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| author | Johannes Ranke <jranke@uni-bremen.de> | 2018-06-06 01:24:15 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-06-06 01:24:15 +0200 |
| commit | 39b2c2c762b03922a2648b1b226d0f308600cc87 (patch) | |
| tree | 4c3ae26ac0fe5360dea329c8815def2fc84dc269 /docs/articles | |
| parent | 6ea7bc3614b9a303f7c38dd63b9f80b8d0ebd95e (diff) | |
Static documentation rebuilt by pkgdown 1.1.0
Diffstat (limited to 'docs/articles')
21 files changed, 230 insertions, 173 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index a83c2f44..8a1f51d1 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -8,8 +8,8 @@ <title>Example evaluation of FOCUS Example Dataset D • mkin</title> <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> -<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS Example Dataset D"> +<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS Example Dataset D"> <meta property="og:description" content=""> <meta name="twitter:card" content="summary"> <!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> @@ -18,7 +18,7 @@ <![endif]--> </head> <body> - <div class="container template-vignette"> + <div class="container template-article"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> @@ -27,8 +27,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">mkin</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -75,17 +79,20 @@ </header><div class="row"> - <div class="col-md-9"> + <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-21</h4> - </div> + <h4 class="date">2018-06-06</h4> + + + <div class="hidden name"><code>FOCUS_D.Rmd</code></div> + + </div> -<div class="contents"> <p>This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using <code>mkin</code>. After loading the library we look a the data. We have observed concentrations in the column named <code>value</code> at the times specified in column <code>time</code> for the two observed variables named <code>parent</code> and <code>m1</code>.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>) <span class="kw">print</span>(FOCUS_<span class="dv">2006</span>_D)</code></pre></div> @@ -153,10 +160,10 @@ <p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p> <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div> -<pre><code>## mkin version: 0.9.46.3 -## R version: 3.4.3 -## Date of fit: Sun Mar 11 22:11:56 2018 -## Date of summary: Sun Mar 11 22:11:57 2018 +<pre><code>## mkin version used for fitting: 0.9.47.1 +## R version used for fitting: 3.5.0 +## Date of fit: Wed Jun 6 01:21:49 2018 +## Date of summary: Wed Jun 6 01:21:50 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -164,7 +171,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.984 s +## Fitted with method Port using 153 model solutions performed in 0.633 s ## ## Weighting: none ## @@ -231,51 +238,46 @@ ## ## Data: ## time variable observed predicted residual -## 0 parent 99.46 9.960e+01 -1.385e-01 -## 0 parent 102.04 9.960e+01 2.442e+00 -## 1 parent 93.50 9.024e+01 3.262e+00 -## 1 parent 92.50 9.024e+01 2.262e+00 -## 3 parent 63.23 7.407e+01 -1.084e+01 -## 3 parent 68.99 7.407e+01 -5.083e+00 -## 7 parent 52.32 4.991e+01 2.408e+00 -## 7 parent 55.13 4.991e+01 5.218e+00 -## 14 parent 27.27 2.501e+01 2.257e+00 -## 14 parent 26.64 2.501e+01 1.627e+00 -## 21 parent 11.50 1.253e+01 -1.035e+00 -## 21 parent 11.64 1.253e+01 -8.946e-01 -## 35 parent 2.85 3.148e+00 -2.979e-01 -## 35 parent 2.91 3.148e+00 -2.379e-01 -## 50 parent 0.69 7.162e-01 -2.624e-02 -## 50 parent 0.63 7.162e-01 -8.624e-02 -## 75 parent 0.05 6.074e-02 -1.074e-02 -## 75 parent 0.06 6.074e-02 -7.382e-04 -## 100 parent NA 5.151e-03 NA -## 100 parent NA 5.151e-03 NA -## 120 parent NA 7.155e-04 NA -## 120 parent NA 7.155e-04 NA -## 0 m1 0.00 0.000e+00 0.000e+00 -## 0 m1 0.00 0.000e+00 0.000e+00 -## 1 m1 4.84 4.803e+00 3.704e-02 -## 1 m1 5.64 4.803e+00 8.370e-01 -## 3 m1 12.91 1.302e+01 -1.140e-01 -## 3 m1 12.96 1.302e+01 -6.400e-02 -## 7 m1 22.97 2.504e+01 -2.075e+00 -## 7 m1 24.47 2.504e+01 -5.748e-01 -## 14 m1 41.69 3.669e+01 5.000e+00 -## 14 m1 33.21 3.669e+01 -3.480e+00 -## 21 m1 44.37 4.165e+01 2.717e+00 -## 21 m1 46.44 4.165e+01 4.787e+00 -## 35 m1 41.22 4.331e+01 -2.093e+00 -## 35 m1 37.95 4.331e+01 -5.363e+00 -## 50 m1 41.19 4.122e+01 -2.831e-02 -## 50 m1 40.01 4.122e+01 -1.208e+00 -## 75 m1 40.09 3.645e+01 3.643e+00 -## 75 m1 33.85 3.645e+01 -2.597e+00 -## 100 m1 31.04 3.198e+01 -9.416e-01 -## 100 m1 33.13 3.198e+01 1.148e+00 -## 120 m1 25.15 2.879e+01 -3.640e+00 -## 120 m1 33.31 2.879e+01 4.520e+00</code></pre> -</div> +## 0 parent 99.46 99.59848 -1.385e-01 +## 0 parent 102.04 99.59848 2.442e+00 +## 1 parent 93.50 90.23787 3.262e+00 +## 1 parent 92.50 90.23787 2.262e+00 +## 3 parent 63.23 74.07320 -1.084e+01 +## 3 parent 68.99 74.07320 -5.083e+00 +## 7 parent 52.32 49.91207 2.408e+00 +## 7 parent 55.13 49.91207 5.218e+00 +## 14 parent 27.27 25.01257 2.257e+00 +## 14 parent 26.64 25.01257 1.627e+00 +## 21 parent 11.50 12.53462 -1.035e+00 +## 21 parent 11.64 12.53462 -8.946e-01 +## 35 parent 2.85 3.14787 -2.979e-01 +## 35 parent 2.91 3.14787 -2.379e-01 +## 50 parent 0.69 0.71624 -2.624e-02 +## 50 parent 0.63 0.71624 -8.624e-02 +## 75 parent 0.05 0.06074 -1.074e-02 +## 75 parent 0.06 0.06074 -7.382e-04 +## 0 m1 0.00 0.00000 0.000e+00 +## 0 m1 0.00 0.00000 0.000e+00 +## 1 m1 4.84 4.80296 3.704e-02 +## 1 m1 5.64 4.80296 8.370e-01 +## 3 m1 12.91 13.02400 -1.140e-01 +## 3 m1 12.96 13.02400 -6.400e-02 +## 7 m1 22.97 25.04476 -2.075e+00 +## 7 m1 24.47 25.04476 -5.748e-01 +## 14 m1 41.69 36.69002 5.000e+00 +## 14 m1 33.21 36.69002 -3.480e+00 +## 21 m1 44.37 41.65310 2.717e+00 +## 21 m1 46.44 41.65310 4.787e+00 +## 35 m1 41.22 43.31312 -2.093e+00 +## 35 m1 37.95 43.31312 -5.363e+00 +## 50 m1 41.19 41.21831 -2.831e-02 +## 50 m1 40.01 41.21831 -1.208e+00 +## 75 m1 40.09 36.44704 3.643e+00 +## 75 m1 33.85 36.44704 -2.597e+00 +## 100 m1 31.04 31.98163 -9.416e-01 +## 100 m1 33.13 31.98163 1.148e+00 +## 120 m1 25.15 28.78984 -3.640e+00 +## 120 m1 33.31 28.78984 4.520e+00</code></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -295,5 +297,7 @@ </footer> </div> + + </body> </html> diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 08e144bd..fcd0719d 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -8,8 +8,8 @@ <title>Example evaluation of FOCUS Laboratory Data L1 to L3 • mkin</title> <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> -<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS Laboratory Data L1 to L3"> +<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS Laboratory Data L1 to L3"> <meta property="og:description" content=""> <meta name="twitter:card" content="summary"> <!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> @@ -18,7 +18,7 @@ <![endif]--> </head> <body> - <div class="container template-vignette"> + <div class="container template-article"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> @@ -27,8 +27,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">mkin</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -75,17 +79,20 @@ </header><div class="row"> - <div class="col-md-9"> + <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-21</h4> - </div> + <h4 class="date">2018-06-06</h4> + + + <div class="hidden name"><code>FOCUS_L.Rmd</code></div> + + </div> -<div class="contents"> <div id="laboratory-data-l1" class="section level1"> <h1 class="hasAnchor"> <a href="#laboratory-data-l1" class="anchor"></a>Laboratory Data L1</h1> @@ -101,17 +108,17 @@ FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span c <p>Since mkin version 0.9-32 (July 2014), we can use shorthand notation like <code>"SFO"</code> for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L1.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_<span class="dv">2006</span>_L1_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">summary</span>(m.L1.SFO)</code></pre></div> -<pre><code>## mkin version: 0.9.46.3 -## R version: 3.4.4 -## Date of fit: Wed Mar 21 18:16:03 2018 -## Date of summary: Wed Mar 21 18:16:03 2018 +<pre><code>## mkin version used for fitting: 0.9.47.1 +## R version used for fitting: 3.5.0 +## Date of fit: Wed Jun 6 01:21:52 2018 +## Date of summary: Wed Jun 6 01:21:52 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.257 s +## Fitted with method Port using 37 model solutions performed in 0.094 s ## ## Weighting: none ## @@ -192,17 +199,17 @@ FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span c <span class="kw">plot</span>(m.L1.FOMC, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - FOMC"</span>)</code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> -<pre><code>## mkin version: 0.9.46.3 -## R version: 3.4.4 -## Date of fit: Wed Mar 21 18:16:05 2018 -## Date of summary: Wed Mar 21 18:16:05 2018 +<pre><code>## mkin version used for fitting: 0.9.47.1 +## R version used for fitting: 3.5.0 +## Date of fit: Wed Jun 6 01:21:53 2018 +## Date of summary: Wed Jun 6 01:21:53 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 611 model solutions performed in 1.404 s +## Fitted with method Port using 611 model solutions performed in 1.369 s ## ## Weighting: none ## @@ -287,17 +294,17 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c <span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> -<pre><code>## mkin version: 0.9.46.3 -## R version: 3.4.4 -## Date of fit: Wed Mar 21 18:16:06 2018 -## Date of summary: Wed Mar 21 18:16:06 2018 +<pre><code>## mkin version used for fitting: 0.9.47.1 +## R version used for fitting: 3.5.0 +## Date of fit: Wed Jun 6 01:21:54 2018 +## Date of summary: Wed Jun 6 01:21:54 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.168 s +## Fitted with method Port using 81 model solutions performed in 0.173 s ## ## Weighting: none ## @@ -358,10 +365,10 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c <span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> -<pre><code>## mkin version: 0.9.46.3 -## R version: 3.4.4 -## Date of fit: Wed Mar 21 18:16:06 2018 -## Date of summary: Wed Mar 21 18:16:06 2018 +<pre><code>## mkin version used for fitting: 0.9.47.1 +## R version used for fitting: 3.5.0 +## Date of fit: Wed Jun 6 01:21:55 2018 +## Date of summary: Wed Jun 6 01:21:55 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -370,7 +377,7 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.719 s +## Fitted with method Port using 336 model solutions performed in 0.76 s ## ## Weighting: none ## @@ -441,7 +448,7 @@ FOCUS_<span class="dv">2006</span>_L3_mkin <-<span class="st"> </span><span c mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin.html">mmkin</a></span>(<span class="kw">c</span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>), <span class="dt">cores =</span> <span class="dv">1</span>, <span class="kw">list</span>(<span class="st">"FOCUS L3"</span> =<span class="st"> </span>FOCUS_<span class="dv">2006</span>_L3_mkin), <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">plot</span>(mm.L3)</code></pre></div> -<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-12-1.png" width="672"></p> +<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-12-1.png" width="700"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 21% as well as the plot suggest that the SFO model does not fit very well. The FOMC model performs better, with an error level at which the <span class="math inline">\(\chi^2\)</span> test passes of 7%. Fitting the four parameter DFOP model further reduces the <span class="math inline">\(\chi^2\)</span> error level considerably.</p> </div> <div id="accessing-mmkin-objects" class="section level2"> @@ -450,10 +457,10 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <p>The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.</p> <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</code></pre></div> -<pre><code>## mkin version: 0.9.46.3 -## R version: 3.4.4 -## Date of fit: Wed Mar 21 18:16:07 2018 -## Date of summary: Wed Mar 21 18:16:07 2018 +<pre><code>## mkin version used for fitting: 0.9.47.1 +## R version used for fitting: 3.5.0 +## Date of fit: Wed Jun 6 01:21:56 2018 +## Date of summary: Wed Jun 6 01:21:56 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -462,7 +469,7 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.283 s +## Fitted with method Port using 137 model solutions performed in 0.33 s ## ## Weighting: none ## @@ -529,7 +536,7 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## 91 parent 15.0 15.18 -0.18181 ## 120 parent 12.0 10.19 1.81395</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]], <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>)</code></pre></div> -<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-13-1.png" width="672"></p> +<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-13-1.png" width="700"></p> <p>Here, a look to the model plot, the confidence intervals of the parameters and the correlation matrix suggest that the parameter estimates are reliable, and the DFOP model can be used as the best-fit model based on the <span class="math inline">\(\chi^2\)</span> error level criterion for laboratory data L3.</p> <p>This is also an example where the standard t-test for the parameter <code>g_ilr</code> is misleading, as it tests for a significant difference from zero. In this case, zero appears to be the correct value for this parameter, and the confidence interval for the backtransformed parameter <code>g</code> is quite narrow.</p> </div> @@ -548,20 +555,20 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <span class="kw">list</span>(<span class="st">"FOCUS L4"</span> =<span class="st"> </span>FOCUS_<span class="dv">2006</span>_L4_mkin), <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">plot</span>(mm.L4)</code></pre></div> -<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="672"></p> +<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="700"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> -<pre><code>## mkin version: 0.9.46.3 -## R version: 3.4.4 -## Date of fit: Wed Mar 21 18:16:08 2018 -## Date of summary: Wed Mar 21 18:16:08 2018 +<pre><code>## mkin version used for fitting: 0.9.47.1 +## R version used for fitting: 3.5.0 +## Date of fit: Wed Jun 6 01:21:56 2018 +## Date of summary: Wed Jun 6 01:21:57 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.092 s +## Fitted with method Port using 46 model solutions performed in 0.099 s ## ## Weighting: none ## @@ -611,17 +618,17 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## DT50 DT90 ## parent 106 352</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> -<pre><code>## mkin version: 0.9.46.3 -## R version: 3.4.4 -## Date of fit: Wed Mar 21 18:16:08 2018 -## Date of summary: Wed Mar 21 18:16:08 2018 +<pre><code>## mkin version used for fitting: 0.9.47.1 +## R version used for fitting: 3.5.0 +## Date of fit: Wed Jun 6 01:21:57 2018 +## Date of summary: Wed Jun 6 01:21:57 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 66 model solutions performed in 0.138 s +## Fitted with method Port using 66 model solutions performed in 0.146 s ## ## Weighting: none ## @@ -681,7 +688,6 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin </div> </div> </div> -</div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -723,5 +729,7 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin </footer> </div> + + </body> </html> diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png Binary files differindex 22f3a530..770db292 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png Binary files differindex 9eb0378f..ac326b45 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png Binary files differindex d8e58169..6badc1bf 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html index a2b88caa..61425745 100644 --- a/docs/articles/FOCUS_Z.html +++ b/docs/articles/FOCUS_Z.html @@ -8,8 +8,8 @@ <title>Example evaluation of FOCUS dataset Z • mkin</title> <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script 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<span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">mkin</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -75,17 +79,20 @@ </header><div class="row"> - <div class="col-md-9"> + <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">2018-03-21</h4> - </div> + <h4 class="date">2018-06-06</h4> + + + <div class="hidden name"><code>FOCUS_Z.Rmd</code></div> + + </div> -<div class="contents"> <p><a href="http://www.jrwb.de">Wissenschaftlicher Berater, Kronacher Str. 12, 79639 Grenzach-Wyhlen, Germany</a><br><a href="http://chem.uft.uni-bremen.de/ranke">Privatdozent at the University of Bremen</a></p> <div id="the-data" class="section level1"> <h1 class="hasAnchor"> @@ -116,7 +123,7 @@ FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span cl <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.Z<span class="fl">.2</span>a <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a)</code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="672"></p> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 9.7015e+01 3.553140 2.7304e+01 1.6793e-21 NA NA @@ -131,7 +138,7 @@ FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span cl <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a.ff, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a.ff)</code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="672"></p> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.Z<span class="fl">.2</span>a.ff, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 97.01488 3.553145 27.3039 1.6793e-21 NA NA @@ -146,7 +153,7 @@ FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span cl <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.Z<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.3</span>)</code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="672"></p> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.Z<span class="fl">.3</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 97.01488 2.681772 36.176 2.3636e-25 91.52152 102.508 @@ -164,7 +171,7 @@ FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span cl <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.Z<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.5</span>)</code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png" width="672"></p> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png" width="700"></p> <p>Finally, metabolite Z3 is added to the model. We use the optimised differential equation parameter values from the previous fit in order to accelerate the optimization.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>), <span class="dt">Z1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>), @@ -175,10 +182,10 @@ FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span cl <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z.FOCUS, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">parms.ini =</span> m.Z<span class="fl">.5</span><span class="op">$</span>bparms.ode, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</code></pre></div> -<pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation by method Port did not converge. -## Convergence code is 1</code></pre> +<pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation by method Port did not converge: +## false convergence (8)</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.FOCUS)</code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="672"></p> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 96.837112 2.058861 47.0343 5.5877e-44 92.703779 100.970445 @@ -215,7 +222,7 @@ FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span cl <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.Z.mkin<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.1</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.1</span>)</code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="672"></p> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</code></pre></div> <pre><code>## NULL</code></pre> <p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p> @@ -225,7 +232,7 @@ FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span cl <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.3</span>)</code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="672"></p> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="700"></p> <p>This results in a much better representation of the behaviour of the parent compound Z0.</p> <p>Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">Z.mkin<span class="fl">.4</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>), @@ -237,7 +244,7 @@ FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span cl <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.3</span><span class="op">$</span>bparms.ode, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.4</span>)</code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png" width="672"></p> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png" width="700"></p> <p>The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">Z.mkin<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>), <span class="dt">Z1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>), @@ -248,7 +255,7 @@ FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span cl <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.4</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>], <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>)</code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png" width="672"></p> +<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"><pre class="sourceCode r"><code class="sourceCode r">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, <span class="dt">parms.ini =</span> <span class="kw">c</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>], @@ -256,11 +263,11 @@ FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span cl <span class="dt">fixed_parms =</span> <span class="st">"k_Z3_bound_free"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>a)</code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png" width="672"></p> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png" width="700"></p> <p>As expected, the residual plots for Z0 and Z3 are more random than in the case of the all SFO model for which they were shown above. In conclusion, the model is proposed as the best-fit model for the dataset from Appendix 7 of the FOCUS report.</p> <p>A graphical representation of the confidence intervals can finally be obtained.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(m.Z.mkin<span class="fl">.5</span>a)</code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png" width="672"></p> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png" width="700"></p> <p>The endpoints obtained with this model are</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/endpoints.html">endpoints</a></span>(m.Z.mkin<span class="fl">.5</span>a)</code></pre></div> <pre><code>## $ff @@ -289,7 +296,6 @@ FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span cl </div> </div> </div> -</div> </div> 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a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png +++ b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 19cb806b..379176bf 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -8,8 +8,8 @@ <title>Performance benefit by using compiled model definitions in mkin • mkin</title> <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> -<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Performance benefit by using compiled model definitions in mkin"> +<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script><meta property="og:title" content="Performance benefit by using compiled model definitions in mkin"> <meta property="og:description" content=""> <meta name="twitter:card" content="summary"> <!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> @@ -18,7 +18,7 @@ <![endif]--> </head> <body> - <div class="container template-vignette"> + <div class="container template-article"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> @@ -27,8 +27,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">mkin</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -75,17 +79,20 @@ </header><div class="row"> - <div class="col-md-9"> + <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-21</h4> - </div> + <h4 class="date">2018-06-06</h4> + + + <div class="hidden name"><code>compiled_models.Rmd</code></div> + + </div> -<div class="contents"> <div id="model-that-can-also-be-solved-with-eigenvalues" class="section level2"> <h2 class="hasAnchor"> <a href="#model-that-can-also-be-solved-with-eigenvalues" class="anchor"></a>Model that can also be solved with Eigenvalues</h2> @@ -118,9 +125,9 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki }</code></pre></div> <pre><code>## Lade nötiges Paket: rbenchmark</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 2.155 1.000 2.152 0 -## 1 deSolve, not compiled 3 15.124 7.018 15.109 0 -## 2 Eigenvalue based 3 2.576 1.195 2.574 0 +## 3 deSolve, compiled 3 2.335 1.000 2.333 0 +## 1 deSolve, not compiled 3 16.810 7.199 16.801 0 +## 2 Eigenvalue based 3 2.882 1.234 2.879 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -149,19 +156,18 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki }</code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 3.419 1.000 3.415 0 -## 1 deSolve, not compiled 3 31.159 9.113 31.130 0 +## 2 deSolve, compiled 3 3.766 1.000 3.764 0 +## 1 deSolve, not compiled 3 37.119 9.856 37.097 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> -<p>Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 0.9.46.3 on</p> -<pre><code>## R version 3.4.4 (2018-03-15) +<p>Here we get a performance benefit of a factor of 10 using the version of the differential equation model compiled from C code!</p> +<p>This vignette was built with mkin 0.9.47.1 on</p> +<pre><code>## R version 3.5.0 (2018-04-23) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 9 (stretch)</code></pre> <pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre> </div> -</div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -189,5 +195,7 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki </footer> </div> + + </body> </html> diff --git a/docs/articles/index.html b/docs/articles/index.html index f338f1b2..59bd221d 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -21,13 +21,19 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Articles" /> + + + <!-- mathjax --> <script 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<h1>Articles <small>version 0.9.47.1</small></h1> -</div> - <div class="row"> - <div class="col-md-9"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Articles</h1> + </div> + <div class="section "> <h3>All vignettes</h3> <p class="section-desc"></p> <ul> - <li><a href="compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> <li><a href="FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li> <li><a href="FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li> <li><a href="FOCUS_Z.html">Example evaluation of FOCUS dataset Z</a></li> + <li><a href="compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> <li><a href="mkin.html">Introduction to mkin</a></li> <li><a href="twa.html">Calculation of time weighted average concentrations with mkin</a></li> </ul> @@ -133,6 +144,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 12ff2e98..28186062 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -8,8 +8,8 @@ <title>Introduction to mkin • mkin</title> <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> -<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Introduction to mkin"> +<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script><meta property="og:title" content="Introduction to mkin"> <meta property="og:description" content=""> <meta name="twitter:card" content="summary"> <!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> @@ -18,7 +18,7 @@ <![endif]--> </head> <body> - <div class="container template-vignette"> + <div class="container template-article"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> @@ -27,8 +27,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">mkin</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -75,17 +79,20 @@ </header><div class="row"> - <div class="col-md-9"> + <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-21</h4> - </div> + <h4 class="date">2018-06-06</h4> + + + <div class="hidden name"><code>mkin.Rmd</code></div> + + </div> -<div class="contents"> <p><a href="http://www.jrwb.de">Wissenschaftlicher Berater, Kronacher Str. 12, 79639 Grenzach-Wyhlen, Germany</a><br><a href="http://chem.uft.uni-bremen.de/ranke">Privatdozent at the University of Bremen</a></p> <div id="abstract" class="section level1"> <h1 class="hasAnchor"> @@ -206,7 +213,6 @@ f_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../referen </div> </div> </div> -</div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -246,5 +252,7 @@ f_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../referen </footer> </div> + + </body> </html> diff --git a/docs/articles/twa.html b/docs/articles/twa.html index 551cf03f..53afcca3 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -8,8 +8,8 @@ <title>Calculation of time weighted average concentrations with mkin • mkin</title> <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> -<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Calculation of time weighted average concentrations with mkin"> +<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script><meta property="og:title" content="Calculation of time weighted average concentrations with mkin"> <meta property="og:description" content=""> <meta name="twitter:card" content="summary"> <!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> @@ -18,7 +18,7 @@ <![endif]--> </head> <body> - <div class="container template-vignette"> + <div class="container template-article"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> @@ -27,8 +27,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">mkin</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -75,17 +79,20 @@ </header><div class="row"> - <div class="col-md-9"> + <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-21</h4> - </div> + <h4 class="date">2018-06-06</h4> + + + <div class="hidden name"><code>twa.Rmd</code></div> + + </div> -<div class="contents"> <p>Since version 0.9.45.1 of the ‘mkin’ package, a function for calculating time weighted average concentrations for decline kinetics (<em>i.e.</em> only for the compound applied in the experiment) is included. Strictly speaking, they are maximum moving window time weighted average concentrations, <em>i.e.</em> the maximum time weighted average concentration that can be found when moving a time window of a specified width over the decline curve.</p> <p>Time weighted average concentrations for the SFO, FOMC and the DFOMP model are calculated using the formulas given in the FOCUS kinetics guidance <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 251)</span>:</p> <p>SFO:</p> @@ -115,7 +122,6 @@ <p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="uri">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> </div> </div> -</div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -135,5 +141,7 @@ </footer> </div> + + </body> </html> |
