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authorJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
commit8d1a84ac2190538ed3bac53a303064e281595868 (patch)
treeacb894d85ab7ec87c4911c355a5264a77e08e34b /docs/reference/sigma_twocomp.html
parent51d63256a7b3020ee11931d61b4db97b9ded02c0 (diff)
parent4200e566ad2600f56bc3987669aeab88582139eb (diff)
Merge branch 'main' into custom_lsoda_call
Diffstat (limited to 'docs/reference/sigma_twocomp.html')
-rw-r--r--docs/reference/sigma_twocomp.html63
1 files changed, 38 insertions, 25 deletions
diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html
index 23102f17..c1db0d30 100644
--- a/docs/reference/sigma_twocomp.html
+++ b/docs/reference/sigma_twocomp.html
@@ -18,7 +18,7 @@ dependence of the measured value \(y\):"><!-- 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">1.1.0</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 @@ dependence of the measured value \(y\):"><!-- mathjax --><script src="https://cd
<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>
@@ -89,23 +95,30 @@ dependence of the measured value \(y\):</p>
</div>
<div id="ref-usage">
- <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">sigma_twocomp</span><span class="op">(</span><span class="va">y</span>, <span class="va">sigma_low</span>, <span class="va">rsd_high</span><span class="op">)</span></code></pre></div>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">sigma_twocomp</span><span class="op">(</span><span class="va">y</span>, <span class="va">sigma_low</span>, <span class="va">rsd_high</span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>y</dt>
<dd><p>The magnitude of the observed value</p></dd>
+
+
<dt>sigma_low</dt>
<dd><p>The asymptotic minimum of the standard deviation for low
observed values</p></dd>
+
+
<dt>rsd_high</dt>
<dd><p>The coefficient describing the increase of the standard
deviation with the magnitude of the observed value</p></dd>
+
</dl></div>
<div id="value">
<h2>Value</h2>
- <p>The standard deviation of the response variable.</p>
+
+
+<p>The standard deviation of the response variable.</p>
</div>
<div id="details">
<h2>Details</h2>
@@ -131,26 +144,26 @@ Degradation Data. <em>Environments</em> 6(12) 124
<div id="ref-examples">
<h2>Examples</h2>
- <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">times</span> <span class="op">&lt;-</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="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span>
-<span class="r-in"><span class="va">d_pred</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="va">times</span>, parent <span class="op">=</span> <span class="fl">100</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp</a></span><span class="op">(</span><span class="op">-</span> <span class="fl">0.03</span> <span class="op">*</span> <span class="va">times</span><span class="op">)</span><span class="op">)</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456</span><span class="op">)</span></span>
-<span class="r-in"><span class="va">d_syn</span> <span class="op">&lt;-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_pred</span>, <span class="kw">function</span><span class="op">(</span><span class="va">y</span><span class="op">)</span> <span class="fu">sigma_twocomp</span><span class="op">(</span><span class="va">y</span>, <span class="fl">1</span>, <span class="fl">0.07</span><span class="op">)</span>,</span>
-<span class="r-in"> reps <span class="op">=</span> <span class="fl">2</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span>
-<span class="r-in"><span class="va">f_nls</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/nls.html" class="external-link">nls</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/stats/SSasymp.html" class="external-link">SSasymp</a></span><span class="op">(</span><span class="va">time</span>, <span class="fl">0</span>, <span class="va">parent_0</span>, <span class="va">lrc</span><span class="op">)</span>, data <span class="op">=</span> <span class="va">d_syn</span>,</span>
-<span class="r-in"> start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>parent_0 <span class="op">=</span> <span class="fl">100</span>, lrc <span class="op">=</span> <span class="op">-</span><span class="fl">3</span><span class="op">)</span><span class="op">)</span></span>
-<span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span>
-<span class="r-in"><span class="va">f_gnls</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/gnls.html" class="external-link">gnls</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/stats/SSasymp.html" class="external-link">SSasymp</a></span><span class="op">(</span><span class="va">time</span>, <span class="fl">0</span>, <span class="va">parent_0</span>, <span class="va">lrc</span><span class="op">)</span>,</span>
-<span class="r-in"> data <span class="op">=</span> <span class="va">d_syn</span>, na.action <span class="op">=</span> <span class="va">na.omit</span>,</span>
-<span class="r-in"> start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>parent_0 <span class="op">=</span> <span class="fl">100</span>, lrc <span class="op">=</span> <span class="op">-</span><span class="fl">3</span><span class="op">)</span><span class="op">)</span></span>
-<span class="r-in"><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">&gt;</span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span></span>
-<span class="r-in"> <span class="va">f_gnls_tc</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_gnls</span>, weights <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/varConstProp.html" class="external-link">varConstProp</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
-<span class="r-in"> <span class="va">f_gnls_tc_sf</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_gnls_tc</span>, control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>sigma <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span>
-<span class="r-in"><span class="op">}</span></span>
-<span class="r-in"><span class="va">f_mkin</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">d_syn</span>, error_model <span class="op">=</span> <span class="st">"const"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in"><span class="va">f_mkin_tc</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">d_syn</span>, error_model <span class="op">=</span> <span class="st">"tc"</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_res</a></span><span class="op">(</span><span class="va">f_mkin_tc</span>, standardized <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">times</span> <span class="op">&lt;-</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="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">d_pred</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="va">times</span>, parent <span class="op">=</span> <span class="fl">100</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp</a></span><span class="op">(</span><span class="op">-</span> <span class="fl">0.03</span> <span class="op">*</span> <span class="va">times</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">d_syn</span> <span class="op">&lt;-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_pred</span>, <span class="kw">function</span><span class="op">(</span><span class="va">y</span><span class="op">)</span> <span class="fu">sigma_twocomp</span><span class="op">(</span><span class="va">y</span>, <span class="fl">1</span>, <span class="fl">0.07</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> reps <span class="op">=</span> <span class="fl">2</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span></span>
+<span class="r-in"><span><span class="va">f_nls</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/nls.html" class="external-link">nls</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/stats/SSasymp.html" class="external-link">SSasymp</a></span><span class="op">(</span><span class="va">time</span>, <span class="fl">0</span>, <span class="va">parent_0</span>, <span class="va">lrc</span><span class="op">)</span>, data <span class="op">=</span> <span class="va">d_syn</span>,</span></span>
+<span class="r-in"><span> start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>parent_0 <span class="op">=</span> <span class="fl">100</span>, lrc <span class="op">=</span> <span class="op">-</span><span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">f_gnls</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/gnls.html" class="external-link">gnls</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/stats/SSasymp.html" class="external-link">SSasymp</a></span><span class="op">(</span><span class="va">time</span>, <span class="fl">0</span>, <span class="va">parent_0</span>, <span class="va">lrc</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> data <span class="op">=</span> <span class="va">d_syn</span>, na.action <span class="op">=</span> <span class="va">na.omit</span>,</span></span>
+<span class="r-in"><span> start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>parent_0 <span class="op">=</span> <span class="fl">100</span>, lrc <span class="op">=</span> <span class="op">-</span><span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">&gt;</span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span></span></span>
+<span class="r-in"><span> <span class="va">f_gnls_tc</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_gnls</span>, weights <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/varConstProp.html" class="external-link">varConstProp</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="va">f_gnls_tc_sf</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_gnls_tc</span>, control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>sigma <span class="op">=</span> <span class="fl">1</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-in"><span><span class="va">f_mkin</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">d_syn</span>, error_model <span class="op">=</span> <span class="st">"const"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">f_mkin_tc</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">d_syn</span>, error_model <span class="op">=</span> <span class="st">"tc"</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="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">f_mkin_tc</span>, standardized <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="sigma_twocomp-1.png" alt="" width="700" height="433"></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_nls</span>, <span class="va">f_gnls</span>, <span class="va">f_gnls_tc</span>, <span class="va">f_gnls_tc_sf</span>, <span class="va">f_mkin</span>, <span class="va">f_mkin_tc</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_nls</span>, <span class="va">f_gnls</span>, <span class="va">f_gnls_tc</span>, <span class="va">f_gnls_tc_sf</span>, <span class="va">f_mkin</span>, <span class="va">f_mkin_tc</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> df AIC</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_nls 3 114.4817</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_gnls 3 114.4817</span>
@@ -172,7 +185,7 @@ Degradation Data. <em>Environments</em> 6(12) 124
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>
</footer></div>

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