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authorJohannes Ranke <jranke@uni-bremen.de>2023-02-17 22:48:18 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2023-02-17 22:48:18 +0100
commitbcd98a1fa3cd2fb4b7105b7ec6c129ca18f872e8 (patch)
tree80ce30d68fb33fe92a0939e1f5be9790263909c1 /docs/dev/reference/summary.saem.mmkin.html
parent5811ab93d856bb339a35eef2d23266fcb781cbe7 (diff)
Update online docs, fix bug that surfaced
Diffstat (limited to 'docs/dev/reference/summary.saem.mmkin.html')
-rw-r--r--docs/dev/reference/summary.saem.mmkin.html47
1 files changed, 32 insertions, 15 deletions
diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html
index 3b5869f1..aa573589 100644
--- a/docs/dev/reference/summary.saem.mmkin.html
+++ b/docs/dev/reference/summary.saem.mmkin.html
@@ -21,13 +21,13 @@ endpoints such as formation fractions and DT50 values. Optionally
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development 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">
@@ -38,6 +38,8 @@ endpoints such as formation fractions and DT50 values. Optionally
<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>
@@ -45,22 +47,29 @@ endpoints such as formation fractions and DT50 values. Optionally
<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>
@@ -68,6 +77,14 @@ endpoints such as formation fractions and DT50 values. Optionally
<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>
@@ -102,7 +119,7 @@ endpoints such as formation fractions and DT50 values. Optionally
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span>
-<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">object</span>, data <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<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">object</span>, data <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for summary.saem.mmkin</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">verbose</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
@@ -292,12 +309,12 @@ saemix authors for the parts inherited from saemix.</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> lower est. upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 0.67696663 0.87777355 1.07858048</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> b.1 0.06363957 0.07878001 0.09392044</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">f_saem_dfop_sfo_2</span>, data <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/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<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: 1.2.2 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting: 1.2.3 </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 Dec 15 14:47:14 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Dec 15 14:47:14 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Fri Feb 17 22:24:21 2023 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Fri Feb 17 22:24:21 2023 </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>
@@ -312,7 +329,7 @@ saemix authors for the parts inherited from saemix.</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 9.623 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 9.426 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: Two-component variance function </span>
@@ -627,7 +644,7 @@ saemix authors for the parts inherited from saemix.</p>
</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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