diff options
author | Johannes Ranke <johannes.ranke@jrwb.de> | 2025-02-16 17:27:18 +0100 |
---|---|---|
committer | Johannes Ranke <johannes.ranke@jrwb.de> | 2025-02-16 17:29:28 +0100 |
commit | 4f62f39b8979cb3a5c52d65d425e530dc0770665 (patch) | |
tree | 895d4bde0773a600943e5c308e17651c12358a67 /docs/dev/articles/web_only | |
parent | 44c30938872bd7cc80a4c84dd4db593e26000fce (diff) |
The special case occurs if not observed data for time zero
are available. Fixes #16. Write NEWS and update docs.
A lot of html was regenerated, because I had checked out
the main branch in between, which made pkgdown believe that
I have changed the help files.
Diffstat (limited to 'docs/dev/articles/web_only')
-rw-r--r-- | docs/dev/articles/web_only/FOCUS_Z.html | 2 | ||||
-rw-r--r-- | docs/dev/articles/web_only/NAFTA_examples.html | 2 | ||||
-rw-r--r-- | docs/dev/articles/web_only/benchmarks.html | 24 | ||||
-rw-r--r-- | docs/dev/articles/web_only/compiled_models.html | 14 | ||||
-rw-r--r-- | docs/dev/articles/web_only/dimethenamid_2018.html | 12 | ||||
-rw-r--r-- | docs/dev/articles/web_only/multistart.html | 2 | ||||
-rw-r--r-- | docs/dev/articles/web_only/saem_benchmarks.html | 22 |
7 files changed, 39 insertions, 39 deletions
diff --git a/docs/dev/articles/web_only/FOCUS_Z.html b/docs/dev/articles/web_only/FOCUS_Z.html index 40ce9e01..9db2cf7e 100644 --- a/docs/dev/articles/web_only/FOCUS_Z.html +++ b/docs/dev/articles/web_only/FOCUS_Z.html @@ -85,7 +85,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 16 January 2018 -(rebuilt 2025-02-14)</h4> +(rebuilt 2025-02-16)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/FOCUS_Z.rmd" class="external-link"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small> <div class="d-none name"><code>FOCUS_Z.rmd</code></div> diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html index 6bf39b2c..54c45b3e 100644 --- a/docs/dev/articles/web_only/NAFTA_examples.html +++ b/docs/dev/articles/web_only/NAFTA_examples.html @@ -85,7 +85,7 @@ Ranke</h4> <h4 data-toc-skip class="date">26 February 2019 (rebuilt -2025-02-14)</h4> +2025-02-16)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/NAFTA_examples.rmd" class="external-link"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> <div class="d-none name"><code>NAFTA_examples.rmd</code></div> diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html index bd6a443a..bb5647d3 100644 --- a/docs/dev/articles/web_only/benchmarks.html +++ b/docs/dev/articles/web_only/benchmarks.html @@ -85,7 +85,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 17 February 2023 -(rebuilt 2025-02-14)</h4> +(rebuilt 2025-02-16)</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="d-none name"><code>benchmarks.rmd</code></div> @@ -428,8 +428,8 @@ models fitted to two datasets, i.e. eight fits for each test.</p> <td align="left">Ryzen 9 7950X</td> <td align="left">4.4.2</td> <td align="left">1.2.10</td> -<td align="right">1.371</td> -<td align="right">1.980</td> +<td align="right">1.407</td> +<td align="right">1.990</td> </tr> </tbody> </table> @@ -717,9 +717,9 @@ for each test.</p> <td align="left">Ryzen 9 7950X</td> <td align="left">4.4.2</td> <td align="left">1.2.10</td> -<td align="right">0.762</td> -<td align="right">2.179</td> -<td align="right">1.131</td> +<td align="right">0.775</td> +<td align="right">2.199</td> +<td align="right">1.161</td> </tr> </tbody> </table> @@ -1097,12 +1097,12 @@ dataset, i.e. one fit for each test.</p> <td align="left">Ryzen 9 7950X</td> <td align="left">4.4.2</td> <td align="left">1.2.10</td> -<td align="right">0.426</td> -<td align="right">0.533</td> -<td align="right">0.565</td> -<td align="right">1.296</td> -<td align="right">0.728</td> -<td align="right">0.978</td> +<td align="right">0.433</td> +<td align="right">0.541</td> +<td align="right">0.576</td> +<td align="right">1.307</td> +<td align="right">0.744</td> +<td align="right">0.988</td> </tr> </tbody> </table> diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html index 113f7b67..a88a19ee 100644 --- a/docs/dev/articles/web_only/compiled_models.html +++ b/docs/dev/articles/web_only/compiled_models.html @@ -84,7 +84,7 @@ <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">2025-02-14</h4> + <h4 data-toc-skip class="date">2025-02-16</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/compiled_models.rmd" class="external-link"><code>vignettes/web_only/compiled_models.rmd</code></a></small> <div class="d-none name"><code>compiled_models.rmd</code></div> @@ -162,10 +162,10 @@ solution is also implemented, which is included in the tests below.</p> <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="st">"R package rbenchmark is not available"</span><span class="op">)</span></span> <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 4 analytical 1 1.000 0.102</span></span> -<span><span class="co">## 3 deSolve, compiled 1 1.324 0.135</span></span> -<span><span class="co">## 2 Eigenvalue based 1 1.706 0.174</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 22.627 2.308</span></span></code></pre> +<span><span class="co">## 4 analytical 1 1.000 0.115</span></span> +<span><span class="co">## 3 deSolve, compiled 1 1.217 0.140</span></span> +<span><span class="co">## 2 Eigenvalue based 1 1.652 0.190</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 20.522 2.360</span></span></code></pre> <p>We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.</p> </div> @@ -196,8 +196,8 @@ compiled code is available.</p> <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 2 deSolve, compiled 1 1.000 0.170</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 23.865 4.057</span></span></code></pre> +<span><span class="co">## 2 deSolve, compiled 1 1.000 0.180</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 23.656 4.258</span></span></code></pre> <p>Here we get a performance benefit of a factor of 24 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 1.2.10 on</p> diff --git a/docs/dev/articles/web_only/dimethenamid_2018.html b/docs/dev/articles/web_only/dimethenamid_2018.html index 572f253d..0bbf0b73 100644 --- a/docs/dev/articles/web_only/dimethenamid_2018.html +++ b/docs/dev/articles/web_only/dimethenamid_2018.html @@ -85,7 +85,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 1 July 2022, -built on 14 Feb 2025</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="d-none name"><code>dimethenamid_2018.rmd</code></div> @@ -586,7 +586,7 @@ attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: -[1] saemix_3.3 npde_3.5 nlme_3.1-166 mkin_1.2.10 knitr_1.49 +[1] nlme_3.1-166 mkin_1.2.10 knitr_1.49 loaded via a namespace (and not attached): [1] gtable_0.3.6 jsonlite_1.8.9 dplyr_1.1.4 compiler_4.4.2 @@ -598,10 +598,10 @@ loaded via a namespace (and not attached): [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] mclust_6.1.1 lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.1 -[41] glue_1.8.0 codetools_0.2-20 ragg_1.3.3 zoo_1.8-12 -[45] fansi_1.0.6 colorspace_2.1-1 rmarkdown_2.29 pkgconfig_2.0.3 -[49] tools_4.4.2 htmltools_0.5.8.1</code></pre> +[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> diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html index 83073979..39bb2947 100644 --- a/docs/dev/articles/web_only/multistart.html +++ b/docs/dev/articles/web_only/multistart.html @@ -85,7 +85,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 20 April 2023 -(rebuilt 2025-02-14)</h4> +(rebuilt 2025-02-16)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/multistart.rmd" class="external-link"><code>vignettes/web_only/multistart.rmd</code></a></small> <div class="d-none name"><code>multistart.rmd</code></div> diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html index d4cd0d6f..b76384da 100644 --- a/docs/dev/articles/web_only/saem_benchmarks.html +++ b/docs/dev/articles/web_only/saem_benchmarks.html @@ -85,7 +85,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 17 February 2023 -(rebuilt 2025-02-14)</h4> +(rebuilt 2025-02-16)</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="d-none name"><code>saem_benchmarks.rmd</code></div> @@ -408,9 +408,9 @@ systems. All trademarks belong to their respective owners.</p> <td align="left">1.2.10</td> <td align="left">3.3</td> <td align="right">1.115</td> -<td align="right">2.277</td> -<td align="right">1.945</td> -<td align="right">2.134</td> +<td align="right">2.263</td> +<td align="right">1.991</td> +<td align="right">2.193</td> </tr> </tbody> </table> @@ -542,10 +542,10 @@ systems. All trademarks belong to their respective owners.</p> <td align="left">Linux</td> <td align="left">1.2.10</td> <td align="left">3.3</td> -<td align="right">2.372</td> -<td align="right">3.137</td> -<td align="right">3.100</td> -<td align="right">3.281</td> +<td align="right">2.380</td> +<td align="right">3.147</td> +<td align="right">3.131</td> +<td align="right">3.331</td> </tr> </tbody> </table> @@ -657,8 +657,8 @@ systems. All trademarks belong to their respective owners.</p> <td align="left">Linux</td> <td align="left">1.2.10</td> <td align="left">3.3</td> -<td align="right">11.590</td> -<td align="right">279.782</td> +<td align="right">11.581</td> +<td align="right">296.184</td> </tr> </tbody> </table> @@ -758,7 +758,7 @@ systems. All trademarks belong to their respective owners.</p> <td align="left">Linux</td> <td align="left">1.2.10</td> <td align="left">3.3</td> -<td align="right">469.036</td> +<td align="right">486.856</td> </tr> </tbody> </table> |