diff options
Diffstat (limited to 'docs/dev')
| -rw-r--r-- | docs/dev/articles/web_only/benchmarks.html | 29 | ||||
| -rw-r--r-- | docs/dev/articles/web_only/saem_benchmarks.html | 29 | ||||
| -rw-r--r-- | docs/dev/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/dev/reference/Rplot001.png | bin | 1011 -> 22432 bytes | |||
| -rw-r--r-- | docs/dev/reference/logLik.saem.mmkin.html | 5 | ||||
| -rw-r--r-- | docs/dev/reference/mkinpredict.html | 13 | ||||
| -rw-r--r-- | docs/dev/reference/saem.html | 11 |
7 files changed, 52 insertions, 37 deletions
diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html index cb048453..5c7aa3dc 100644 --- a/docs/dev/articles/web_only/benchmarks.html +++ b/docs/dev/articles/web_only/benchmarks.html @@ -78,7 +78,10 @@ <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -109,7 +112,7 @@ <h1 data-toc-skip>Benchmark timings for mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-11-14)</h4> + <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-11-15)</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> @@ -348,8 +351,8 @@ <td align="left">Ryzen 7 1700</td> <td align="left">4.2.2</td> <td align="left">1.2.0</td> -<td align="right">2.030</td> -<td align="right">3.791</td> +<td align="right">2.129</td> +<td align="right">3.784</td> </tr> </tbody> </table> @@ -527,9 +530,9 @@ <td align="left">Ryzen 7 1700</td> <td align="left">4.2.2</td> <td align="left">1.2.0</td> -<td align="right">1.579</td> -<td align="right">6.591</td> -<td align="right">3.107</td> +<td align="right">1.559</td> +<td align="right">6.097</td> +<td align="right">2.841</td> </tr> </tbody> </table> @@ -761,12 +764,12 @@ <td align="left">Ryzen 7 1700</td> <td align="left">4.2.2</td> <td align="left">1.2.0</td> -<td align="right">0.915</td> -<td align="right">1.426</td> -<td align="right">1.613</td> -<td align="right">3.224</td> -<td align="right">2.068</td> -<td align="right">2.962</td> +<td align="right">0.911</td> +<td align="right">1.328</td> +<td align="right">1.519</td> +<td align="right">2.986</td> +<td align="right">1.957</td> +<td align="right">2.769</td> </tr> </tbody> </table> diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html index 97ea6fd4..e54bc38c 100644 --- a/docs/dev/articles/web_only/saem_benchmarks.html +++ b/docs/dev/articles/web_only/saem_benchmarks.html @@ -78,7 +78,10 @@ <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -109,7 +112,7 @@ <h1 data-toc-skip>Benchmark timings for saem.mmkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-14)</h4> + <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-15)</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> @@ -306,10 +309,10 @@ <td align="left">Linux</td> <td align="left">1.2.0</td> <td align="left">3.2</td> -<td align="right">2.589</td> -<td align="right">4.945</td> -<td align="right">4.786</td> -<td align="right">4.484</td> +<td align="right">2.11</td> +<td align="right">4.632</td> +<td align="right">4.264</td> +<td align="right">4.93</td> </tr></tbody> </table> <p>Two-component error fits for SFO, DFOP, SFORB and HS.</p> @@ -329,10 +332,10 @@ <td align="left">Linux</td> <td align="left">1.2.0</td> <td align="left">3.2</td> -<td align="right">5.645</td> -<td align="right">8.115</td> -<td align="right">7.737</td> -<td align="right">7.782</td> +<td align="right">5.602</td> +<td align="right">7.373</td> +<td align="right">7.815</td> +<td align="right">7.831</td> </tr></tbody> </table> </div> @@ -354,8 +357,8 @@ <td align="left">Linux</td> <td align="left">1.2.0</td> <td align="left">3.2</td> -<td align="right">25.921</td> -<td align="right">766.034</td> +<td align="right">24.014</td> +<td align="right">749.699</td> </tr></tbody> </table> </div> @@ -376,7 +379,7 @@ <td align="left">Linux</td> <td align="left">1.2.0</td> <td align="left">3.2</td> -<td align="right">1269.799</td> +<td align="right">1249.834</td> </tr></tbody> </table> </div> diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index ad0d8b19..e0c11a84 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -13,7 +13,7 @@ articles: dimethenamid_2018: web_only/dimethenamid_2018.html multistart: web_only/multistart.html saem_benchmarks: web_only/saem_benchmarks.html -last_built: 2022-11-14T20:49Z +last_built: 2022-11-14T23:45Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex 17a35806..b3448db0 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/logLik.saem.mmkin.html b/docs/dev/reference/logLik.saem.mmkin.html index b1ea22ef..ebef3b10 100644 --- a/docs/dev/reference/logLik.saem.mmkin.html +++ b/docs/dev/reference/logLik.saem.mmkin.html @@ -59,7 +59,10 @@ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html index 14f2b75b..37930912 100644 --- a/docs/dev/reference/mkinpredict.html +++ b/docs/dev/reference/mkinpredict.html @@ -61,7 +61,10 @@ kinetic parameters and initial values for the state variables."><meta name="robo <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -371,10 +374,10 @@ as these always return mapped output.</p></dd> <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 1.00 0.004</span> -<span class="r-out co"><span class="r-pr">#></span> 4 analytical 5.25 0.021</span> -<span class="r-out co"><span class="r-pr">#></span> 1 eigen 6.00 0.024</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 52.50 0.210</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> 1 eigen 4.2 0.021</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 4.2 0.021</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 40.8 0.204</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> diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 968dc68c..73382cba 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -61,7 +61,10 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -429,8 +432,8 @@ using <a href="mmkin.html">mmkin</a>.</p> <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: 1.2.0 </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: Mon Nov 14 21:06:30 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Nov 14 21:06:30 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Tue Nov 15 00:45:58 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Tue Nov 15 00:45:58 2022 </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> @@ -445,7 +448,7 @@ 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 9.625 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.189 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> |
