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-rw-r--r--docs/reference/mkinfit.html39
1 files changed, 22 insertions, 17 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 3b27ac7f..62e4bd8d 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -25,7 +25,7 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
</span>
</div>
@@ -52,19 +52,25 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/
<a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
</li>
<li>
- <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
</li>
<li>
<a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
</li>
<li>
<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>
@@ -378,17 +384,17 @@ Degradation Data. <em>Environments</em> 6(12) 124
<span class="r-in"><span><span class="co"># Use shorthand notation for parent only degradation</span></span></span>
<span class="r-in"><span><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting: 1.1.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting: 4.2.1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Wed Aug 10 13:14:25 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Aug 10 13:14:25 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for 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: Thu Nov 17 13:58:19 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Nov 17 13:58:19 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 = - (alpha/beta) * 1/((time/beta) + 1) * parent</span>
<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 using 222 model solutions performed in 0.046 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 222 model solutions performed in 0.044 s</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Error model: Constant variance </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -528,11 +534,10 @@ Degradation Data. <em>Environments</em> 6(12) 124
<span class="r-in"><span> analytical <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span></span>
<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span></span>
<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> 3 analytical 1.000 0.540</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 deSolve_compiled 1.537 0.830</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2 eigen 2.687 1.451</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3 analytical 1.000 0.570</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 deSolve_compiled 1.682 0.959</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 eigen 2.609 1.487</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span>
@@ -559,10 +564,10 @@ Degradation Data. <em>Environments</em> 6(12) 124
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NaNs produced</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NaNs produced</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting: 1.1.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting: 4.2.1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Wed Aug 10 13:14:36 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Aug 10 13:14:36 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for 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: Thu Nov 17 13:58:30 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Nov 17 13:58:30 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 = - (alpha/beta) * 1/((time/beta) + 1) * parent</span>
@@ -571,7 +576,7 @@ Degradation Data. <em>Environments</em> 6(12) 124
<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 deSolve </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 using 3729 model solutions performed in 2.488 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 3729 model solutions performed in 2.464 s</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Error model: Two-component variance function </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>

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