diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-09-18 13:03:50 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-09-18 13:03:50 +0200 |
| commit | e05656d57668688b971c28e32b4cfd4d3eac4662 (patch) | |
| tree | 597df9a638c0ce68ae9efcb5b45d42b2f2927a15 /docs/articles/web_only/FOCUS_Z.html | |
| parent | 0818986e2d9a0e68d3d1de26ac381836e0cf5a6f (diff) | |
Correct and rebuild docs
- Reconcile docs and code for max_twa_parent
- Correct links to docs in twa vignette
- Static documentation rebuilt by pkgdown
Diffstat (limited to 'docs/articles/web_only/FOCUS_Z.html')
| -rw-r--r-- | docs/articles/web_only/FOCUS_Z.html | 39 |
1 files changed, 22 insertions, 17 deletions
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 8f3fe97e..aed1debc 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -7,8 +7,9 @@ <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Example evaluation of FOCUS dataset Z • mkin</title> <!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous"> -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link 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property="og:title" content="Example evaluation of FOCUS dataset Z"> <meta property="og:description" content=""> <meta name="twitter:card" content="summary"> @@ -82,13 +83,14 @@ <!--/.navbar --> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-07-09</h4> + <h4 class="date">2019-09-18</h4> <div class="hidden name"><code>FOCUS_Z.Rmd</code></div> @@ -102,18 +104,18 @@ <h1 class="hasAnchor"> <a href="#the-data" class="anchor"></a>The data</h1> <p>The following code defines the example dataset from Appendix 7 to the FOCUS kinetics report <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 354)</span>.</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(mkin, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> +<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(mkin, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> <a class="sourceLine" id="cb1-2" title="2">LOD =<span class="st"> </span><span class="fl">0.5</span></a> -<a class="sourceLine" id="cb1-3" title="3">FOCUS_<span class="dv">2006</span>_Z =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> -<a class="sourceLine" id="cb1-4" title="4"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">3</span>, <span class="dv">4</span>, <span class="dv">7</span>, <span class="dv">10</span>, <span class="dv">14</span>, <span class="dv">21</span>,</a> +<a class="sourceLine" id="cb1-3" title="3">FOCUS_<span class="dv">2006</span>_Z =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(</a> +<a class="sourceLine" id="cb1-4" title="4"> <span class="dt">t =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">3</span>, <span class="dv">4</span>, <span class="dv">7</span>, <span class="dv">10</span>, <span class="dv">14</span>, <span class="dv">21</span>,</a> <a class="sourceLine" id="cb1-5" title="5"> <span class="dv">42</span>, <span class="dv">61</span>, <span class="dv">96</span>, <span class="dv">124</span>),</a> -<a class="sourceLine" id="cb1-6" title="6"> <span class="dt">Z0 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,</a> +<a class="sourceLine" id="cb1-6" title="6"> <span class="dt">Z0 =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,</a> <a class="sourceLine" id="cb1-7" title="7"> <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span>),</a> -<a class="sourceLine" id="cb1-8" title="8"> <span class="dt">Z1 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="dv">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,</a> +<a class="sourceLine" id="cb1-8" title="8"> <span class="dt">Z1 =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="dv">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,</a> <a class="sourceLine" id="cb1-9" title="9"> <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>),</a> -<a class="sourceLine" id="cb1-10" title="10"> <span class="dt">Z2 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,</a> +<a class="sourceLine" id="cb1-10" title="10"> <span class="dt">Z2 =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,</a> <a class="sourceLine" id="cb1-11" title="11"> <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>),</a> -<a class="sourceLine" id="cb1-12" title="12"> <span class="dt">Z3 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,</a> +<a class="sourceLine" id="cb1-12" title="12"> <span class="dt">Z3 =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,</a> <a class="sourceLine" id="cb1-13" title="13"> <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span>))</a> <a class="sourceLine" id="cb1-14" title="14"></a> <a class="sourceLine" id="cb1-15" title="15">FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span class="kw"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_Z)</a></code></pre></div> @@ -130,7 +132,7 @@ ## with value of zero were removed from the data</code></pre> <div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p> -<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 9.7015e+01 3.393176 2.8591e+01 6.4352e-21 91.66556 102.3642 ## k_Z0_sink 7.2231e-10 0.225254 3.2067e-09 5.0000e-01 0.00000 Inf @@ -148,7 +150,7 @@ ## with value of zero were removed from the data</code></pre> <div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a.ff)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></p> -<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a.ff, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.Z<span class="fl">.2</span>a.ff, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642 ## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600 @@ -166,7 +168,7 @@ ## value of zero were removed from the data</code></pre> <div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.3</span>)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p> -<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.3</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.Z<span class="fl">.3</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 97.01488 2.597342 37.352 2.0106e-24 91.67597 102.3538 ## k_Z0 2.23601 0.146904 15.221 9.1477e-15 1.95354 2.5593 @@ -201,7 +203,7 @@ ## 5$bparms.ode, : Observations with value of zero were removed from the data</code></pre> <div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb32-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.FOCUS)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p> -<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 96.838607 1.994273 48.5584 4.0283e-42 92.826626 100.850589 ## k_Z0 2.215405 0.118459 18.7018 1.0415e-23 1.989465 2.467003 @@ -241,7 +243,7 @@ ## with value of zero were removed from the data</code></pre> <div class="sourceCode" id="cb41"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb41-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.1</span>)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> -<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div> +<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div> <pre><code>## Z0_0 log_k_Z0_Z1 log_k_Z1_Z2 log_k_Z2_sink ## Z0_0 3.8375e+00 5.4918e-03 3.0584e-02 1.2969e-01 ## log_k_Z0_Z1 5.4918e-03 2.7613e-03 -1.8820e-04 2.6634e-04 @@ -312,7 +314,7 @@ <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png" width="700"></p> <p>The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized is excessively small, it seems reasonable to fix it to zero.</p> <div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" title="1">m.Z.mkin<span class="fl">.5</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb59-2" title="2"> <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(m.Z.mkin<span class="fl">.5</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">7</span>],</a> +<a class="sourceLine" id="cb59-2" title="2"> <span class="dt">parms.ini =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(m.Z.mkin<span class="fl">.5</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">7</span>],</a> <a class="sourceLine" id="cb59-3" title="3"> <span class="dt">k_Z3_bound_free =</span> <span class="dv">0</span>),</a> <a class="sourceLine" id="cb59-4" title="4"> <span class="dt">fixed_parms =</span> <span class="st">"k_Z3_bound_free"</span>,</a> <a class="sourceLine" id="cb59-5" title="5"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> @@ -372,17 +374,20 @@ </div> + <footer><div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> + </footer> </div> + </body> </html> |