diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-11-15 08:01:52 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-11-15 08:01:52 +0100 |
| commit | 679cf716192cdfd91dfd232578cbd4e30d7eac12 (patch) | |
| tree | 24dce01d75cd0dce7d2605ec600e0bcc49cf6ef5 /docs/dev/reference | |
| parent | 2b16f6cc5aae9a57362db2add0e3263c65afc7e2 (diff) | |
Import saemix for easier profiling, update online docs
Diffstat (limited to 'docs/dev/reference')
| -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 |
4 files changed, 19 insertions, 10 deletions
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> |
