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Diffstat (limited to 'docs/articles/web_only/dimethenamid_2018.html')
| -rw-r--r-- | docs/articles/web_only/dimethenamid_2018.html | 55 |
1 files changed, 29 insertions, 26 deletions
diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html index 4575067b..a89631a2 100644 --- a/docs/articles/web_only/dimethenamid_2018.html +++ b/docs/articles/web_only/dimethenamid_2018.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -135,7 +135,7 @@ from 2018</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change 1 July 2022, -built on 20 Apr 2023</h4> +built on 19 May 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/dimethenamid_2018.rmd" class="external-link"><code>vignettes/web_only/dimethenamid_2018.rmd</code></a></small> <div class="hidden name"><code>dimethenamid_2018.rmd</code></div> @@ -222,12 +222,12 @@ least in some datasets the degradation slows down towards later time points, and that the scatter of the residuals error is smaller for smaller values (panel to the right):</p> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_sfo_const-1.png" width="700"></p> <p>Using biexponential decline (DFOP) results in a slightly more random scatter of the residuals:</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/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const-1.png" width="700"></p> <p>The population curve (bold line) in the above plot results from taking the mean of the individual transformed parameters, i.e. of log k1 @@ -239,7 +239,7 @@ dominates the average. This is alleviated if only rate constants that pass the t-test for significant difference from zero (on the untransformed scale) are considered in the averaging:</p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const_test-1.png" width="700"></p> <p>While this is visually much more satisfactory, such an average procedure could introduce a bias, as not all results from the individual @@ -251,7 +251,7 @@ degradation model and the error model (see below).</p> predicted residues is reduced by using the two-component error model:</p> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_tc_test-1.png" width="700"></p> <p>However, note that in the case of using this error model, the fits to the Flaach and BBA 2.3 datasets appear to be ill-defined, indicated by @@ -341,7 +341,7 @@ effects does not improve the fits.</p> <p>The selected model (DFOP with two-component error) fitted to the data assuming no correlations between random effects is shown below.</p> <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">f_parent_nlme_dfop_tc</span><span class="op">)</span></span></code></pre></div> +<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">f_parent_nlme_dfop_tc</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/plot_parent_nlme-1.png" width="700"></p> </div> <div class="section level4"> @@ -549,7 +549,7 @@ iterations second phase, 15 chains).</p> <span> saemix_is <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>,</span> <span> <span class="va">f_parent_saemix_dfop_const</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span>, <span class="va">AIC</span>, method <span class="op">=</span> <span class="st">"is"</span><span class="op">)</span></span> <span><span class="op">)</span></span> -<span><span class="fu">kable</span><span class="op">(</span><span class="va">AIC_all</span><span class="op">)</span></span></code></pre></div> +<span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="va">AIC_all</span><span class="op">)</span></span></code></pre></div> <table class="table"> <thead><tr class="header"> <th align="left">Degradation model</th> @@ -614,13 +614,13 @@ satisfactory precision.</p> </h2> <div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> -<pre><code>R version 4.2.3 (2023-03-15) +<pre><code>R version 4.3.0 Patched (2023-05-18 r84448) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so +BLAS: /home/jranke/svn/R/r-patched/build/lib/libRblas.so +LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3; LAPACK version 3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -630,27 +630,30 @@ locale: [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C +time zone: Europe/Berlin +tzcode source: system (glibc) + attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: -[1] saemix_3.2 npde_3.3 nlme_3.1-162 mkin_1.2.3 knitr_1.42 +[1] nlme_3.1-162 mkin_1.2.4 knitr_1.42 loaded via a namespace (and not attached): - [1] highr_0.10 pillar_1.9.0 bslib_0.4.2 compiler_4.2.3 - [5] jquerylib_0.1.4 tools_4.2.3 mclust_6.0.0 digest_0.6.31 - [9] tibble_3.2.1 jsonlite_1.8.4 evaluate_0.20 memoise_2.0.1 -[13] lifecycle_1.0.3 gtable_0.3.3 lattice_0.21-8 pkgconfig_2.0.3 -[17] rlang_1.1.0 DBI_1.1.3 cli_3.6.1 yaml_2.3.7 -[21] parallel_4.2.3 pkgdown_2.0.7 xfun_0.38 fastmap_1.1.1 -[25] gridExtra_2.3 dplyr_1.1.1 stringr_1.5.0 generics_0.1.3 -[29] desc_1.4.2 fs_1.6.1 vctrs_0.6.1 sass_0.4.5 -[33] systemfonts_1.0.4 tidyselect_1.2.0 rprojroot_2.0.3 lmtest_0.9-40 -[37] grid_4.2.3 glue_1.6.2 R6_2.5.1 textshaping_0.3.6 -[41] fansi_1.0.4 rmarkdown_2.21 purrr_1.0.1 ggplot2_3.4.2 -[45] magrittr_2.0.3 codetools_0.2-19 scales_1.2.1 htmltools_0.5.5 -[49] colorspace_2.1-0 ragg_1.2.5 utf8_1.2.3 stringi_1.7.12 -[53] munsell_0.5.0 cachem_1.0.7 zoo_1.8-12 </code></pre> + [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 saemix_3.2 + [5] stringi_1.7.12 lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 + [9] evaluate_0.21 grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 +[13] jsonlite_1.8.4 DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 +[17] purrr_1.0.1 fansi_1.0.4 scales_1.2.1 textshaping_0.3.6 +[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 munsell_0.5.0 +[25] cachem_1.0.8 yaml_2.3.7 tools_4.3.0 parallel_4.3.0 +[29] memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 +[33] vctrs_0.6.2 R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 +[37] stringr_1.5.0 fs_1.6.2 ragg_1.2.5 pkgconfig_2.0.3 +[41] desc_1.4.2 pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 +[45] gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 xfun_0.39 +[49] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 npde_3.3 +[53] htmltools_0.5.5 rmarkdown_2.21 compiler_4.3.0 </code></pre> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> |