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authorJohannes Ranke <jranke@uni-bremen.de>2022-11-17 14:54:20 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-11-17 14:56:25 +0100
commite5d1df9a9b1f0951d7dfbaf24eee4294470b73e2 (patch)
tree18740ef050a68d1a6fe91f1bd2fdfdd97ac6448b /docs/reference/test_data_from_UBA_2014.html
parent90354f5cd9e095f9ef98424689a2716770b248d4 (diff)
Complete update of online docs for v1.2.0
Diffstat (limited to 'docs/reference/test_data_from_UBA_2014.html')
-rw-r--r--docs/reference/test_data_from_UBA_2014.html75
1 files changed, 42 insertions, 33 deletions
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 327e8ae9..a76f23ab 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -18,7 +18,7 @@
</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">1.1.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
</span>
</div>
@@ -45,19 +45,25 @@
<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>
@@ -89,7 +95,7 @@
</div>
<div id="ref-usage">
- <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">test_data_from_UBA_2014</span></code></pre></div>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">test_data_from_UBA_2014</span></span></code></pre></div>
</div>
<div id="format">
@@ -111,21 +117,23 @@
<div id="ref-examples">
<h2>Examples</h2>
- <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"> <span class="co"># \dontrun{</span></span>
-<span class="r-in"> <span class="co"># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span></span>
-<span class="r-in"> <span class="co"># guidance. Due to the strong correlation of the parameter estimates, the</span></span>
-<span class="r-in"> <span class="co"># covariance matrix is not returned. Note that level P-II evaluations are</span></span>
-<span class="r-in"> <span class="co"># generally considered deprecated due to the frequent occurrence of such</span></span>
-<span class="r-in"> <span class="co"># large parameter correlations, among other reasons (e.g. the adequacy of the</span></span>
-<span class="r-in"> <span class="co"># model).</span></span>
-<span class="r-in"> <span class="va">m_ws</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent_w <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"parent_s"</span><span class="op">)</span>,</span>
-<span class="r-in"> parent_s <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"parent_w"</span><span class="op">)</span><span class="op">)</span></span>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span> <span class="co"># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span></span></span>
+<span class="r-in"><span> <span class="co"># guidance. Due to the strong correlation of the parameter estimates, the</span></span></span>
+<span class="r-in"><span> <span class="co"># covariance matrix is not returned. Note that level P-II evaluations are</span></span></span>
+<span class="r-in"><span> <span class="co"># generally considered deprecated due to the frequent occurrence of such</span></span></span>
+<span class="r-in"><span> <span class="co"># large parameter correlations, among other reasons (e.g. the adequacy of the</span></span></span>
+<span class="r-in"><span> <span class="co"># model).</span></span></span>
+<span class="r-in"><span> <span class="va">m_ws</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent_w <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"parent_s"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> parent_s <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"parent_w"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
-<span class="r-in"> <span class="va">f_river</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_ws</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in"> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span>
+<span class="r-in"><span> <span class="va">f_river</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_ws</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
+<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="test_data_from_UBA_2014-1.png" alt="" width="700" height="433"></span>
-<span class="r-in"></span>
-<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Could not calculate correlation; no covariance matrix</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Estimate se_notrans t value Pr(&gt;t) Lower Upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_w_0 95.91998118 NA NA NA NA NA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_w 0.41145375 NA NA NA NA NA</span>
@@ -133,25 +141,26 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_w_to_parent_s 0.12467894 NA NA NA NA NA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_s_to_parent_w 0.50000000 NA NA NA NA NA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 3.13612618 NA NA NA NA NA</span>
-<span class="r-in"> <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span>
+<span class="r-in"><span> <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> err.min n.optim df</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> All data 0.1090929 5 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_w 0.0817436 3 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_s 0.1619965 2 3</span>
-<span class="r-in"></span>
-<span class="r-in"> <span class="co"># This is the evaluation used for the validation of software packages</span></span>
-<span class="r-in"> <span class="co"># in the expertise from 2014</span></span>
-<span class="r-in"> <span class="va">m_soil</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span>
-<span class="r-in"> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</span><span class="op">)</span>,</span>
-<span class="r-in"> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</span><span class="op">)</span>,</span>
-<span class="r-in"> M3 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span>
-<span class="r-in"> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="co"># This is the evaluation used for the validation of software packages</span></span></span>
+<span class="r-in"><span> <span class="co"># in the expertise from 2014</span></span></span>
+<span class="r-in"><span> <span class="va">m_soil</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> M3 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
-<span class="r-in"></span>
-<span class="r-in"> <span class="va">f_soil</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_soil</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in"> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_soil</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="va">f_soil</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_soil</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
+<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_soil</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="test_data_from_UBA_2014-2.png" alt="" width="700" height="433"></span>
-<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Estimate se_notrans t value Pr(&gt;t) Lower</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent 0.12081956 0.004601918 26.2541722 1.077359e-16 0.111561575</span>
@@ -174,14 +183,14 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> f_M1_to_M3 0.86450775</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_M2_to_M3 0.99489895</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 1.45337221</span>
-<span class="r-in"> <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span></span>
+<span class="r-in"><span> <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> err.min n.optim df</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> All data 0.09649963 9 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent 0.04721283 2 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> M1 0.26551208 2 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> M2 0.20327575 2 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> M3 0.05196550 3 4</span>
-<span class="r-in"> <span class="co"># }</span></span>
+<span class="r-in"><span> <span class="co"># }</span></span></span>
</code></pre></div>
</div>
</div>
@@ -196,7 +205,7 @@
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
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