally <div id="ref-usage"> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, data <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span> +<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">object</span>, data <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for summary.saem.mmkin</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 class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">verbose</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> @@ -292,12 +309,12 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> <span class="r-out co"><span class="r-pr">#></span> a.1 0.67696663 0.87777355 1.07858048</span> <span class="r-out co"><span class="r-pr">#></span> b.1 0.06363957 0.07878001 0.09392044</span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><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_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.3 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Dec 15 14:47:14 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Dec 15 14:47:14 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Feb 17 22:24:21 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Feb 17 22:24:21 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -312,7 +329,7 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.623 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.426 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> @@ -627,7 +644,7 @@ saemix authors for the parts inherited from saemix.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer></div> diff --git a/docs/dev/reference/summary_listing.html b/docs/dev/reference/summary_listing.html index 876412cc..e584416a 100644 --- a/docs/dev/reference/summary_listing.html +++ b/docs/dev/reference/summary_listing.html @@ -18,13 +18,13 @@ option results = "asis".'><meta name="robots" content="noindex"><!-- mathjax --> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Functions and data</a> + <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -35,6 +35,8 @@ option results = "asis".'><meta name="robots" content="noindex"><!-- mathjax --> <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -42,22 +44,29 @@ option results = "asis".'><meta name="robots" content="noindex"><!-- mathjax --> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + <li class="dropdown-header">Performance</li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -65,6 +74,14 @@ option results = "asis".'><meta name="robots" content="noindex"><!-- mathjax --> <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul></li> <li> <a href="../news/index.html">News</a> diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda Binary files differindex 0a88d04f..533271cf 100644 --- a/vignettes/web_only/mkin_benchmarks.rda +++ b/vignettes/web_only/mkin_benchmarks.rda diff --git a/vignettes/web_only/saem_benchmarks.rda b/vignettes/web_only/saem_benchmarks.rda Binary files differindex 564c851b..319b2f5f 100644 --- a/vignettes/web_only/saem_benchmarks.rda +++ b/vignettes/web_only/saem_benchmarks.rda |
