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- </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Example evaluations of the dimethenamid data -from 2018</h1> + + +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + + <h1>Example evaluations of the dimethenamid data from 2018</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change 1 July 2022, -built on 19 May 2023</h4> +built on 16 Feb 2025</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> - + <div class="d-none name"><code>dimethenamid_2018.rmd</code></div> </div> @@ -264,7 +212,7 @@ Status of individual fits: dataset model Calke Borstel Flaach BBA 2.2 BBA 2.3 Elliot - DFOP OK OK C OK C OK + DFOP OK OK OK OK C OK C: Optimisation did not converge: iteration limit reached without convergence (10) @@ -320,7 +268,7 @@ indicates that this difference is significant as the p-value is below <pre><code> Model df AIC BIC logLik Test L.Ratio p-value f_parent_nlme_sfo_const 1 5 796.60 811.82 -393.30 f_parent_nlme_sfo_tc 2 6 798.60 816.86 -393.30 1 vs 2 0.00 0.998 -f_parent_nlme_dfop_tc 3 10 671.91 702.34 -325.96 2 vs 3 134.69 <.0001</code></pre> +f_parent_nlme_dfop_tc 3 10 671.91 702.34 -325.95 2 vs 3 134.69 <.0001</code></pre> <p>In addition to these fits, attempts were also made to include correlations between random effects by using the log Cholesky parameterisation of the matrix specifying them. The code used for these @@ -409,11 +357,11 @@ DMTA_0 97.99583 96.50079 99.4909 k1 0.06377 0.03432 0.0932 k2 0.00848 0.00444 0.0125 g 0.95701 0.91313 1.0009 -a.1 1.82141 1.65122 1.9916 -SD.DMTA_0 1.64787 0.45772 2.8380 +a.1 1.82141 1.60516 2.0377 +SD.DMTA_0 1.64787 0.45729 2.8384 SD.k1 0.57439 0.24731 0.9015 -SD.k2 0.03296 -2.50195 2.5679 -SD.g 1.10266 0.32369 1.8816</code></pre> +SD.k2 0.03296 -2.50524 2.5712 +SD.g 1.10266 0.32354 1.8818</code></pre> <p>While the other parameters converge to credible values, the variance of k2 (<code>omega2.k2</code>) converges to a very small value. The printout of the <code>saem.mmkin</code> model shows that the estimated @@ -447,17 +395,17 @@ Likelihood computed by importance sampling 666 664 -323 Fitted parameters: - estimate lower upper -DMTA_0 98.27617 96.3088 100.2436 -k1 0.06437 0.0337 0.0950 -k2 0.00880 0.0063 0.0113 -g 0.95249 0.9100 0.9949 -a.1 1.06161 0.8625 1.2607 -b.1 0.02967 0.0226 0.0367 -SD.DMTA_0 2.06075 0.4187 3.7028 -SD.k1 0.59357 0.2561 0.9310 -SD.k2 0.00292 -10.2960 10.3019 -SD.g 1.05725 0.3808 1.7337</code></pre> + estimate lower upper +DMTA_0 98.24165 96.29190 100.1914 +k1 0.06421 0.03352 0.0949 +k2 0.00866 0.00617 0.0111 +g 0.95340 0.91218 0.9946 +a.1 1.06463 0.87979 1.2495 +b.1 0.02964 0.02266 0.0366 +SD.DMTA_0 2.03611 0.40361 3.6686 +SD.k1 0.59534 0.25692 0.9338 +SD.k2 0.00042 -73.00540 73.0062 +SD.g 1.04234 0.37189 1.7128</code></pre> <p>Doubling the number of iterations in the first phase of the algorithm leads to a slightly lower likelihood, and therefore to slightly higher AIC and BIC values. With even more iterations, the algorithm stops with @@ -489,8 +437,8 @@ comparison function of the saemix package:</p> SFO const 796.38 795.34 SFO tc 798.38 797.13 DFOP const 705.75 703.88 -DFOP tc 665.65 663.57 -DFOP tc more iterations 665.88 663.80</code></pre> +DFOP tc 665.67 663.59 +DFOP tc more iterations 665.85 663.76</code></pre> <p>In order to check the influence of the likelihood calculation algorithms implemented in saemix, the likelihood from Gaussian quadrature is added to the best fit, and the AIC values obtained from @@ -505,7 +453,7 @@ the three methods are compared.</p> <span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix_methods</span><span class="op">)</span></span></code></pre></div> <pre><code> is gq lin -665.65 665.68 665.11 </code></pre> +665.67 665.74 665.13 </code></pre> <p>The AIC values based on importance sampling and Gaussian quadrature are very similar. Using linearisation is known to be less accurate, but still gives a similar value.</p> @@ -530,7 +478,7 @@ using defaults for the fit.</p> <span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix_methods_defaults</span><span class="op">)</span></span></code></pre></div> <pre><code> is gq lin -669.77 669.36 670.95 </code></pre> +670.09 669.37 671.29 </code></pre> </div> </div> <div class="section level3"> @@ -578,15 +526,15 @@ iterations second phase, 15 chains).</p> <td align="left">DFOP</td> <td align="left">const</td> <td align="right">NA</td> -<td align="right">709.26</td> +<td align="right">704.95</td> <td align="right">705.75</td> </tr> <tr class="even"> <td align="left">DFOP</td> <td align="left">tc</td> <td align="right">671.91</td> -<td align="right">665.11</td> -<td align="right">665.65</td> +<td align="right">665.13</td> +<td align="right">665.67</td> </tr> </tbody> </table> @@ -615,13 +563,13 @@ 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 4.3.0 (2023-04-21) -Platform: x86_64-pc-linux-gnu (64-bit) +<pre><code>R version 4.4.2 (2024-10-31) +Platform: x86_64-pc-linux-gnu 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; LAPACK version 3.11.0 +BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -638,23 +586,22 @@ 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_1.2.5 knitr_1.42 +[1] nlme_3.1-166 mkin_1.2.10 knitr_1.49 loaded via a namespace (and not attached): - [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 - [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 - [9] grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4 -[13] DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 purrr_1.0.1 -[17] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 -[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 munsell_0.5.0 -[25] cachem_1.0.8 yaml_2.3.7 tools_4.3.0 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 highr_0.10 -[49] xfun_0.39 tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 -[53] htmltools_0.5.5 rmarkdown_2.21 compiler_4.3.0 </code></pre> + [1] gtable_0.3.6 jsonlite_1.8.9 dplyr_1.1.4 compiler_4.4.2 + [5] tidyselect_1.2.1 parallel_4.4.2 gridExtra_2.3 jquerylib_0.1.4 + [9] systemfonts_1.1.0 scales_1.3.0 textshaping_0.4.1 yaml_2.3.10 +[13] fastmap_1.2.0 lattice_0.22-6 ggplot2_3.5.1 R6_2.5.1 +[17] generics_0.1.3 lmtest_0.9-40 MASS_7.3-61 htmlwidgets_1.6.4 +[21] tibble_3.2.1 desc_1.4.3 munsell_0.5.1 bslib_0.8.0 +[25] pillar_1.9.0 rlang_1.1.4 utf8_1.2.4 cachem_1.1.0 +[29] xfun_0.49 fs_1.6.5 sass_0.4.9 cli_3.6.3 +[33] pkgdown_2.1.1 magrittr_2.0.3 digest_0.6.37 grid_4.4.2 +[37] npde_3.5 mclust_6.1.1 lifecycle_1.0.4 vctrs_0.6.5 +[41] evaluate_1.0.1 glue_1.8.0 ragg_1.3.3 zoo_1.8-12 +[45] saemix_3.3 fansi_1.0.6 colorspace_2.1-1 rmarkdown_2.29 +[49] pkgconfig_2.0.3 tools_4.4.2 htmltools_0.5.8.1</code></pre> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> @@ -679,35 +626,26 @@ November 2017</span>.”</span> <a href="https://open.efsa.europa.eu/study-inven </div> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> -</div> - + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside> </div> - <footer><div class="copyright"> - <p></p> -<p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> - </footer> + </footer> </div> - - + </body> </html> |