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Diffstat (limited to 'docs/dev/articles/prebuilt/2022_dmta_pathway.html')
| -rw-r--r-- | docs/dev/articles/prebuilt/2022_dmta_pathway.html | 79 |
1 files changed, 45 insertions, 34 deletions
diff --git a/docs/dev/articles/prebuilt/2022_dmta_pathway.html b/docs/dev/articles/prebuilt/2022_dmta_pathway.html index 0285a193..959f3429 100644 --- a/docs/dev/articles/prebuilt/2022_dmta_pathway.html +++ b/docs/dev/articles/prebuilt/2022_dmta_pathway.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span> </span> </div> @@ -135,8 +135,8 @@ residue data on dimethenamid and dimethenamid-P</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change on 8 January -2023, last compiled on 16 April 2023</h4> + <h4 data-toc-skip class="date">Last change on 20 April 2023, +last compiled on 20 April 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_dmta_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_dmta_pathway.rmd</code></a></small> <div class="hidden name"><code>2022_dmta_pathway.rmd</code></div> @@ -156,7 +156,7 @@ can be fitted with the mkin package.</p> 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data) of the German Environment Agency carried out in 2022 and 2023.</p> -<p>The mkin package is used in version 1.2.3, which is currently under +<p>The mkin package is used in version 1.2.4, 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 @@ -171,10 +171,17 @@ processing, the <code>parallel</code> package is used.</p> <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span> <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">parallel</span><span class="op">)</span></span> <span><span class="va">n_cores</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span></span> -<span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="op">{</span></span> -<span> <span class="va">cl</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makePSOCKcluster</a></span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span></span> -<span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span> -<span> <span class="va">cl</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makeForkCluster</a></span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># We need to start a new cluster after defining a compiled model that is</span></span> +<span><span class="co"># saved as a DLL to the user directory, therefore we define a function</span></span> +<span><span class="co"># This is used again after defining the pathway model</span></span> +<span><span class="va">start_cluster</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="va">ret</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makePSOCKcluster</a></span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span></span> +<span> <span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span> +<span> <span class="va">ret</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makeForkCluster</a></span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span></span> +<span> <span class="op">}</span></span> +<span> <span class="kw"><a href="https://rdrr.io/r/base/function.html" class="external-link">return</a></span><span class="op">(</span><span class="va">ret</span><span class="op">)</span></span> <span><span class="op">}</span></span></code></pre></div> </div> <div class="section level2"> @@ -1441,6 +1448,8 @@ of parent models tested here.</p> <span> unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> quiet <span class="op">=</span> <span class="cn">TRUE</span></span> <span><span class="op">)</span></span> +<span><span class="va">cl</span> <span class="op"><-</span> <span class="fu">start_cluster</span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span></span> +<span></span> <span><span class="va">deg_mods_1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span> <span> sfo_path_1 <span class="op">=</span> <span class="va">m_sfo_path_1</span>,</span> <span> fomc_path_1 <span class="op">=</span> <span class="va">m_fomc_path_1</span>,</span> @@ -1883,6 +1892,8 @@ SFORB pathway fit with two-component error, reduced parameter model </div> <p>Plots of the remaining fits and listings for all successful fits are shown in the Appendix.</p> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></code></pre></div> </div> <div class="section level2"> <h2 id="conclusions">Conclusions<a class="anchor" aria-label="anchor" href="#conclusions"></a> @@ -1921,24 +1932,24 @@ Level with Nonlinear Mixed-Effects Models.”</span> <em>Environments</em> <div class="section level3"> <h3 id="plots-of-hierarchical-fits-not-selected-for-refinement">Plots of hierarchical fits not selected for refinement<a class="anchor" aria-label="anchor" href="#plots-of-hierarchical-fits-not-selected-for-refinement"></a> </h3> -<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"sfo_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> -<img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-5-1.png" alt="SFO pathway fit with two-component error" width="700"><p class="caption"> +<img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-6-1.png" alt="SFO pathway fit with two-component error" width="700"><p class="caption"> SFO pathway fit with two-component error </p> </div> -<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"fomc_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> -<img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-6-1.png" alt="FOMC pathway fit with two-component error" width="700"><p class="caption"> +<img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-7-1.png" alt="FOMC pathway fit with two-component error" width="700"><p class="caption"> FOMC pathway fit with two-component error </p> </div> -<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"sforb_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> -<img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-7-1.png" alt="HS pathway fit with two-component error" width="700"><p class="caption"> +<img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-8-1.png" alt="HS pathway fit with two-component error" width="700"><p class="caption"> HS pathway fit with two-component error </p> </div> @@ -1961,9 +1972,9 @@ error<a class="anchor" aria-label="anchor" href="#improved-fit-of-the-sforb-path <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.2.2 Patched (2022-11-10 r83330) +<pre><code>R version 4.2.3 (2023-03-15) Platform: x86_64-pc-linux-gnu (64-bit) -Running under: Debian GNU/Linux bookworm/sid +Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 @@ -1982,31 +1993,31 @@ 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_1.42 mkin_1.2.4 loaded via a namespace (and not attached): - [1] deSolve_1.34 zoo_1.8-11 tidyselect_1.2.0 xfun_0.35 - [5] bslib_0.4.2 purrr_1.0.0 lattice_0.20-45 colorspace_2.0-3 - [9] vctrs_0.5.1 generics_0.1.3 htmltools_0.5.4 yaml_2.3.6 -[13] pkgbuild_1.4.0 utf8_1.2.2 rlang_1.0.6 pkgdown_2.0.7 -[17] jquerylib_0.1.4 pillar_1.8.1 glue_1.6.2 DBI_1.1.3 -[21] lifecycle_1.0.3 stringr_1.5.0 munsell_0.5.0 gtable_0.3.1 -[25] ragg_1.2.4 codetools_0.2-18 memoise_2.0.1 evaluate_0.19 -[29] inline_0.3.19 callr_3.7.3 fastmap_1.1.0 ps_1.7.2 -[33] lmtest_0.9-40 fansi_1.0.3 highr_0.9 scales_1.2.1 -[37] cachem_1.0.6 desc_1.4.2 jsonlite_1.8.4 systemfonts_1.0.4 -[41] fs_1.5.2 textshaping_0.3.6 gridExtra_2.3 ggplot2_3.4.0 -[45] digest_0.6.31 stringi_1.7.8 processx_3.8.0 dplyr_1.0.10 -[49] grid_4.2.2 rprojroot_2.0.3 cli_3.5.0 tools_4.2.2 -[53] magrittr_2.0.3 sass_0.4.4 tibble_3.1.8 crayon_1.5.2 -[57] pkgconfig_2.0.3 prettyunits_1.1.1 assertthat_0.2.1 rmarkdown_2.19 -[61] R6_2.5.1 mclust_6.0.0 nlme_3.1-161 compiler_4.2.2 </code></pre> + [1] deSolve_1.35 zoo_1.8-12 tidyselect_1.2.0 xfun_0.38 + [5] bslib_0.4.2 purrr_1.0.1 lattice_0.21-8 colorspace_2.1-0 + [9] vctrs_0.6.1 generics_0.1.3 htmltools_0.5.5 yaml_2.3.7 +[13] utf8_1.2.3 rlang_1.1.0 pkgbuild_1.4.0 pkgdown_2.0.7 +[17] jquerylib_0.1.4 pillar_1.9.0 glue_1.6.2 DBI_1.1.3 +[21] lifecycle_1.0.3 stringr_1.5.0 munsell_0.5.0 gtable_0.3.3 +[25] ragg_1.2.5 codetools_0.2-19 memoise_2.0.1 evaluate_0.20 +[29] inline_0.3.19 callr_3.7.3 fastmap_1.1.1 ps_1.7.4 +[33] lmtest_0.9-40 fansi_1.0.4 highr_0.10 scales_1.2.1 +[37] cachem_1.0.7 desc_1.4.2 jsonlite_1.8.4 systemfonts_1.0.4 +[41] fs_1.6.1 textshaping_0.3.6 gridExtra_2.3 ggplot2_3.4.2 +[45] digest_0.6.31 stringi_1.7.12 processx_3.8.0 dplyr_1.1.1 +[49] grid_4.2.3 rprojroot_2.0.3 cli_3.6.1 tools_4.2.3 +[53] magrittr_2.0.3 sass_0.4.5 tibble_3.2.1 crayon_1.5.2 +[57] pkgconfig_2.0.3 prettyunits_1.1.1 rmarkdown_2.21 R6_2.5.1 +[61] mclust_6.0.0 nlme_3.1-162 compiler_4.2.3 </code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> <pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64940452 kB</code></pre> +<pre><code>MemTotal: 64936316 kB</code></pre> </div> </div> </div> |