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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 | |
| parent | 6ea7bc3614b9a303f7c38dd63b9f80b8d0ebd95e (diff) | |
Static documentation rebuilt by pkgdown 1.1.0
87 files changed, 2042 insertions, 949 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index e3c7de4e..7158f2e0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -27,3 +27,4 @@ Encoding: UTF-8 VignetteBuilder: knitr BugReports: http://github.com/jranke/mkin/issues URL: https://cgit.jrwb.de/mkin/about +RoxygenNote: 6.0.1 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 src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -40,7 +46,7 @@ </head> <body> - <div class="container template-vignette-index"> + <div class="container template-article-index"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> @@ -50,8 +56,12 @@ <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> @@ -92,6 +102,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -99,21 +110,21 @@ </header> - <div class="page-header"> - <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> diff --git a/docs/authors.html b/docs/authors.html index a9712678..492c3a18 100644 --- a/docs/authors.html +++ b/docs/authors.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="Authors" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -50,8 +56,12 @@ <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> @@ -92,6 +102,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -99,15 +110,15 @@ </header> - <div class="row"> - <div class="contents col-md-12"> +<div class="row"> + <div class="contents col-md-9"> <div class="page-header"> <h1>Authors</h1> </div> <ul class="list-unstyled"> <li> - <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. <a href='https://orcid.org/0000-0003-4371-6538' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid'></a> + <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. <a href='https://orcid.org/0000-0003-4371-6538' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' height='16'></a> </p> </li> <li> @@ -141,6 +152,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/docsearch.css b/docs/docsearch.css new file mode 100644 index 00000000..e5f1fe1d --- /dev/null +++ b/docs/docsearch.css @@ -0,0 +1,148 @@ +/* Docsearch -------------------------------------------------------------- */ +/* + Source: https://github.com/algolia/docsearch/ + License: MIT +*/ + +.algolia-autocomplete { + display: block; + -webkit-box-flex: 1; + -ms-flex: 1; + flex: 1 +} + +.algolia-autocomplete .ds-dropdown-menu { + width: 100%; + min-width: none; + max-width: none; + padding: .75rem 0; + background-color: #fff; + background-clip: padding-box; + border: 1px solid rgba(0, 0, 0, .1); + box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175); +} + +@media (min-width:768px) { + 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= words.concat(content.matchedWords); + } + + // return unique words + var words_uniq = [...new Set(words)]; + return words_uniq; +} + +function updateHitURL(hit) { + + var words = matchedWords(hit); + var url = ""; + + if (hit.anchor) { + url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor; + } else { + url = hit.url + '?q=' + escape(words.join(" ")); + } + + return url; +} diff --git a/docs/index.html b/docs/index.html index 9caba262..2a5f5107 100644 --- a/docs/index.html +++ b/docs/index.html @@ -8,8 +8,8 @@ <title>Kinetic Evaluation of Chemical Degradation Data • 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" 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Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical @@ -34,8 +34,12 @@ <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> @@ -135,7 +139,7 @@ <div id="news" class="section level2"> <h2 class="hasAnchor"> <a href="#news" class="anchor"></a>News</h2> -<p>There is a ChangeLog, for the latest <a href="https://cran.r-project.org/package=mkin/news.html">CRAN release</a> and one for the <a href="https://github.com/jranke/mkin/blob/master/NEWS.md">github master branch</a>.</p> +<p>There is a ChangeLog, for the latest <a href="https://cran.r-project.org/package=mkin/news.html">CRAN release</a> and one for the <a href="https://github.com/jranke/mkin/blob/master/NEWS.html">github master branch</a>.</p> </div> <div id="credits-and-historical-remarks" class="section level2"> <h2 class="hasAnchor"> @@ -158,26 +162,37 @@ </div> <div class="col-md-3" id="sidebar"> - <h2>Links</h2> + <div class="links"> +<h2>Links</h2> <ul class="list-unstyled"> -<li>Download from CRAN at <br><a href="https://cran.r-project.org/package=mkin">https://cran.r-project.org/package=mkin</a> +<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=mkin">https://cloud.r-project.org/package=mkin</a> </li> <li>Report a bug at <br><a href="http://github.com/jranke/mkin/issues">http://github.com/jranke/mkin/issues</a> </li> </ul> +</div> +<div class="license"> <h2>License</h2> -<p>GPL</p> +<ul class="list-unstyled"> +<li>GPL</li> +</ul> +</div> +<div class="developers"> <h2>Developers</h2> <ul class="list-unstyled"> -<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid"></a> </li> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" height="16"></a> </li> <li><a href="authors.html">All authors...</a></li> </ul> +</div> + + <div class="dev-status"> <h2>Dev status</h2> <ul class="list-unstyled"> <li><a href="https://cran.r-project.org/package=mkin"><img src="https://www.r-pkg.org/badges/version/mkin"></a></li> </ul> </div> </div> +</div> <footer><div class="copyright"> @@ -191,5 +206,7 @@ </footer> </div> + + </body> </html> diff --git a/docs/news/index.html b/docs/news/index.html index c4605ae1..cc837f1e 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>All news • mkin</title> +<title>Changelog • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -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="All news" /> + + + +<meta property="og:title" content="Changelog" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -50,8 +56,12 @@ <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> @@ -92,6 +102,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -99,17 +110,17 @@ </header> - <div class="row"> - - <div class="col-md-9"> +<div class="row"> + <div class="col-md-9 contents"> <div class="page-header"> - <h1>Change log <small>All releases</small></h1> + <h1>Changelog <small></small></h1> + </div> - <div class="contents"> <div id="mkin-0-9-47-1-2018-02-06" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-47-1-2018-02-06" class="anchor"></a>mkin 0.9.47.1 (2018-02-06)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-47-1-2018-02-06" class="anchor"></a>mkin 0.9.47.1 (2018-02-06)<small> 2018-02-06 </small> +</h1> <ul> <li><p>Skip some test on CRAN and winbuilder to avoid timeouts</p></li> <li><p>‘test_data_from_UBA_2014’: Added this list of datasets containing experimental data used in the expertise from 2014</p></li> @@ -120,24 +131,27 @@ </ul> </div> <div id="mkin-0-9-46-3-2017-11-16" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-46-3-2017-11-16" class="anchor"></a>mkin 0.9.46.3 (2017-11-16)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-46-3-2017-11-16" class="anchor"></a>mkin 0.9.46.3 (2017-11-16)<small> 2017-11-16 </small> +</h1> <ul> <li><p><code>README.md</code>, <code>vignettes/mkin.Rmd</code>: URLs were updated</p></li> <li><p><code>synthetic_data_for_UBA</code>: Add the code used to generate the data in the interest of reproducibility</p></li> </ul> </div> <div id="mkin-0-9-46-2-2017-10-10" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-46-2-2017-10-10" class="anchor"></a>mkin 0.9.46.2 (2017-10-10)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-46-2-2017-10-10" class="anchor"></a>mkin 0.9.46.2 (2017-10-10)<small> 2017-10-10 </small> +</h1> <ul> <li><p>Converted the vignette FOCUS_Z from tex/pdf to markdown/html</p></li> <li><p><code>DESCRIPTION</code>: Add ORCID</p></li> </ul> </div> <div id="mkin-0-9-46-1-2017-09-14" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-46-1-2017-09-14" class="anchor"></a>mkin 0.9.46.1 (2017-09-14)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-46-1-2017-09-14" class="anchor"></a>mkin 0.9.46.1 (2017-09-14)<small> 2017-09-14 </small> +</h1> <ul> <li><p><code>plot.mkinfit</code>: Fix scaling of residual plots for the case of separate plots for each observed variable</p></li> <li><p><code>plot.mkinfit</code>: Use all data points of the fitted curve for y axis scaling for the case of separate plots for each observed variable</p></li> @@ -145,15 +159,17 @@ </ul> </div> <div id="mkin-0-9-46-2017-07-24" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-46-2017-07-24" class="anchor"></a>mkin 0.9.46 (2017-07-24)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-46-2017-07-24" class="anchor"></a>mkin 0.9.46 (2017-07-24)<small> 2017-07-29 </small> +</h1> <ul> <li>Remove <code>test_FOMC_ill-defined.R</code> as it is too platform dependent</li> </ul> </div> <div id="mkin-0-9-45-2-2017-07-24" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-45-2-2017-07-24" class="anchor"></a>mkin 0.9.45.2 (2017-07-24)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-45-2-2017-07-24" class="anchor"></a>mkin 0.9.45.2 (2017-07-24)<small> 2017-07-22 </small> +</h1> <ul> <li><p>Rename <code>twa</code> to <code>max_twa_parent</code> to avoid conflict with <code>twa</code> from my <code>pfm</code> package</p></li> <li><p>Update URLs in documentation</p></li> @@ -162,8 +178,9 @@ </ul> </div> <div id="mkin-0-9-45-1-2016-12-20" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-45-1-2016-12-20" class="anchor"></a>mkin 0.9.45.1 (2016-12-20)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-45-1-2016-12-20" class="anchor"></a>mkin 0.9.45.1 (2016-12-20)<small> Unreleased </small> +</h1> <div id="new-features" class="section level2"> <h2 class="hasAnchor"> <a href="#new-features" class="anchor"></a>New features</h2> @@ -173,8 +190,9 @@ </div> </div> <div id="mkin-0-9-45-2016-12-08" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-45-2016-12-08" class="anchor"></a>mkin 0.9.45 (2016-12-08)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-45-2016-12-08" class="anchor"></a>mkin 0.9.45 (2016-12-08)<small> 2016-12-08 </small> +</h1> <div id="minor-changes" class="section level2"> <h2 class="hasAnchor"> <a href="#minor-changes" class="anchor"></a>Minor changes</h2> @@ -186,8 +204,9 @@ </div> </div> <div id="mkin-0-9-44-2016-06-29" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-44-2016-06-29" class="anchor"></a>mkin 0.9.44 (2016-06-29)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-44-2016-06-29" class="anchor"></a>mkin 0.9.44 (2016-06-29)<small> 2016-06-29 </small> +</h1> <div id="bug-fixes" class="section level2"> <h2 class="hasAnchor"> <a href="#bug-fixes" class="anchor"></a>Bug fixes</h2> @@ -197,8 +216,9 @@ </div> </div> <div id="mkin-0-9-43-2016-06-28" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-43-2016-06-28" class="anchor"></a>mkin 0.9.43 (2016-06-28)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-43-2016-06-28" class="anchor"></a>mkin 0.9.43 (2016-06-28)<small> 2016-06-28 </small> +</h1> <div id="major-changes" class="section level2"> <h2 class="hasAnchor"> <a href="#major-changes" class="anchor"></a>Major changes</h2> @@ -235,8 +255,9 @@ </div> </div> <div id="mkin-0-9-42-2016-03-25" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-42-2016-03-25" class="anchor"></a>mkin 0.9.42 (2016-03-25)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-42-2016-03-25" class="anchor"></a>mkin 0.9.42 (2016-03-25)<small> 2016-03-25 </small> +</h1> <div id="major-changes-1" class="section level2"> <h2 class="hasAnchor"> <a href="#major-changes-1" class="anchor"></a>Major changes</h2> @@ -255,8 +276,9 @@ </div> </div> <div id="mkin-0-9-41-2015-11-09" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-41-2015-11-09" class="anchor"></a>mkin 0.9-41 (2015-11-09)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-41-2015-11-09" class="anchor"></a>mkin 0.9-41 (2015-11-09)<small> 2015-11-09 </small> +</h1> <div id="minor-changes-3" class="section level2"> <h2 class="hasAnchor"> <a href="#minor-changes-3" class="anchor"></a>Minor changes</h2> @@ -277,8 +299,9 @@ </div> </div> <div id="mkin-0-9-40-2015-07-21" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-40-2015-07-21" class="anchor"></a>mkin 0.9-40 (2015-07-21)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-40-2015-07-21" class="anchor"></a>mkin 0.9-40 (2015-07-21)<small> 2015-07-21 </small> +</h1> <div id="bug-fixes-3" class="section level2"> <h2 class="hasAnchor"> <a href="#bug-fixes-3" class="anchor"></a>Bug fixes</h2> @@ -297,8 +320,9 @@ </div> </div> <div id="mkin-0-9-39-2015-06-26" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-39-2015-06-26" class="anchor"></a>mkin 0.9-39 (2015-06-26)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-39-2015-06-26" class="anchor"></a>mkin 0.9-39 (2015-06-26)<small> 2015-06-26 </small> +</h1> <div id="major-changes-2" class="section level2"> <h2 class="hasAnchor"> <a href="#major-changes-2" class="anchor"></a>Major changes</h2> @@ -317,8 +341,9 @@ </div> </div> <div id="mkin-0-9-38-2015-06-24" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-38-2015-06-24" class="anchor"></a>mkin 0.9-38 (2015-06-24)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-38-2015-06-24" class="anchor"></a>mkin 0.9-38 (2015-06-24)<small> 2015-06-23 </small> +</h1> <div id="minor-changes-4" class="section level2"> <h2 class="hasAnchor"> <a href="#minor-changes-4" class="anchor"></a>Minor changes</h2> @@ -337,8 +362,9 @@ </div> </div> <div id="mkin-0-9-36-2015-06-21" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-36-2015-06-21" class="anchor"></a>mkin 0.9-36 (2015-06-21)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-36-2015-06-21" class="anchor"></a>mkin 0.9-36 (2015-06-21)<small> 2015-06-21 </small> +</h1> <div id="major-changes-3" class="section level2"> <h2 class="hasAnchor"> <a href="#major-changes-3" class="anchor"></a>Major changes</h2> @@ -358,8 +384,9 @@ </div> </div> <div id="mkin-0-9-35-2015-05-15" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-35-2015-05-15" class="anchor"></a>mkin 0.9-35 (2015-05-15)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-35-2015-05-15" class="anchor"></a>mkin 0.9-35 (2015-05-15)<small> 2015-05-15 </small> +</h1> <div id="major-changes-4" class="section level2"> <h2 class="hasAnchor"> <a href="#major-changes-4" class="anchor"></a>Major changes</h2> @@ -389,8 +416,9 @@ </div> </div> <div id="mkin-0-9-34-2014-11-22" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-34-2014-11-22" class="anchor"></a>mkin 0.9-34 (2014-11-22)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-34-2014-11-22" class="anchor"></a>mkin 0.9-34 (2014-11-22)<small> 2014-11-22 </small> +</h1> <div id="new-features-2" class="section level2"> <h2 class="hasAnchor"> <a href="#new-features-2" class="anchor"></a>New features</h2> @@ -410,8 +438,9 @@ </div> </div> <div id="mkin-0-9-33-2014-10-22" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-33-2014-10-22" class="anchor"></a>mkin 0.9-33 (2014-10-22)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-33-2014-10-22" class="anchor"></a>mkin 0.9-33 (2014-10-22)<small> 2014-10-12 </small> +</h1> <div id="new-features-3" class="section level2"> <h2 class="hasAnchor"> <a href="#new-features-3" class="anchor"></a>New features</h2> @@ -442,8 +471,9 @@ </div> </div> <div id="mkin-0-9-32-2014-07-24" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-32-2014-07-24" class="anchor"></a>mkin 0.9-32 (2014-07-24)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-32-2014-07-24" class="anchor"></a>mkin 0.9-32 (2014-07-24)<small> 2014-07-24 </small> +</h1> <div id="new-features-4" class="section level2"> <h2 class="hasAnchor"> <a href="#new-features-4" class="anchor"></a>New features</h2> @@ -478,8 +508,9 @@ </div> </div> <div id="mkin-0-9-31-2014-07-14" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-31-2014-07-14" class="anchor"></a>mkin 0.9-31 (2014-07-14)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-31-2014-07-14" class="anchor"></a>mkin 0.9-31 (2014-07-14)<small> 2014-07-14 </small> +</h1> <div id="bug-fixes-9" class="section level2"> <h2 class="hasAnchor"> <a href="#bug-fixes-9" class="anchor"></a>Bug fixes</h2> @@ -489,8 +520,9 @@ </div> </div> <div id="mkin-0-9-30-2014-07-11" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-30-2014-07-11" class="anchor"></a>mkin 0.9-30 (2014-07-11)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-30-2014-07-11" class="anchor"></a>mkin 0.9-30 (2014-07-11)<small> 2014-07-11 </small> +</h1> <div id="new-features-5" class="section level2"> <h2 class="hasAnchor"> <a href="#new-features-5" class="anchor"></a>New features</h2> @@ -520,8 +552,9 @@ </div> </div> <div id="mkin-0-9-29-2014-06-27" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-29-2014-06-27" class="anchor"></a>mkin 0.9-29 (2014-06-27)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-29-2014-06-27" class="anchor"></a>mkin 0.9-29 (2014-06-27)<small> 2014-06-27 </small> +</h1> <ul> <li><p>R/mkinresplot.R: Make it possible to specify <code>xlim</code></p></li> <li><p>R/geometric_mean.R, man/geometric_mean.Rd: Add geometric mean function</p></li> @@ -529,8 +562,9 @@ </ul> </div> <div id="mkin-0-9-28-2014-05-20" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-28-2014-05-20" class="anchor"></a>mkin 0.9-28 (2014-05-20)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-28-2014-05-20" class="anchor"></a>mkin 0.9-28 (2014-05-20)<small> 2014-05-20 </small> +</h1> <ul> <li><p>Do not backtransform confidence intervals for formation fractions if more than one compound is formed, as such parameters only define the pathways as a set</p></li> <li><p>Add historical remarks and some background to the main package vignette</p></li> @@ -538,8 +572,9 @@ </ul> </div> <div id="mkin-0-9-27-2014-05-10" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-27-2014-05-10" class="anchor"></a>mkin 0.9-27 (2014-05-10)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-27-2014-05-10" class="anchor"></a>mkin 0.9-27 (2014-05-10)<small> 2014-05-10 </small> +</h1> <ul> <li><p>Fork the GUI into a separate package <a href="http://github.com/jranke/gmkin">gmkin</a></p></li> <li><p>DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information</p></li> @@ -561,8 +596,9 @@ </ul> </div> <div id="mkin-0-9-24-2013-11-06" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-24-2013-11-06" class="anchor"></a>mkin 0.9-24 (2013-11-06)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-24-2013-11-06" class="anchor"></a>mkin 0.9-24 (2013-11-06)<small> 2013-11-06 </small> +</h1> <ul> <li><p>Bugfix re-enabling the fixing of any combination of initial values for state variables</p></li> <li><p>Default values for kinetic rate constants are not all 0.1 any more but are “salted” with a small increment to avoid numeric artefacts with the eigenvalue based solutions</p></li> @@ -570,8 +606,9 @@ </ul> </div> <div id="mkin-0-9-22-2013-10-26" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-22-2013-10-26" class="anchor"></a>mkin 0.9-22 (2013-10-26)</h1> +<h1 class="page-header"> +<a href="#mkin-0-9-22-2013-10-26" class="anchor"></a>mkin 0.9-22 (2013-10-26)<small> 2013-10-26 </small> +</h1> <ul> <li><p>Get rid of the optimisation step in <code>mkinerrmin</code> - this was unnecessary. Thanks to KinGUII for the inspiration - actually this is equation 6-2 in FOCUS kinetics p. 91 that I had overlooked originally</p></li> <li><p>Fix <code>plot.mkinfit</code> as it passed graphical arguments like main to the solver</p></li> @@ -587,7 +624,6 @@ </ul> <p>For a detailed list of changes to the mkin source please consult the commit history on <a href="http://github.com/jranke/mkin" class="uri">http://github.com/jranke/mkin</a></p> </div> - </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -639,6 +675,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 181fe639..6ca2f37a 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -1,13 +1,32 @@ -/* Sticker footer */ +/* Sticky footer */ + +/** + * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/ + * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css + * + * .Site -> body > .container + * .Site-content -> body > .container .row + * .footer -> footer + * + * Key idea seems to be to ensure that .container and __all its parents__ + * have height set to 100% + * + */ + +html, body { + height: 100%; +} + body > .container { display: flex; - padding-top: 60px; - min-height: calc(100vh); + height: 100%; flex-direction: column; + + padding-top: 60px; } body > .container .row { - flex: 1; + flex: 1 0 auto; } footer { @@ -16,6 +35,7 @@ footer { border-top: 1px solid #e5e5e5; color: #666; display: flex; + flex-shrink: 0; } footer p { margin-bottom: 0; @@ -38,6 +58,12 @@ img { max-width: 100%; } +/* Typographic tweaking ---------------------------------*/ + +.contents h1.page-header { + margin-top: calc(-60px + 1em); +} + /* Section anchors ---------------------------------*/ a.anchor { @@ -68,7 +94,7 @@ a.anchor { .contents h1, .contents h2, .contents h3, .contents h4 { padding-top: 60px; - margin-top: -60px; + margin-top: -40px; } /* Static header placement on mobile devices */ @@ -108,7 +134,6 @@ a.anchor { /* Reference index & topics ----------------------------------------------- */ .ref-index th {font-weight: normal;} -.ref-index h2 {font-size: 20px;} .ref-index td {vertical-align: top;} .ref-index .alias {width: 40%;} @@ -192,3 +217,16 @@ a.sourceLine:hover { .hasCopyButton:hover button.btn-copy-ex { visibility: visible; } + +/* mark.js ----------------------------*/ + +mark { + background-color: rgba(255, 255, 51, 0.5); + border-bottom: 2px solid rgba(255, 153, 51, 0.3); + padding: 1px; +} + +/* vertical spacing after htmlwidgets */ +.html-widget { + margin-bottom: 10px; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 64b20df4..de9bd724 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -1,94 +1,110 @@ -$(function() { - - $("#sidebar") - .stick_in_parent({offset_top: 40}) - .on('sticky_kit:bottom', function(e) { - $(this).parent().css('position', 'static'); - }) - .on('sticky_kit:unbottom', function(e) { - $(this).parent().css('position', 'relative'); +/* http://gregfranko.com/blog/jquery-best-practices/ */ +(function($) { + $(function() { + + $("#sidebar") + .stick_in_parent({offset_top: 40}) + .on('sticky_kit:bottom', function(e) { + $(this).parent().css('position', 'static'); + }) + .on('sticky_kit:unbottom', function(e) { + $(this).parent().css('position', 'relative'); + }); + + $('body').scrollspy({ + target: '#sidebar', + offset: 60 }); - $('body').scrollspy({ - target: '#sidebar', - offset: 60 - }); + $('[data-toggle="tooltip"]').tooltip(); + + var cur_path = paths(location.pathname); + var links = $("#navbar ul li a"); + var max_length = -1; + var pos = -1; + for (var i = 0; i < links.length; i++) { + if (links[i].getAttribute("href") === "#") + continue; + var path = paths(links[i].pathname); + + var length = prefix_length(cur_path, path); + if (length > max_length) { + max_length = length; + pos = i; + } + } - var cur_path = paths(location.pathname); - $("#navbar ul li a").each(function(index, value) { - if (value.text == "Home") - return; - if (value.getAttribute("href") === "#") - return; - - var path = paths(value.pathname); - if (is_prefix(cur_path, path)) { - // Add class to parent <li>, and enclosing <li> if in dropdown - var menu_anchor = $(value); + // Add class to parent <li>, and enclosing <li> if in dropdown + if (pos >= 0) { + var menu_anchor = $(links[pos]); menu_anchor.parent().addClass("active"); menu_anchor.closest("li.dropdown").addClass("active"); } }); -}); -function paths(pathname) { - var pieces = pathname.split("/"); - pieces.shift(); // always starts with / + function paths(pathname) { + var pieces = pathname.split("/"); + pieces.shift(); // always starts with / + + var end = pieces[pieces.length - 1]; + if (end === "index.html" || end === "") + pieces.pop(); + return(pieces); + } - var end = pieces[pieces.length - 1]; - if (end === "index.html" || end === "") - pieces.pop(); - return(pieces); -} + function prefix_length(needle, haystack) { + if (needle.length > haystack.length) + return(0); -function is_prefix(needle, haystack) { - if (needle.length > haystack.lengh) - return(false); + // Special case for length-0 haystack, since for loop won't run + if (haystack.length === 0) { + return(needle.length === 0 ? 1 : 0); + } - for (var i = 0; i < haystack.length; i++) { - if (needle[i] != haystack[i]) - return(false); - } + for (var i = 0; i < haystack.length; i++) { + if (needle[i] != haystack[i]) + return(i); + } - return(true); -} + return(haystack.length); + } -/* Clipboard --------------------------*/ + /* Clipboard --------------------------*/ -function changeTooltipMessage(element, msg) { - var tooltipOriginalTitle=element.getAttribute('data-original-title'); - element.setAttribute('data-original-title', msg); - $(element).tooltip('show'); - element.setAttribute('data-original-title', tooltipOriginalTitle); -} + function changeTooltipMessage(element, msg) { + var tooltipOriginalTitle=element.getAttribute('data-original-title'); + element.setAttribute('data-original-title', msg); + $(element).tooltip('show'); + element.setAttribute('data-original-title', tooltipOriginalTitle); + } -if(Clipboard.isSupported()) { - 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// Initialize clipboard: - var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', { - text: function(trigger) { - return trigger.parentNode.textContent; - } - }); + // Initialize clipboard: + var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', { + text: function(trigger) { + return trigger.parentNode.textContent; + } + }); - clipboardBtnCopies.on('success', function(e) { - changeTooltipMessage(e.trigger, 'Copied!'); - e.clearSelection(); - }); + clipboardBtnCopies.on('success', function(e) { + changeTooltipMessage(e.trigger, 'Copied!'); + e.clearSelection(); + }); - clipboardBtnCopies.on('error', function() { - changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); + clipboardBtnCopies.on('error', function() { + changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); + }); }); - }); -} - + } +})(window.jQuery || window.$) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 974e3585..485b80de 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,20 +1,11 @@ pandoc: 1.19.2.4 -pkgdown: 0.1.0.9000 +pkgdown: 1.1.0 pkgdown_sha: ~ articles: FOCUS_D: FOCUS_D.html - FOCUS_D.html: FOCUS_D.html FOCUS_L: FOCUS_L.html - FOCUS_L.html: FOCUS_L.html FOCUS_Z: FOCUS_Z.html - FOCUS_Z.html: FOCUS_Z.html - FOCUS_Z.pdf: FOCUS_Z.pdf compiled_models: compiled_models.html - compiled_models.html: compiled_models.html mkin: mkin.html - mkin.html: mkin.html - mkin_vignettes.css: mkin_vignettes.css - references.bib: references.bib twa: twa.html - twa.html: twa.html diff --git a/docs/reference/DFOP.solution-1.png b/docs/reference/DFOP.solution-1.png Binary files differindex e9268f94..0fbc1da1 100644 --- a/docs/reference/DFOP.solution-1.png +++ b/docs/reference/DFOP.solution-1.png diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index b1b3cf50..cd8f29e9 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -21,17 +21,23 @@ <!-- 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="Double First-Order in Parallel kinetics — DFOP.solution" /> <meta property="og:description" content="Function describing decline from a defined starting value using the sum of two exponential decline functions." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <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> @@ -96,6 +106,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -103,20 +114,24 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Double First-Order in Parallel kinetics</h1> + + <div class="hidden name"><code>DFOP.solution.Rd</code></div> </div> + <div class="ref-description"> <p>Function describing decline from a defined starting value using the sum of two exponential decline functions.</p> + </div> <pre class="usage"><span class='fu'>DFOP.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>g</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -156,7 +171,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>DFOP.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>5</span>, <span class='fl'>0.5</span>, <span class='fl'>0.3</span>), <span class='fl'>0</span>, <span class='fl'>4</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='DFOP.solution-1.png' alt='' width='700' height='432.632880098887' /></div></pre> + <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>DFOP.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>5</span>, <span class='fl'>0.5</span>, <span class='fl'>0.3</span>), <span class='fl'>0</span>, <span class='fl'>4</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='DFOP.solution-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -185,6 +200,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 2a3b1c78..deb418c2 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -21,16 +21,22 @@ <!-- 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="Subsetting method for mmkin objects — [.mmkin" /> <meta property="og:description" content="Subsetting method for mmkin objects." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <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> @@ -95,6 +105,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -102,20 +113,24 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Subsetting method for mmkin objects</h1> + + <div class="hidden name"><code>Extract.mmkin.Rd</code></div> </div> + <div class="ref-description"> <p>Subsetting method for mmkin objects.</p> + </div> <pre class="usage"># S3 method for mmkin [(x, i, j, ..., drop = FALSE)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -262,8 +277,8 @@ #> [1] 29 #> #> $time -#> user system elapsed -#> 0.242 0.000 0.244 +#> User System verstrichen +#> 0.179 0.000 0.184 #> #> $mkinmod #> <mkinmod> model generated with @@ -452,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x5555578ff9d0> -#> <environment: 0x555559a0da40> +#> <bytecode: 0x55555b9b9d58> +#> <environment: 0x55555be59518> #> #> $cost_notrans #> function (P) @@ -475,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x555559b90d60> -#> <environment: 0x555559a0da40> +#> <bytecode: 0x55555c2673f8> +#> <environment: 0x55555be59518> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -495,7 +510,7 @@ #> #> $fixed #> [1] value type -#> <0 rows> (or 0-length row.names) +#> <0 Zeilen> (oder row.names mit Länge 0) #> #> $data #> time variable observed predicted residual @@ -543,13 +558,13 @@ #> 99.17407 #> #> $date -#> [1] "Wed Mar 21 18:14:20 2018" +#> [1] "Wed Jun 6 01:21:24 2018" #> #> $version #> [1] "0.9.47.1" #> #> $Rversion -#> [1] "3.4.4" +#> [1] "3.5.0" #> #> attr(,"class") #> [1] "mkinfit" "modFit" @@ -584,6 +599,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index f392bf64..78caf48d 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -21,12 +21,15 @@ <!-- 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="Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B" /> <meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values @@ -35,6 +38,9 @@ The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -57,8 +63,12 @@ in this fit." /> <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> @@ -99,6 +109,7 @@ in this fit." /> <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -106,12 +117,15 @@ in this fit." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</h1> + + <div class="hidden name"><code>FOCUS_2006_DFOP_ref_A_to_B.Rd</code></div> </div> + <div class="ref-description"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -119,6 +133,7 @@ The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> + </div> <pre class="usage"><span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span></pre> @@ -173,6 +188,8 @@ in this fit.</p> </footer> </div> + + </body> </html> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index 6e4c8d64..c854c11c 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -21,12 +21,15 @@ <!-- 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="Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F" /> <meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values @@ -35,6 +38,9 @@ The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -57,8 +63,12 @@ in this fit." /> <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> @@ -99,6 +109,7 @@ in this fit." /> <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -106,12 +117,15 @@ in this fit." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</h1> + + <div class="hidden name"><code>FOCUS_2006_FOMC_ref_A_to_F.Rd</code></div> </div> + <div class="ref-description"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -119,6 +133,7 @@ The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> + </div> <pre class="usage"><span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span></pre> @@ -172,6 +187,8 @@ in this fit.</p> </footer> </div> + + </body> </html> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index ed38ccae..89ee9ae9 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -21,12 +21,15 @@ <!-- 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="Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F" /> <meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values @@ -35,6 +38,9 @@ The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -57,8 +63,12 @@ in this fit." /> <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> @@ -99,6 +109,7 @@ in this fit." /> <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -106,12 +117,15 @@ in this fit." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Results of fitting the HS model to Datasets A to F of FOCUS (2006)</h1> + + <div class="hidden name"><code>FOCUS_2006_HS_ref_A_to_F.Rd</code></div> </div> + <div class="ref-description"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -119,6 +133,7 @@ The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> + </div> <pre class="usage"><span class='no'>FOCUS_2006_HS_ref_A_to_F</span></pre> @@ -173,6 +188,8 @@ in this fit.</p> </footer> </div> + + </body> </html> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index 107f3e5f..182c7003 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -21,12 +21,15 @@ <!-- 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="Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F" /> <meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values @@ -35,6 +38,9 @@ The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -57,8 +63,12 @@ in this fit." /> <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> @@ -99,6 +109,7 @@ in this fit." /> <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -106,12 +117,15 @@ in this fit." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</h1> + + <div class="hidden name"><code>FOCUS_2006_SFO_ref_A_to_F.Rd</code></div> </div> + <div class="ref-description"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -119,6 +133,7 @@ The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> + </div> <pre class="usage"><span class='no'>FOCUS_2006_SFO_ref_A_to_F</span></pre> @@ -171,6 +186,8 @@ in this fit.</p> </footer> </div> + + </body> </html> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index cc310ee3..aa84e14b 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -21,16 +21,22 @@ <!-- 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="Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets" /> <meta property="og:description" content="Data taken from FOCUS (2006), p. 258." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <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> @@ -95,6 +105,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -102,15 +113,19 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Datasets A to F from the FOCUS Kinetics report from 2006</h1> + + <div class="hidden name"><code>FOCUS_2006_datasets.Rd</code></div> </div> + <div class="ref-description"> <p>Data taken from FOCUS (2006), p. 258.</p> + </div> <pre class="usage"><span class='no'>FOCUS_2006_datasets</span></pre> @@ -169,6 +184,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/FOMC.solution-1.png b/docs/reference/FOMC.solution-1.png Binary files differindex f10cff4e..127f3085 100644 --- a/docs/reference/FOMC.solution-1.png +++ b/docs/reference/FOMC.solution-1.png diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 397dc82d..4b8f1c92 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -21,12 +21,15 @@ <!-- 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="First-Order Multi-Compartment kinetics — FOMC.solution" /> <meta property="og:description" content="Function describing exponential decline from a defined starting value, with @@ -35,6 +38,9 @@ The form given here differs slightly from the original reference by Gustafson and Holden (1990). The parameter beta corresponds to 1/beta in the original equation." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -57,8 +63,12 @@ The form given here differs slightly from the original reference by Gustafson <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> @@ -99,6 +109,7 @@ The form given here differs slightly from the original reference by Gustafson <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -106,12 +117,15 @@ The form given here differs slightly from the original reference by Gustafson </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>First-Order Multi-Compartment kinetics</h1> + + <div class="hidden name"><code>FOMC.solution.Rd</code></div> </div> + <div class="ref-description"> <p>Function describing exponential decline from a defined starting value, with a decreasing rate constant.</p> @@ -119,10 +133,11 @@ The form given here differs slightly from the original reference by Gustafson and Holden (1990). The parameter <code>beta</code> corresponds to 1/beta in the original equation.</p> + </div> <pre class="usage"><span class='fu'>FOMC.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>alpha</span>, <span class='no'>beta</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -168,7 +183,7 @@ The form given here differs slightly from the original reference by Gustafson <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>FOMC.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>10</span>, <span class='fl'>2</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='FOMC.solution-1.png' alt='' width='700' height='432.632880098887' /></div></pre> + <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>FOMC.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>10</span>, <span class='fl'>2</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='FOMC.solution-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -199,6 +214,8 @@ The form given here differs slightly from the original reference by Gustafson </footer> </div> + + </body> </html> diff --git a/docs/reference/HS.solution-1.png b/docs/reference/HS.solution-1.png Binary files differindex 5e04d343..4dc42c31 100644 --- a/docs/reference/HS.solution-1.png +++ b/docs/reference/HS.solution-1.png diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index f633aa67..d06a839e 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -21,17 +21,23 @@ <!-- 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="Hockey-Stick kinetics — HS.solution" /> <meta property="og:description" content="Function describing two exponential decline functions with a break point between them." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <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> @@ -96,6 +106,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -103,20 +114,24 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Hockey-Stick kinetics</h1> + + <div class="hidden name"><code>HS.solution.Rd</code></div> </div> + <div class="ref-description"> <p>Function describing two exponential decline functions with a break point between them.</p> + </div> <pre class="usage"><span class='fu'>HS.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>tb</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -157,7 +172,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>HS.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>2</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='HS.solution-1.png' alt='' width='700' height='432.632880098887' /></div></pre> + <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>HS.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>2</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='HS.solution-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -186,6 +201,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/IORE.solution-1.png b/docs/reference/IORE.solution-1.png Binary files differindex e421d562..d8b6e8e3 100644 --- a/docs/reference/IORE.solution-1.png +++ b/docs/reference/IORE.solution-1.png diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 687dee5a..c037a8d2 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -21,17 +21,23 @@ <!-- 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="Indeterminate order rate equation kinetics — IORE.solution" /> <meta property="og:description" content="Function describing exponential decline from a defined starting value, with a concentration dependent rate constant." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <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> @@ -96,6 +106,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -103,20 +114,24 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Indeterminate order rate equation kinetics</h1> + + <div class="hidden name"><code>IORE.solution.Rd</code></div> </div> + <div class="ref-description"> <p>Function describing exponential decline from a defined starting value, with a concentration dependent rate constant.</p> + </div> <pre class="usage"><span class='fu'>IORE.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k__iore</span>, <span class='no'>N</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -157,7 +172,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>IORE.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.2</span>, <span class='fl'>1.3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, - <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='IORE.solution-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> <span class='no'>fit.fomc</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='IORE.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='no'>fit.fomc</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>fit.iore</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>fit.iore.deS</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) @@ -200,6 +215,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 1156c16f..32ef9f29 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -21,16 +21,22 @@ <!-- 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="Single First-Order kinetics — SFO.solution" /> <meta property="og:description" content="Function describing exponential decline from a defined starting value." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <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> @@ -95,6 +105,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -102,19 +113,23 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Single First-Order kinetics</h1> + + <div class="hidden name"><code>SFO.solution.Rd</code></div> </div> + <div class="ref-description"> <p>Function describing exponential decline from a defined starting value.</p> + </div> <pre class="usage"><span class='fu'>SFO.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -176,6 +191,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 6901c435..aee32558 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -21,12 +21,15 @@ <!-- 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="Single First-Order Reversible Binding kinetics — SFORB.solution" /> <meta property="og:description" content="Function describing the solution of the differential equations describing @@ -35,6 +38,9 @@ fraction. The initial condition is a defined amount in the free fraction and no substance in the bound fraction." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -57,8 +63,12 @@ <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> @@ -99,6 +109,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -106,12 +117,15 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Single First-Order Reversible Binding kinetics</h1> + + <div class="hidden name"><code>SFORB.solution.Rd</code></div> </div> + <div class="ref-description"> <p>Function describing the solution of the differential equations describing the kinetic model with first-order terms for a two-way transfer from a free @@ -119,10 +133,11 @@ fraction. The initial condition is a defined amount in the free fraction and no substance in the bound fraction.</p> + </div> <pre class="usage"><span class='fu'>SFORB.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k_12</span>, <span class='no'>k_21</span>, <span class='no'>k_1output</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -193,6 +208,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png Binary files differindex fecfc52d..d099898c 100644 --- a/docs/reference/add_err-1.png +++ b/docs/reference/add_err-1.png diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png Binary files differindex 907001ed..f6de95a0 100644 --- a/docs/reference/add_err-2.png +++ b/docs/reference/add_err-2.png diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png Binary files differindex 3786d934..13f54e65 100644 --- a/docs/reference/add_err-3.png +++ b/docs/reference/add_err-3.png diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 6d830113..063234b3 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -21,18 +21,24 @@ <!-- 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="Add normally distributed errors to simulated kinetic degradation data — add_err" /> <meta property="og:description" content="Normally distributed errors are added to data predicted for a specific degradation model using mkinpredict. The variance of the error may depend on the predicted value and is specified as a standard deviation." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -55,8 +61,12 @@ <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> @@ -97,6 +107,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -104,23 +115,27 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Add normally distributed errors to simulated kinetic degradation data</h1> + + <div class="hidden name"><code>add_err.Rd</code></div> </div> + <div class="ref-description"> <p>Normally distributed errors are added to data predicted for a specific degradation model using <code><a href='mkinpredict.html'>mkinpredict</a></code>. The variance of the error may depend on the predicted value and is specified as a standard deviation.</p> + </div> <pre class="usage"><span class='fu'>add_err</span>(<span class='no'>prediction</span>, <span class='no'>sdfunc</span>, <span class='kw'>secondary</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>), <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -204,14 +219,14 @@ <span class='no'>d_SFO_SFO_err</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) -<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>)</div><div class='img'><img src='add_err-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> +<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>)</div><div class='img'><img src='add_err-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># We would like to inspect the fit for dataset 3 more closely</span> <span class='co'># Using double brackets makes the returned object an mkinfit object</span> <span class='co'># instead of a list of mkinfit objects, so plot.mkinfit is used</span> -<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span><span class='kw'>[[</span><span class='fl'>3</span>]], <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='add_err-2.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> +<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span><span class='kw'>[[</span><span class='fl'>3</span>]], <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='add_err-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># If we use single brackets, we should give two indices (model and dataset),</span> <span class='co'># and plot.mmkin is used</span> -<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><div class='img'><img src='add_err-3.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> +<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><div class='img'><img src='add_err-3.png' alt='' width='700' height='433' /></div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -245,6 +260,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 0f5ba0a4..b10998fb 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -21,12 +21,15 @@ <!-- 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="Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints" /> <meta property="og:description" content="This function calculates DT50 and DT90 values as well as formation fractions from kinetic models @@ -34,6 +37,9 @@ fitted with mkinfit. If the SFORB model was specified for one of the parents or the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but with the advantage that the SFORB model can also be used for metabolites." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -56,8 +62,12 @@ with the advantage that the SFORB model can also be used for metabolites." /> <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> @@ -98,6 +108,7 @@ with the advantage that the SFORB model can also be used for metabolites." /> <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -105,22 +116,26 @@ with the advantage that the SFORB model can also be used for metabolites." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</h1> + + <div class="hidden name"><code>endpoints.Rd</code></div> </div> + <div class="ref-description"> <p>This function calculates DT50 and DT90 values as well as formation fractions from kinetic models fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but with the advantage that the SFORB model can also be used for metabolites.</p> + </div> <pre class="usage"><span class='fu'>endpoints</span>(<span class='no'>fit</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -182,6 +197,8 @@ with the advantage that the SFORB model can also be used for metabolites.</p> </footer> </div> + + </body> </html> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 9d91b5a8..90b6fd9d 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -21,16 +21,22 @@ <!-- 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="Calculate the geometric mean — geometric_mean" /> <meta property="og:description" content="Function calculating the geometric mean of numeric vectors" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <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> @@ -95,6 +105,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -102,19 +113,23 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate the geometric mean</h1> + + <div class="hidden name"><code>geometric_mean.Rd</code></div> </div> + <div class="ref-description"> <p>Function calculating the geometric mean of numeric vectors</p> + </div> <pre class="usage"><span class='fu'>geometric_mean</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -160,6 +175,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 33d749ce..8f337595 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -21,16 +21,22 @@ <!-- 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="Function to perform isometric log-ratio transformation — ilr" /> <meta property="og:description" content="This implementation is a special case of the class of isometric log-ratio transformations." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <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> @@ -95,6 +105,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -102,20 +113,24 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to perform isometric log-ratio transformation</h1> + + <div class="hidden name"><code>ilr.Rd</code></div> </div> + <div class="ref-description"> <p>This implementation is a special case of the class of isometric log-ratio transformations.</p> + </div> <pre class="usage"><span class='fu'>ilr</span>(<span class='no'>x</span>) <span class='fu'>invilr</span>(<span class='no'>x</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -136,7 +151,7 @@ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p>Another implementation can be found in R package <code>robCompositions</code>.</p> + <div class='dont-index'><p>Another implementation can be found in R package <code>robCompositions</code>.</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -184,6 +199,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/index.html b/docs/reference/index.html index 6c05941d..5785b5aa 100644 --- a/docs/reference/index.html +++ b/docs/reference/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="Function reference" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -50,8 +56,12 @@ <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> @@ -92,6 +102,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -99,330 +110,326 @@ </header> - <div class="row"> - <div class="col-md-9"> +<div class="row"> + <div class="contents col-md-9"> <div class="page-header"> - <h1> - Reference - <small>version 0.9.47.1</small> - </h1> + <h1>Reference</h1> </div> - <div class="contents"> - <table class="ref-index"> + <table class="ref-index"> - <colgroup> - <col class="alias" /> - <col class="title" /> - </colgroup> + <colgroup> + + <col class="alias" /> + <col class="title" /> + </colgroup> - <tbody> - <tr> - <th colspan="2"> - <h2 id="section-main-functions" class="hasAnchor"><a href="#section-main-functions" class="anchor"></a>Main functions</h2> - <p class="section-desc"><p>Essential functionality</p></p> - </th> - </tr> - <tr> - <!-- --> - <td> - <p><code><a href="mkinmod.html">mkinmod</a></code> </p> - </td> - <td><p>Function to set up a kinetic model with one or more state variables</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="mkinfit.html">mkinfit</a></code> </p> - </td> - <td><p>Fit a kinetic model to data with one or more state variables</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="mmkin.html">mmkin</a></code> </p> - </td> - <td><p>Fit one or more kinetic models with one or more state variables to one or more datasets</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-show-results" class="hasAnchor"><a href="#section-show-results" class="anchor"></a>Show results</h2> - <p class="section-desc"><p>Functions working with mkinfit objects</p></p> - </th> - </tr> - <tr> - <!-- --> - <td> - <p><code><a href="plot.mkinfit.html">plot.mkinfit</a></code> </p> - </td> - <td><p>Plot the observed data and the fitted model of an mkinfit object</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="summary.mkinfit.html">summary</a></code> <code><a href="summary.mkinfit.html">print</a></code> </p> - </td> - <td><p>Summary method for class "mkinfit"</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="mkinresplot.html">mkinresplot</a></code> </p> - </td> - <td><p>Function to plot residuals stored in an mkin object</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="mkinparplot.html">mkinparplot</a></code> </p> - </td> - <td><p>Function to plot the confidence intervals obtained using mkinfit</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="endpoints.html">endpoints</a></code> </p> - </td> - <td><p>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="mkinerrmin.html">mkinerrmin</a></code> </p> - </td> - <td><p>Calculate the minimum error to assume in order to pass the variance test</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-work-with-mmkin-objects" class="hasAnchor"><a href="#section-work-with-mmkin-objects" class="anchor"></a>Work with mmkin objects</h2> - <p class="section-desc"><p>Functions working with aggregated results</p></p> - </th> - </tr> - <tr> - <!-- --> - <td> - <p><code><a href="Extract.mmkin.html">[.mmkin</a></code> </p> - </td> - <td><p>Subsetting method for mmkin objects</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="plot.mmkin.html">plot</a></code> </p> - </td> - <td><p>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-datasets-and-known-results" class="hasAnchor"><a href="#section-datasets-and-known-results" class="anchor"></a>Datasets and known results</h2> - <p class="section-desc"></p> - </th> - </tr> - <tr> - <!-- --> - <td> - <p><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_datasets</a></code> </p> - </td> - <td><p>Datasets A to F from the FOCUS Kinetics report from 2006</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code> </p> - </td> - <td><p>Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code> </p> - </td> - <td><p>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code> </p> - </td> - <td><p>Results of fitting the HS model to Datasets A to F of FOCUS (2006)</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code> </p> - </td> - <td><p>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="mccall81_245T.html">mccall81_245T</a></code> </p> - </td> - <td><p>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code> </p> - </td> - <td><p>Metabolism data set used for checking the software quality of KinGUI</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code> </p> - </td> - <td><p>Synthetic datasets for one parent compound with two metabolites</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="test_data_from_UBA_2014.html">test_data_from_UBA_2014</a></code> </p> - </td> - <td><p>Three experimental datasets from two water sediment systems and one soil</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="mkinds.html">mkinds</a></code> </p> - </td> - <td><p>A dataset class for mkin</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="print.mkinds.html">print</a></code> </p> - </td> - <td><p>Print mkinds objects</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2> - <p class="section-desc"></p> - </th> - </tr> - <tr> - <!-- --> - <td> - <p><code><a href="geometric_mean.html">geometric_mean</a></code> </p> - </td> - <td><p>Calculate the geometric mean</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="mkinsub.html">mkinsub</a></code> </p> - </td> - <td><p>Function to set up a kinetic submodel for one state variable</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="max_twa_parent.html">max_twa_parent</a></code> </p> - </td> - <td><p>Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="mkinpredict.html">mkinpredict</a></code> </p> - </td> - <td><p>Produce predictions from a kinetic model using specific parameters</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code> </p> - </td> - <td><p>Convert a dataframe with observations over time into long format</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code> </p> - </td> - <td><p>Convert a dataframe from long to wide format</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="print.mkinmod.html">print</a></code> </p> - </td> - <td><p>Print mkinmod objects</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="transform_odeparms.html">transform_odeparms</a></code> <code><a href="transform_odeparms.html">backtransform_odeparms</a></code> </p> - </td> - <td><p>Functions to transform and backtransform kinetic parameters for fitting</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="ilr.html">ilr</a></code> <code><a href="ilr.html">invilr</a></code> </p> - </td> - <td><p>Function to perform isometric log-ratio transformation</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="sigma_rl.html">sigma_rl</a></code> </p> - </td> - <td><p>Two component error model of Rocke and Lorenzato</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-analytical-solutions" class="hasAnchor"><a href="#section-analytical-solutions" class="anchor"></a>Analytical solutions</h2> - <p class="section-desc"><p>Parent only model solutions</p></p> - </th> - </tr> - <tr> - <!-- --> - <td> - <p><code><a href="SFO.solution.html">SFO.solution</a></code> </p> - </td> - <td><p>Single First-Order kinetics</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="FOMC.solution.html">FOMC.solution</a></code> </p> - </td> - <td><p>First-Order Multi-Compartment kinetics</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="DFOP.solution.html">DFOP.solution</a></code> </p> - </td> - <td><p>Double First-Order in Parallel kinetics</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="SFORB.solution.html">SFORB.solution</a></code> </p> - </td> - <td><p>Single First-Order Reversible Binding kinetics</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="HS.solution.html">HS.solution</a></code> </p> - </td> - <td><p>Hockey-Stick kinetics</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="IORE.solution.html">IORE.solution</a></code> </p> - </td> - <td><p>Indeterminate order rate equation kinetics</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-generate-synthetic-datasets" class="hasAnchor"><a href="#section-generate-synthetic-datasets" class="anchor"></a>Generate synthetic datasets</h2> - <p class="section-desc"></p> - </th> - </tr> - <tr> - <!-- --> - <td> - <p><code><a href="add_err.html">add_err</a></code> </p> - </td> - <td><p>Add normally distributed errors to simulated kinetic degradation data</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2> - <p class="section-desc"><p>Functions that have been superseeded</p></p> - </th> - </tr> - <tr> - <!-- --> - <td> - <p><code><a href="mkinplot.html">mkinplot</a></code> </p> - </td> - <td><p>Plot the observed data and the fitted model of an mkinfit object</p></td> - </tr> - </tbody> - </table> - </div> + <tbody> + <tr> + <th colspan="2"> + <h2 id="section-main-functions" class="hasAnchor"><a href="#section-main-functions" class="anchor"></a>Main functions</h2> + <p class="section-desc"><p>Essential functionality</p></p> + </th> + </tr> + <tr> + + <td> + <p><code><a href="mkinmod.html">mkinmod()</a></code> </p> + </td> + <td><p>Function to set up a kinetic model with one or more state variables</p></td> + </tr><tr> + + <td> + <p><code><a href="mkinfit.html">mkinfit()</a></code> </p> + </td> + <td><p>Fit a kinetic model to data with one or more state variables</p></td> + </tr><tr> + + <td> + <p><code><a href="mmkin.html">mmkin()</a></code> </p> + </td> + <td><p>Fit one or more kinetic models with one or more state variables to one or more datasets</p></td> + </tr> + </tbody><tbody> + <tr> + <th colspan="2"> + <h2 id="section-show-results" class="hasAnchor"><a href="#section-show-results" class="anchor"></a>Show results</h2> + <p class="section-desc"><p>Functions working with mkinfit objects</p></p> + </th> + </tr> + <tr> + + <td> + <p><code><a href="plot.mkinfit.html">plot(<i><mkinfit></i>)</a></code> <code><a href="plot.mkinfit.html">plot_sep()</a></code> </p> + </td> + <td><p>Plot the observed data and the fitted model of an mkinfit object</p></td> + </tr><tr> + + <td> + <p><code><a href="summary.mkinfit.html">summary(<i><mkinfit></i>)</a></code> <code><a href="summary.mkinfit.html">print(<i><summary.mkinfit></i>)</a></code> </p> + </td> + <td><p>Summary method for class "mkinfit"</p></td> + </tr><tr> + + <td> + <p><code><a href="mkinresplot.html">mkinresplot()</a></code> </p> + </td> + <td><p>Function to plot residuals stored in an mkin object</p></td> + </tr><tr> + + <td> + <p><code><a href="mkinparplot.html">mkinparplot()</a></code> </p> + </td> + <td><p>Function to plot the confidence intervals obtained using mkinfit</p></td> + </tr><tr> + + <td> + <p><code><a href="endpoints.html">endpoints()</a></code> </p> + </td> + <td><p>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</p></td> + </tr><tr> + + <td> + <p><code><a href="mkinerrmin.html">mkinerrmin()</a></code> </p> + </td> + <td><p>Calculate the minimum error to assume in order to pass the variance test</p></td> + </tr> + </tbody><tbody> + <tr> + <th colspan="2"> + <h2 id="section-work-with-mmkin-objects" class="hasAnchor"><a href="#section-work-with-mmkin-objects" class="anchor"></a>Work with mmkin objects</h2> + <p class="section-desc"><p>Functions working with aggregated results</p></p> + </th> + </tr> + <tr> + + <td> + <p><code><a href="Extract.mmkin.html">`[`(<i><mmkin></i>)</a></code> </p> + </td> + <td><p>Subsetting method for mmkin objects</p></td> + </tr><tr> + + <td> + <p><code><a href="plot.mmkin.html">plot(<i><mmkin></i>)</a></code> </p> + </td> + <td><p>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</p></td> + </tr> + </tbody><tbody> + <tr> + <th colspan="2"> + <h2 id="section-datasets-and-known-results" class="hasAnchor"><a href="#section-datasets-and-known-results" class="anchor"></a>Datasets and known results</h2> + <p class="section-desc"></p> + </th> + </tr> + <tr> + + <td> + <p><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_datasets</a></code> </p> + </td> + <td><p>Datasets A to F from the FOCUS Kinetics report from 2006</p></td> + </tr><tr> + + <td> + <p><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code> </p> + </td> + <td><p>Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</p></td> + </tr><tr> + + <td> + <p><code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code> </p> + </td> + <td><p>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</p></td> + </tr><tr> + + <td> + <p><code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code> </p> + </td> + <td><p>Results of fitting the HS model to Datasets A to F of FOCUS (2006)</p></td> + </tr><tr> + + <td> + <p><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code> </p> + </td> + <td><p>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</p></td> + </tr><tr> + + <td> + <p><code><a href="mccall81_245T.html">mccall81_245T</a></code> </p> + </td> + <td><p>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</p></td> + </tr><tr> + + <td> + <p><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code> </p> + </td> + <td><p>Metabolism data set used for checking the software quality of KinGUI</p></td> + </tr><tr> + + <td> + <p><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code> </p> + </td> + <td><p>Synthetic datasets for one parent compound with two metabolites</p></td> + </tr><tr> + + <td> + <p><code><a href="test_data_from_UBA_2014.html">test_data_from_UBA_2014</a></code> </p> + </td> + <td><p>Three experimental datasets from two water sediment systems and one soil</p></td> + </tr><tr> + + <td> + <p><code><a href="mkinds.html">mkinds</a></code> </p> + </td> + <td><p>A dataset class for mkin</p></td> + </tr><tr> + + <td> + <p><code><a href="print.mkinds.html">print(<i><mkinds></i>)</a></code> </p> + </td> + <td><p>Print mkinds objects</p></td> + </tr> + </tbody><tbody> + <tr> + <th colspan="2"> + <h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2> + <p class="section-desc"></p> + </th> + </tr> + <tr> + + <td> + <p><code><a href="geometric_mean.html">geometric_mean()</a></code> </p> + </td> + <td><p>Calculate the geometric mean</p></td> + </tr><tr> + + <td> + <p><code><a href="mkinsub.html">mkinsub()</a></code> </p> + </td> + <td><p>Function to set up a kinetic submodel for one state variable</p></td> + </tr><tr> + + <td> + <p><code><a href="max_twa_parent.html">max_twa_parent()</a></code> </p> + </td> + <td><p>Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit</p></td> + </tr><tr> + + <td> + <p><code><a href="mkinpredict.html">mkinpredict()</a></code> </p> + </td> + <td><p>Produce predictions from a kinetic model using specific parameters</p></td> + </tr><tr> + + <td> + <p><code><a href="mkin_wide_to_long.html">mkin_wide_to_long()</a></code> </p> + </td> + <td><p>Convert a dataframe with observations over time into long format</p></td> + </tr><tr> + + <td> + <p><code><a href="mkin_long_to_wide.html">mkin_long_to_wide()</a></code> </p> + </td> + <td><p>Convert a dataframe from long to wide format</p></td> + </tr><tr> + + <td> + <p><code><a href="print.mkinmod.html">print(<i><mkinmod></i>)</a></code> </p> + </td> + <td><p>Print mkinmod objects</p></td> + </tr><tr> + + <td> + <p><code><a href="transform_odeparms.html">transform_odeparms()</a></code> <code><a href="transform_odeparms.html">backtransform_odeparms()</a></code> </p> + </td> + <td><p>Functions to transform and backtransform kinetic parameters for fitting</p></td> + </tr><tr> + + <td> + <p><code><a href="ilr.html">ilr()</a></code> <code><a href="ilr.html">invilr()</a></code> </p> + </td> + <td><p>Function to perform isometric log-ratio transformation</p></td> + </tr><tr> + + <td> + <p><code><a href="sigma_rl.html">sigma_rl()</a></code> </p> + </td> + <td><p>Two component error model of Rocke and Lorenzato</p></td> + </tr> + </tbody><tbody> + <tr> + <th colspan="2"> + <h2 id="section-analytical-solutions" class="hasAnchor"><a href="#section-analytical-solutions" class="anchor"></a>Analytical solutions</h2> + <p class="section-desc"><p>Parent only model solutions</p></p> + </th> + </tr> + <tr> + + <td> + <p><code><a href="SFO.solution.html">SFO.solution()</a></code> </p> + </td> + <td><p>Single First-Order kinetics</p></td> + </tr><tr> + + <td> + <p><code><a href="FOMC.solution.html">FOMC.solution()</a></code> </p> + </td> + <td><p>First-Order Multi-Compartment kinetics</p></td> + </tr><tr> + + <td> + <p><code><a href="DFOP.solution.html">DFOP.solution()</a></code> </p> + </td> + <td><p>Double First-Order in Parallel kinetics</p></td> + </tr><tr> + + <td> + <p><code><a href="SFORB.solution.html">SFORB.solution()</a></code> </p> + </td> + <td><p>Single First-Order Reversible Binding kinetics</p></td> + </tr><tr> + + <td> + <p><code><a href="HS.solution.html">HS.solution()</a></code> </p> + </td> + <td><p>Hockey-Stick kinetics</p></td> + </tr><tr> + + <td> + <p><code><a href="IORE.solution.html">IORE.solution()</a></code> </p> + </td> + <td><p>Indeterminate order rate equation kinetics</p></td> + </tr> + </tbody><tbody> + <tr> + <th colspan="2"> + <h2 id="section-generate-synthetic-datasets" class="hasAnchor"><a href="#section-generate-synthetic-datasets" class="anchor"></a>Generate synthetic datasets</h2> + <p class="section-desc"></p> + </th> + </tr> + <tr> + + <td> + <p><code><a href="add_err.html">add_err()</a></code> </p> + </td> + <td><p>Add normally distributed errors to simulated kinetic degradation data</p></td> + </tr> + </tbody><tbody> + <tr> + <th colspan="2"> + <h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2> + <p class="section-desc"><p>Functions that have been superseeded</p></p> + </th> + </tr> + <tr> + + <td> + <p><code><a href="mkinplot.html">mkinplot()</a></code> </p> + </td> + <td><p>Plot the observed data and the fitted model of an mkinfit object</p></td> + </tr> + </tbody> + </table> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -452,6 +459,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 696ca729..7b3ef8ea 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -21,12 +21,15 @@ <!-- 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="Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit — max_twa_parent" /> <meta property="og:description" content="This function calculates maximum moving window time weighted average concentrations @@ -35,6 +38,9 @@ calculations for the parent are implemented for the SFO, FOMC and DFOP models, using the analytical formulas given in the PEC soil section of the FOCUS guidance." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -57,8 +63,12 @@ guidance." /> <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> @@ -99,6 +109,7 @@ guidance." /> <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -106,12 +117,15 @@ guidance." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit</h1> + + <div class="hidden name"><code>max_twa_parent.Rd</code></div> </div> + <div class="ref-description"> <p>This function calculates maximum moving window time weighted average concentrations (TWAs) for kinetic models fitted with <code><a href='mkinfit.html'>mkinfit</a></code>. Currently, only @@ -119,10 +133,11 @@ calculations for the parent are implemented for the SFO, FOMC and DFOP models, using the analytical formulas given in the PEC soil section of the FOCUS guidance.</p> + </div> <pre class="usage"><span class='fu'>max_twa_parent</span>(<span class='no'>fit</span>, <span class='no'>windows</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -184,6 +199,8 @@ guidance.</p> </footer> </div> + + </body> </html> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index cb70e68c..3326a225 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -21,18 +21,24 @@ <!-- 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="Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T" /> <meta property="og:description" content="Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether extracts." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -55,8 +61,12 @@ <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> @@ -97,6 +107,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -104,17 +115,21 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</h1> + + <div class="hidden name"><code>mccall81_245T.Rd</code></div> </div> + <div class="ref-description"> <p>Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether extracts.</p> + </div> <pre class="usage"><span class='no'>mccall81_245T</span></pre> @@ -150,9 +165,9 @@ <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.1 -#> R version used for fitting: 3.4.4 -#> Date of fit: Wed Mar 21 18:14:30 2018 -#> Date of summary: Wed Mar 21 18:14:30 2018 +#> R version used for fitting: 3.5.0 +#> Date of fit: Wed Jun 6 01:21:34 2018 +#> Date of summary: Wed Jun 6 01:21:34 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -162,7 +177,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.403 s +#> Fitted with method Port using 246 model solutions performed in 1.452 s #> #> Weighting: none #> @@ -270,6 +285,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 3c498a76..7f4431f5 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -21,18 +21,24 @@ <!-- 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="Convert a dataframe from long to wide format — mkin_long_to_wide" /> <meta property="og:description" content="This function takes a dataframe in the long form as required by modCost and converts it into a dataframe with one independent variable and several dependent variables as columns." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -55,8 +61,12 @@ <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> @@ -97,6 +107,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -104,21 +115,25 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Convert a dataframe from long to wide format</h1> + + <div class="hidden name"><code>mkin_long_to_wide.Rd</code></div> </div> + <div class="ref-description"> <p>This function takes a dataframe in the long form as required by <code>modCost</code> and converts it into a dataframe with one independent variable and several dependent variables as columns.</p> + </div> <pre class="usage"><span class='fu'>mkin_long_to_wide</span>(<span class='no'>long_data</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>, <span class='kw'>outtime</span> <span class='kw'>=</span> <span class='st'>"time"</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -196,6 +211,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index f40cb7cf..d52f582b 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -21,17 +21,23 @@ <!-- 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="Convert a dataframe with observations over time into long format — mkin_wide_to_long" /> <meta property="og:description" content="This function simply takes a dataframe with one independent variable and several dependent variable and converts it into the long form as required by modCost." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <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> @@ -96,6 +106,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -103,20 +114,24 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Convert a dataframe with observations over time into long format</h1> + + <div class="hidden name"><code>mkin_wide_to_long.Rd</code></div> </div> + <div class="ref-description"> <p>This function simply takes a dataframe with one independent variable and several dependent variable and converts it into the long form as required by <code>modCost</code>.</p> + </div> <pre class="usage"><span class='fu'>mkin_wide_to_long</span>(<span class='no'>wide_data</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"t"</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -174,6 +189,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 7f5ec78e..43cd51f7 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -21,16 +21,22 @@ <!-- 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="A dataset class for mkin — mkinds" /> <meta property="og:description" content="A dataset class for mkin" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <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> @@ -95,6 +105,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -102,15 +113,19 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>A dataset class for mkin</h1> + + <div class="hidden name"><code>mkinds.Rd</code></div> </div> + <div class="ref-description"> <p>A dataset class for mkin</p> + </div> <pre class="usage"><span class='no'>mkinds</span></pre> @@ -162,6 +177,8 @@ in order to be compatible with mkinfit</p></dd> </footer> </div> + + </body> </html> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index f172cba1..e6fd8807 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -21,17 +21,23 @@ <!-- 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="Calculate the minimum error to assume in order to pass the variance test — mkinerrmin" /> <meta property="og:description" content="This function finds the smallest relative error still resulting in passing the chi-squared test as defined in the FOCUS kinetics report from 2006." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> <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> @@ -96,6 +106,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -103,20 +114,24 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate the minimum error to assume in order to pass the variance test</h1> + + <div class="hidden name"><code>mkinerrmin.Rd</code></div> </div> + <div class="ref-description"> <p>This function finds the smallest relative error still resulting in passing the chi-squared test as defined in the FOCUS kinetics report from 2006.</p> + </div> <pre class="usage"><span class='fu'>mkinerrmin</span>(<span class='no'>fit</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -198,6 +213,8 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p> </footer> </div> + + </body> </html> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 8ac8295f..d0b54098 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -21,12 +21,15 @@ <!-- 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="Fit a kinetic model to data with one or more state variables — mkinfit" /> <meta property="og:description" content="This function uses the Flexible Modelling Environment package @@ -39,8 +42,11 @@ In each step of the optimsation, the kinetic model is solved using the function mkinpredict. The variance of the residuals for each observed variable can optionally be iteratively reweighted until convergence - using the argument reweight.method = "obs"." /> + using the argument reweight.method = "obs"." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -63,8 +69,12 @@ <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> @@ -105,6 +115,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -112,12 +123,15 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Fit a kinetic model to data with one or more state variables</h1> + + <div class="hidden name"><code>mkinfit.Rd</code></div> </div> + <div class="ref-description"> <p>This function uses the Flexible Modelling Environment package <code>FME</code> to create a function calculating the model cost, i.e. the @@ -131,6 +145,7 @@ observed variable can optionally be iteratively reweighted until convergence using the argument <code>reweight.method = "obs"</code>.</p> + </div> <pre class="usage"><span class='fu'>mkinfit</span>(<span class='no'>mkinmod</span>, <span class='no'>observed</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, @@ -154,7 +169,7 @@ <span class='kw'>reweight.tol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>reweight.max.iter</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>trace_parms</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -384,10 +399,10 @@ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and + <div class='dont-index'><p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinparplot.html'>mkinparplot</a></code>.</p> <p>Fitting of several models to several datasets in a single call to - <code><a href='mmkin.html'>mmkin</a></code>.</p> + <code><a href='mmkin.html'>mmkin</a></code>.</p></div> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> @@ -413,16 +428,16 @@ <pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.1 -#> R version used for fitting: 3.4.4 -#> Date of fit: Wed Mar 21 18:14:33 2018 -#> Date of summary: Wed Mar 21 18:14:33 2018 +#> R version used for fitting: 3.5.0 +#> Date of fit: Wed Jun 6 01:21:36 2018 +#> Date of summary: Wed Jun 6 01:21:36 2018 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.14 s +#> Fitted with method Port using 64 model solutions performed in 0.143 s #> #> Weighting: none #> @@ -490,8 +505,8 @@ <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, - <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> user system elapsed -#> 0.834 0.000 0.835 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> User System verstrichen +#> 0.927 0.000 0.929 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -597,6 +612,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 7d3c0f94..04050367 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -21,12 +21,15 @@ <!-- 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="Function to set up a kinetic model with one or more state variables — mkinmod" /> <meta property="og:description" content="The function usually takes several expressions, each assigning a compound name to @@ -36,6 +39,9 @@ For the definition of model types and their parameters, the equations given in the FOCUS and NAFTA guidance documents are used." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -58,8 +64,12 @@ For the definition of model types and their parameters, the equations given <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> @@ -100,6 +110,7 @@ For the definition of model types and their parameters, the equations given <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -107,12 +118,15 @@ For the definition of model types and their parameters, the equations given </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to set up a kinetic model with one or more state variables</h1> + + <div class="hidden name"><code>mkinmod.Rd</code></div> </div> + <div class="ref-description"> <p>The function usually takes several expressions, each assigning a compound name to a list, specifying the kinetic model type and reaction or transfer to other @@ -121,10 +135,11 @@ For the definition of model types and their parameters, the equations given <p>For the definition of model types and their parameters, the equations given in the FOCUS and NAFTA guidance documents are used.</p> + </div> <pre class="usage"><span class='fu'>mkinmod</span>(<span class='no'>...</span>, <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>, <span class='kw'>speclist</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -262,6 +277,8 @@ For the definition of model types and their parameters, the equations given </footer> </div> + + </body> </html> diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png Binary files differindex 1e7603d7..ba7212c5 100644 --- a/docs/reference/mkinparplot-1.png +++ b/docs/reference/mkinparplot-1.png diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 81f52fc3..5a843c0e 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -21,17 +21,23 @@ <!-- 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="Function to plot the confidence intervals obtained using mkinfit — mkinparplot" /> <meta property="og:description" content="This function plots the confidence intervals for the parameters fitted using mkinfit." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <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> @@ -96,6 +106,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -103,20 +114,24 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to plot the confidence intervals obtained using mkinfit</h1> + + <div class="hidden name"><code>mkinparplot.Rd</code></div> </div> + <div class="ref-description"> <p>This function plots the confidence intervals for the parameters fitted using <code><a href='mkinfit.html'>mkinfit</a></code>.</p> + </div> <pre class="usage"><span class='fu'>mkinparplot</span>(<span class='no'>object</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -135,7 +150,7 @@ <span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"phenol"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"anisole"</span>)), <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='432.632880098887' /></div></pre> +<span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -166,6 +181,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index cfd72521..3a55ceae 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -21,16 +21,22 @@ <!-- 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="Plot the observed data and the fitted model of an mkinfit object — mkinplot" /> <meta property="og:description" content="Deprecated function. It now only calls the plot method plot.mkinfit." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <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> @@ -95,6 +105,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -102,19 +113,23 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot the observed data and the fitted model of an mkinfit object</h1> + + <div class="hidden name"><code>mkinplot.Rd</code></div> </div> + <div class="ref-description"> <p>Deprecated function. It now only calls the plot method <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p> + </div> <pre class="usage"><span class='fu'>mkinplot</span>(<span class='no'>fit</span>, <span class='no'>...</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -160,6 +175,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 4768215b..946e0dfc 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -21,18 +21,24 @@ <!-- 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="Produce predictions from a kinetic model using specific parameters — mkinpredict" /> <meta property="og:description" content="This function produces a time series for all the observed variables in a kinetic model as specified by mkinmod, using a specific set of kinetic parameters and initial values for the state variables." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -55,8 +61,12 @@ <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> @@ -97,6 +107,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -104,23 +115,27 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Produce predictions from a kinetic model using specific parameters</h1> + + <div class="hidden name"><code>mkinpredict.Rd</code></div> </div> + <div class="ref-description"> <p>This function produces a time series for all the observed variables in a kinetic model as specified by <code><a href='mkinmod.html'>mkinmod</a></code>, using a specific set of kinetic parameters and initial values for the state variables.</p> + </div> <pre class="usage"><span class='fu'>mkinpredict</span>(<span class='no'>mkinmod</span>, <span class='no'>odeparms</span>, <span class='no'>odeini</span>, <span class='no'>outtimes</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -305,18 +320,18 @@ <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 -#> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.003 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>( +#> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen +#> 0.004 0.000 0.004 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 -#> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.002 0.000 0.001 </div><div class='input'> <span class='fu'>system.time</span>( +#> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen +#> 0.002 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 -#> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.033 0.000 0.032 </div></pre> +#> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen +#> 0.035 0.000 0.035 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -347,6 +362,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png Binary files differindex 5b201616..b53869c7 100644 --- a/docs/reference/mkinresplot-1.png +++ b/docs/reference/mkinresplot-1.png diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index df83f693..c288bf7c 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -21,12 +21,15 @@ <!-- 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="Function to plot residuals stored in an mkin object — mkinresplot" /> <meta property="og:description" content="This function plots the residuals for the specified subset of the @@ -34,6 +37,9 @@ model and the residuals can be obtained using plot.mkinfit using the argument show_residuals = TRUE." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -56,8 +62,12 @@ <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> @@ -98,6 +108,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -105,18 +116,22 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to plot residuals stored in an mkin object</h1> + + <div class="hidden name"><code>mkinresplot.Rd</code></div> </div> + <div class="ref-description"> <p>This function plots the residuals for the specified subset of the observed variables from an mkinfit object. A combined plot of the fitted model and the residuals can be obtained using <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> using the argument <code>show_residuals = TRUE</code>.</p> + </div> <pre class="usage"><span class='fu'>mkinresplot</span>(<span class='no'>object</span>, <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'>names</span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), @@ -124,7 +139,7 @@ <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residual"</span>, <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, <span class='no'>...</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -174,13 +189,13 @@ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted lines of the - mkinfit object.</p> + <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted lines of the + mkinfit object.</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>mkinresplot</span>(<span class='no'>fit</span>, <span class='st'>"m1"</span>)</div><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='432.632880098887' /></div></pre> +<span class='fu'>mkinresplot</span>(<span class='no'>fit</span>, <span class='st'>"m1"</span>)</div><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -213,6 +228,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index db727427..9f98a077 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -21,17 +21,23 @@ <!-- 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="Function to set up a kinetic submodel for one state variable — mkinsub" /> <meta property="og:description" content="This is a convenience function to set up the lists used as arguments for mkinmod." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <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> @@ -96,6 +106,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -103,20 +114,24 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to set up a kinetic submodel for one state variable</h1> + + <div class="hidden name"><code>mkinsub.Rd</code></div> </div> + <div class="ref-description"> <p>This is a convenience function to set up the lists used as arguments for <code><a href='mkinmod.html'>mkinmod</a></code>.</p> + </div> <pre class="usage"><span class='fu'>mkinsub</span>(<span class='no'>submodel</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -191,6 +206,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 6c99f07b..74b6adad 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -21,17 +21,23 @@ <!-- 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="Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin" /> <meta property="og:description" content="This function calls mkinfit on all combinations of models and datasets specified in its first two arguments." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <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> @@ -96,6 +106,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -103,21 +114,25 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Fit one or more kinetic models with one or more state variables to one or more datasets</h1> + + <div class="hidden name"><code>mmkin.Rd</code></div> </div> + <div class="ref-description"> <p>This function calls <code><a href='mkinfit.html'>mkinfit</a></code> on all combinations of models and datasets specified in its first two arguments.</p> + </div> <pre class="usage"><span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>round</span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -156,7 +171,7 @@ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p><code><a href='Extract.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for plotting.</p> + <div class='dont-index'><p><code><a href='Extract.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for plotting.</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -225,6 +240,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png Binary files differindex 0d54d2fe..f7404448 100644 --- a/docs/reference/plot.mkinfit-1.png +++ b/docs/reference/plot.mkinfit-1.png diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png Binary files differindex 377d63b6..93c9efe0 100644 --- a/docs/reference/plot.mkinfit-2.png +++ b/docs/reference/plot.mkinfit-2.png diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png Binary files differindex b23ddfe7..7b8a81e2 100644 --- a/docs/reference/plot.mkinfit-3.png +++ b/docs/reference/plot.mkinfit-3.png diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png Binary files differindex 0dd9f4d6..d44b6f9f 100644 --- a/docs/reference/plot.mkinfit-4.png +++ b/docs/reference/plot.mkinfit-4.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 319ba75b..525a8453 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -21,12 +21,15 @@ <!-- 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="Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit" /> <meta property="og:description" content="Solves the differential equations with the optimised and fixed parameters @@ -36,6 +39,9 @@ If the current plot device is a tikz device, then latex is being used for the formatting of the chi2 error level, if show_errmin = TRUE." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -58,8 +64,12 @@ If the current plot device is a tikz device, <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> @@ -100,6 +110,7 @@ If the current plot device is a tikz device, <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -107,12 +118,15 @@ If the current plot device is a tikz device, </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot the observed data and the fitted model of an mkinfit object</h1> + + <div class="hidden name"><code>plot.mkinfit.Rd</code></div> </div> + <div class="ref-description"> <p>Solves the differential equations with the optimised and fixed parameters from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots @@ -121,6 +135,7 @@ If the current plot device is a tikz device, then latex is being used for the formatting of the chi2 error level, if <code>show_errmin = TRUE</code>.</p> + </div> <pre class="usage"># S3 method for mkinfit plot(x, fit = x, @@ -137,7 +152,7 @@ plot(x, fit = x, show_errmin = FALSE, errmin_digits = 3, …) plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -244,12 +259,12 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … <span class='co'># parent to sink included, use Levenberg-Marquardt for speed</span> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span> ))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) -<span class='fu'>plot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> +<span class='fu'>plot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Show the observed variables separately</span> -<span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> +<span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Show the observed variables separately, with residuals</span> <span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>), - <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># The same can be obtained with less typing, using the convenience function plot_sep</span> <span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div></pre> </div> @@ -282,6 +297,8 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … </footer> </div> + + </body> </html> diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png Binary files differindex c2c25e90..2aa7aad9 100644 --- a/docs/reference/plot.mmkin-1.png +++ b/docs/reference/plot.mmkin-1.png diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png Binary files differindex b40ae0d5..94b1332a 100644 --- a/docs/reference/plot.mmkin-2.png +++ b/docs/reference/plot.mmkin-2.png diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png Binary files differindex dfbe014f..ca78fa42 100644 --- a/docs/reference/plot.mmkin-3.png +++ b/docs/reference/plot.mmkin-3.png diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index f1aa789f..a554a489 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -21,12 +21,15 @@ <!-- 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="Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin" /> <meta property="og:description" content="When x is a row selected from an mmkin object ([.mmkin), the same model @@ -35,6 +38,9 @@ If the current plot device is a tikz device, then latex is being used for the formatting of the chi2 error level." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -57,8 +63,12 @@ If the current plot device is a tikz device, <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> @@ -99,6 +109,7 @@ If the current plot device is a tikz device, <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -106,12 +117,15 @@ If the current plot device is a tikz device, </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</h1> + + <div class="hidden name"><code>plot.mmkin.Rd</code></div> </div> + <div class="ref-description"> <p>When x is a row selected from an mmkin object (<code><a href='Extract.mmkin.html'>[.mmkin</a></code>), the same model fitted for at least one dataset is shown. When it is a column, the fit of at least one model @@ -119,12 +133,13 @@ If the current plot device is a tikz device, <p>If the current plot device is a <code><a href='http://www.rdocumentation.org/packages/tikzDevice/topics/tikz'>tikz</a></code> device, then latex is being used for the formatting of the chi2 error level.</p> + </div> <pre class="usage"><span class='co'># S3 method for mmkin</span> <span class='fu'>plot</span>(<span class='no'>x</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>errmin_var</span> <span class='kw'>=</span> <span class='st'>"All data"</span>, <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, <span class='no'>...</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -171,11 +186,11 @@ If the current plot device is a tikz device, <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>c</span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>), <span class='fu'>list</span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='co'># named list for titles</span> <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) - <span class='fu'>plot</span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='img'><img src='plot.mmkin-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><div class='img'><img src='plot.mmkin-2.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> + <span class='fu'>plot</span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='img'><img src='plot.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><div class='img'><img src='plot.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span> <span class='co'># height should be smaller than the plot width (this is not possible for the html pages</span> <span class='co'># generated by pkgdown, as far as I know).</span> - <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span>]) <span class='co'># same as plot(fits[1, 2])</span></div><div class='img'><img src='plot.mmkin-3.png' alt='' width='700' height='432.632880098887' /></div></pre> + <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span>]) <span class='co'># same as plot(fits[1, 2])</span></div><div class='img'><img src='plot.mmkin-3.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -206,6 +221,8 @@ If the current plot device is a tikz device, </footer> </div> + + </body> </html> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 2a469fc2..ade048f0 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -21,16 +21,22 @@ <!-- 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="Print mkinds objects — print.mkinds" /> <meta property="og:description" content="Print mkinds objects." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <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> @@ -95,6 +105,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -102,20 +113,24 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Print mkinds objects</h1> + + <div class="hidden name"><code>print.mkinds.Rd</code></div> </div> + <div class="ref-description"> <p>Print mkinds objects.</p> + </div> <pre class="usage"><span class='co'># S3 method for mkinds</span> <span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -151,6 +166,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 30703dfd..64d3a03c 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -21,16 +21,22 @@ <!-- 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="Print mkinmod objects — print.mkinmod" /> <meta property="og:description" content="Print mkinmod objects in a way that the user finds his way to get to its components." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <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> @@ -95,6 +105,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -102,20 +113,24 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Print mkinmod objects</h1> + + <div class="hidden name"><code>print.mkinmod.Rd</code></div> </div> + <div class="ref-description"> <p>Print mkinmod objects in a way that the user finds his way to get to its components.</p> + </div> <pre class="usage"><span class='co'># S3 method for mkinmod</span> <span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -172,6 +187,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 2c06b1dd..06b3c049 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -21,18 +21,24 @@ <!-- 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="Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case" /> <meta property="og:description" content="This dataset was used for a comparison of KinGUI and ModelMaker to check the software quality of KinGUI in the original publication (Schäfer et al., 2007). The results from the fitting are also included." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -55,8 +61,12 @@ <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> @@ -97,6 +107,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -104,17 +115,21 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Metabolism data set used for checking the software quality of KinGUI</h1> + + <div class="hidden name"><code>schaefer07_complex_case.Rd</code></div> </div> + <div class="ref-description"> <p>This dataset was used for a comparison of KinGUI and ModelMaker to check the software quality of KinGUI in the original publication (Schäfer et al., 2007). The results from the fitting are also included.</p> + </div> <pre class="usage"><span class='no'>schaefer07_complex_case</span></pre> @@ -192,6 +207,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/sigma_rl.html b/docs/reference/sigma_rl.html index fd714224..bb9fd396 100644 --- a/docs/reference/sigma_rl.html +++ b/docs/reference/sigma_rl.html @@ -21,18 +21,24 @@ <!-- 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="Two component error model of Rocke and Lorenzato — sigma_rl" /> <meta property="og:description" content="Function describing the standard deviation of the measurement error in dependence of the measured value \(y\): $$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -55,8 +61,12 @@ $$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$" /> <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> @@ -97,6 +107,7 @@ $$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$" /> <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -104,21 +115,25 @@ $$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$" /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Two component error model of Rocke and Lorenzato</h1> + + <div class="hidden name"><code>sigma_rl.Rd</code></div> </div> + <div class="ref-description"> <p>Function describing the standard deviation of the measurement error in dependence of the measured value \(y\):</p> <p>$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$</p> + </div> <pre class="usage"><span class='fu'>sigma_rl</span>(<span class='no'>y</span>, <span class='no'>sigma_low</span>, <span class='no'>rsd_high</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -172,6 +187,8 @@ $$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$" /> </footer> </div> + + </body> </html> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 37b8fff8..c8919f1c 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -21,12 +21,15 @@ <!-- 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="Summary method for class "mkinfit" — summary.mkinfit" /> <meta property="og:description" content="Lists model equations, the summary as returned by summary.modFit, @@ -34,6 +37,9 @@ as defined therein, and optionally the data, consisting of observed, predicted and residual values." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -56,8 +62,12 @@ <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> @@ -98,6 +108,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -105,25 +116,29 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Summary method for class "mkinfit"</h1> + + <div class="hidden name"><code>summary.mkinfit.Rd</code></div> </div> + <div class="ref-description"> <p>Lists model equations, the summary as returned by <code>summary.modFit</code>, the chi2 error levels calculated according to FOCUS guidance (2006) as far as defined therein, and optionally the data, consisting of observed, predicted and residual values.</p> + </div> <pre class="usage"><span class='co'># S3 method for mkinfit</span> <span class='fu'>summary</span>(<span class='no'>object</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distimes</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='no'>...</span>) <span class='co'># S3 method for summary.mkinfit</span> <span class='fu'>print</span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'>max</span>(<span class='fl'>3</span>, <span class='fu'>getOption</span>(<span class='st'>"digits"</span>) - <span class='fl'>3</span>), <span class='no'>...</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -190,16 +205,16 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.47.1 -#> R version used for fitting: 3.4.4 -#> Date of fit: Wed Mar 21 18:14:42 2018 -#> Date of summary: Wed Mar 21 18:14:42 2018 +#> R version used for fitting: 3.5.0 +#> Date of fit: Wed Jun 6 01:21:46 2018 +#> Date of summary: Wed Jun 6 01:21:46 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.072 s +#> Fitted with method Port using 35 model solutions performed in 0.075 s #> #> Weighting: none #> @@ -291,6 +306,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 18da9ff6..6e0ac227 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -21,12 +21,15 @@ <!-- 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="Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014" /> <meta property="og:description" content="The 12 datasets were generated using four different models and three different @@ -43,6 +46,9 @@ As an example, the first dataset has the title SFO_lin_a and is based on the SFO with two sequential metabolites (linear pathway), with added variance component 'a'. Compare also the code in the example section to see the degradation models." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -65,8 +71,12 @@ Compare also the code in the example section to see the degradation models." /> <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> @@ -107,6 +117,7 @@ Compare also the code in the example section to see the degradation models." /> <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -114,12 +125,15 @@ Compare also the code in the example section to see the degradation models." /> </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Synthetic datasets for one parent compound with two metabolites</h1> + + <div class="hidden name"><code>synthetic_data_for_UBA.Rd</code></div> </div> + <div class="ref-description"> <p>The 12 datasets were generated using four different models and three different variance components. The four models are either the SFO or the DFOP model with either @@ -135,6 +149,7 @@ Compare also the code in the example section to see the degradation models." /> with two sequential metabolites (linear pathway), with added variance component 'a'.</p> <p>Compare also the code in the example section to see the degradation models.</p> + </div> <pre class="usage"><span class='no'>synthetic_data_for_UBA_2014</span></pre> @@ -283,6 +298,8 @@ summary(fit) </footer> </div> + + </body> </html> diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index b1b5e617..090b0c22 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -21,17 +21,23 @@ <!-- 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="Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014" /> <meta property="og:description" content="The datasets were used for the comparative validation of several kinetic evaluation software packages (Ranke, 2014)." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <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> @@ -96,6 +106,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -103,16 +114,20 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Three experimental datasets from two water sediment systems and one soil</h1> + + <div class="hidden name"><code>test_data_from_UBA_2014.Rd</code></div> </div> + <div class="ref-description"> <p>The datasets were used for the comparative validation of several kinetic evaluation software packages (Ranke, 2014).</p> + </div> <pre class="usage"><span class='no'>test_data_from_UBA_2014</span></pre> @@ -187,6 +202,8 @@ </footer> </div> + + </body> </html> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index fb03cdac..3adb3a10 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -21,12 +21,15 @@ <!-- 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="Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms" /> <meta property="og:description" content="The transformations are intended to map parameters that should only take @@ -39,6 +42,9 @@ The transformation of sets of formation fractions is fragile, as it supposes the same ordering of the components in forward and backward transformation. This is no problem for the internal use in mkinfit." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -61,8 +67,12 @@ The transformation of sets of formation fractions is fragile, as it supposes <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> @@ -103,6 +113,7 @@ The transformation of sets of formation fractions is fragile, as it supposes <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -110,12 +121,15 @@ The transformation of sets of formation fractions is fragile, as it supposes </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Functions to transform and backtransform kinetic parameters for fitting</h1> + + <div class="hidden name"><code>transform_odeparms.Rd</code></div> </div> + <div class="ref-description"> <p>The transformations are intended to map parameters that should only take on restricted values to the full scale of real numbers. For kinetic rate @@ -127,13 +141,14 @@ The transformation of sets of formation fractions is fragile, as it supposes the same ordering of the components in forward and backward transformation. This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit</a></code>.</p> + </div> <pre class="usage"><span class='fu'>transform_odeparms</span>(<span class='no'>parms</span>, <span class='no'>mkinmod</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>backtransform_odeparms</span>(<span class='no'>transparms</span>, <span class='no'>mkinmod</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -184,9 +199,9 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version used for fitting: 0.9.47.1 -#> R version used for fitting: 3.4.4 -#> Date of fit: Wed Mar 21 18:14:43 2018 -#> Date of summary: Wed Mar 21 18:14:43 2018 +#> R version used for fitting: 3.5.0 +#> Date of fit: Wed Jun 6 01:21:47 2018 +#> Date of summary: Wed Jun 6 01:21:47 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -194,7 +209,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.585 s +#> Fitted with method Port using 153 model solutions performed in 0.628 s #> #> Weighting: none #> @@ -322,6 +337,8 @@ The transformation of sets of formation fractions is fragile, as it supposes </footer> </div> + + </body> </html> |
