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authorJohannes Ranke <johannes.ranke@jrwb.de>2025-02-16 17:27:18 +0100
committerJohannes Ranke <johannes.ranke@jrwb.de>2025-02-16 17:29:28 +0100
commit4f62f39b8979cb3a5c52d65d425e530dc0770665 (patch)
tree895d4bde0773a600943e5c308e17651c12358a67 /docs/dev/articles/web_only
parent44c30938872bd7cc80a4c84dd4db593e26000fce (diff)
Fix solution type "deSolve" for a special caseHEADdev
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.html2
-rw-r--r--docs/dev/articles/web_only/NAFTA_examples.html2
-rw-r--r--docs/dev/articles/web_only/benchmarks.html24
-rw-r--r--docs/dev/articles/web_only/compiled_models.html14
-rw-r--r--docs/dev/articles/web_only/dimethenamid_2018.html12
-rw-r--r--docs/dev/articles/web_only/multistart.html2
-rw-r--r--docs/dev/articles/web_only/saem_benchmarks.html22
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>

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