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authorJohannes Ranke <jranke@uni-bremen.de>2023-04-20 20:17:12 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2023-04-20 20:17:12 +0200
commit7b7c4bf493ba15824ea43bed764661678b4aca03 (patch)
tree48de1e32327c36ee49fc476dc76ece8397ab55c6 /docs/reference/confint.mkinfit.html
parent842998b688037c007d8876d7e1110c929fe2374c (diff)
parent9ae42bd20bc2543a94cf1581ba9820c2f9e3afbd (diff)
Merge branch 'v1.2.3_pkgdown'
Diffstat (limited to 'docs/reference/confint.mkinfit.html')
-rw-r--r--docs/reference/confint.mkinfit.html39
1 files changed, 28 insertions, 11 deletions
diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html
index 8d7c272f..dd6409b6 100644
--- a/docs/reference/confint.mkinfit.html
+++ b/docs/reference/confint.mkinfit.html
@@ -24,13 +24,13 @@ method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cd
</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">1.2.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.3</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
- <a href="../reference/index.html">Functions and data</a>
+ <a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
@@ -41,6 +41,8 @@ method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cd
<ul class="dropdown-menu" role="menu"><li>
<a href="../articles/mkin.html">Introduction to mkin</a>
</li>
+ <li class="divider">
+ <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li>
<li>
<a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
</li>
@@ -48,22 +50,29 @@ method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cd
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
- <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
</li>
+ <li class="divider">
+ <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li>
<li>
- <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+ <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
</li>
<li>
- <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
</li>
<li>
- <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
</li>
<li>
- <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a>
</li>
<li>
- <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+ </li>
+ <li class="divider">
+ <li class="dropdown-header">Performance</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/benchmarks.html">Benchmark timings for mkin</a>
@@ -71,6 +80,14 @@ method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cd
<li>
<a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
</li>
+ <li class="divider">
+ <li class="dropdown-header">Miscellaneous</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>
</ul></li>
<li>
<a href="../news/index.html">News</a>
@@ -237,7 +254,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
<span class="r-in"><span><span class="va">f_d_1</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</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/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> user system elapsed </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3.931 0.000 3.932 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1.26 0.00 1.26 </span>
<span class="r-in"><span><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span></span>
<span class="r-in"><span><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span></span>
<span class="r-in"><span><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span></span>
@@ -245,7 +262,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
<span class="r-in"><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">"k_parent_sink"</span>, <span class="st">"k_parent_m1"</span>, <span class="st">"k_m1_sink"</span>, <span class="st">"sigma"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Profiling the likelihood</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> user system elapsed </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2.219 0.000 2.219 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0.417 0.103 0.291 </span>
<span class="r-in"><span><span class="va">ci_profile</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2.5% 97.5%</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 96.456003640 1.027703e+02</span>
@@ -392,7 +409,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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