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authorJohannes Ranke <jranke@uni-bremen.de>2022-11-15 08:01:52 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-11-15 08:01:52 +0100
commit679cf716192cdfd91dfd232578cbd4e30d7eac12 (patch)
tree24dce01d75cd0dce7d2605ec600e0bcc49cf6ef5 /docs/dev/reference
parent2b16f6cc5aae9a57362db2add0e3263c65afc7e2 (diff)
Import saemix for easier profiling, update online docs
Diffstat (limited to 'docs/dev/reference')
-rw-r--r--docs/dev/reference/Rplot001.pngbin1011 -> 22432 bytes
-rw-r--r--docs/dev/reference/logLik.saem.mmkin.html5
-rw-r--r--docs/dev/reference/mkinpredict.html13
-rw-r--r--docs/dev/reference/saem.html11
4 files changed, 19 insertions, 10 deletions
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index 17a35806..b3448db0 100644
--- a/docs/dev/reference/Rplot001.png
+++ b/docs/dev/reference/Rplot001.png
Binary files differ
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">#&gt;</span> Loading required package: rbenchmark</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> test relative elapsed</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled 1.00 0.004</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4 analytical 5.25 0.021</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 eigen 6.00 0.024</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3 deSolve 52.50 0.210</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled 1.0 0.005</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 eigen 4.2 0.021</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4 analytical 4.2 0.021</span>
+<span class="r-out co"><span class="r-pr">#&gt;</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">#&gt;</span> saemix version used for fitting: 3.2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting: 1.2.0 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting: 4.2.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Mon Nov 14 21:06:30 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Mon Nov 14 21:06:30 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Tue Nov 15 00:45:58 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Tue Nov 15 00:45:58 2022 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
<span class="r-out co"><span class="r-pr">#&gt;</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">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 9.625 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 9.189 s</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 10 chains</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Constant variance </span>

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