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diff --git a/docs/articles/FOCUS_D.R b/docs/articles/FOCUS_D.R new file mode 100644 index 00000000..c3881e80 --- /dev/null +++ b/docs/articles/FOCUS_D.R @@ -0,0 +1,24 @@ +## ---- include = FALSE---------------------------------------------------- +library(knitr) +opts_chunk$set(tidy = FALSE, cache = TRUE) + +## ----data---------------------------------------------------------------- +library("mkin") +print(FOCUS_2006_D) + +## ----model--------------------------------------------------------------- +SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) +print(SFO_SFO$diffs) + +## ----fit----------------------------------------------------------------- +fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) + +## ----plot, fig.height = 5------------------------------------------------ +plot(fit, show_residuals = TRUE) + +## ----plot_2, fig.height = 4---------------------------------------------- +mkinparplot(fit) + +## ------------------------------------------------------------------------ +summary(fit) + diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 02c3aa69..df259e21 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -1,10 +1,10 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" 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"><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><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"><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body> - <div class="container"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container template-vignette"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -30,6 +30,7 @@ </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header><div class="row"> <div class="col-md-9"> @@ -37,11 +38,12 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-10-06</h4> + <h4 class="date">2016-10-26</h4> </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="kw">print</span>(FOCUS_2006_D)</code></pre></div> @@ -103,16 +105,16 @@ <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">fit <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_2006_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</code></pre></div> <p>A plot of the fit including a residual plot for both observed variables is obtained using the <code>plot</code> method for <code>mkinfit</code> objects.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(fit, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-5-1.png" width="672"></p> +<p><img src="FOCUS_D_files/figure-html/unnamed-chunk-5-1.png" width="672"></p> <p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-6-1.png" width="672"></p> +<p><img src="FOCUS_D_files/figure-html/unnamed-chunk-6-1.png" width="672"></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: 0.9.44.9000 ## R version: 3.3.1 -## Date of fit: Thu Oct 6 08:54:04 2016 -## Date of summary: Thu Oct 6 08:54:04 2016 +## Date of fit: Wed Oct 26 23:18:10 2016 +## Date of summary: Wed Oct 26 23:18:10 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -120,7 +122,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.637 s +## Fitted with method Port using 153 model solutions performed in 0.628 s ## ## Weighting: none ## @@ -231,15 +233,23 @@ ## 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> </div> - <div class="col-md-3 hidden-xs"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> </div> </div> - <footer><p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <footer><div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer></div> </body></html> diff --git a/docs/articles/FOCUS_D_cache/html/__packages b/docs/articles/FOCUS_D_cache/html/__packages new file mode 100644 index 00000000..8042c1f3 --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/__packages @@ -0,0 +1,8 @@ +base +minpack.lm +rootSolve +inline +mkin +knitr +microbenchmark +ggplot2 diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_97560c30ad0c097f3807f1e18320a130.RData b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_97560c30ad0c097f3807f1e18320a130.RData Binary files differnew file mode 100644 index 00000000..ab5bdfb2 --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_97560c30ad0c097f3807f1e18320a130.RData diff --git 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FOCUS_2006_L2_mkin, quiet = TRUE) +plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE, + main = "FOCUS L2 - DFOP") +summary(m.L2.DFOP, data = FALSE) + +## ------------------------------------------------------------------------ +FOCUS_2006_L3 = data.frame( + t = c(0, 3, 7, 14, 30, 60, 91, 120), + parent = c(97.8, 60, 51, 43, 35, 22, 15, 12)) +FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3) + +## ----fig.height = 8------------------------------------------------------ +# Only use one core here, not to offend the CRAN checks +mm.L3 <- mmkin(c("SFO", "FOMC", "DFOP"), cores = 1, + list("FOCUS L3" = FOCUS_2006_L3_mkin), quiet = TRUE) +plot(mm.L3) + +## ----fig.height = 5------------------------------------------------------ +summary(mm.L3[["DFOP", 1]]) +plot(mm.L3[["DFOP", 1]], show_errmin = TRUE) + +## ------------------------------------------------------------------------ +FOCUS_2006_L4 = data.frame( + t = c(0, 3, 7, 14, 30, 60, 91, 120), + parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0)) +FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4) + +## ----fig.height = 6------------------------------------------------------ +# Only use one core here, not to offend the CRAN checks +mm.L4 <- mmkin(c("SFO", "FOMC"), cores = 1, + list("FOCUS L4" = FOCUS_2006_L4_mkin), + quiet = TRUE) +plot(mm.L4) + +## ----fig.height = 8------------------------------------------------------ +summary(mm.L4[["SFO", 1]], data = FALSE) +summary(mm.L4[["FOMC", 1]], data = FALSE) + diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 5d586799..cb3096e0 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -1,10 +1,10 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Example 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class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -30,6 +30,7 @@ </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header><div class="row"> <div class="col-md-9"> @@ -37,13 +38,14 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-10-06</h4> + <h4 class="date">2016-10-26</h4> </div> +<div class="contents"> <div id="laboratory-data-l1" class="section level1"> -<h1>Laboratory Data L1</h1> +<h1 class="hasAnchor"><html><body><a href="#laboratory-data-l1" class="anchor"> </a></body></html>Laboratory Data L1</h1> <p>The following code defines example dataset L1 from the FOCUS kinetics report, p. 284:</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>) FOCUS_2006_L1 =<span class="st"> </span><span class="kw">data.frame</span>( @@ -58,15 +60,15 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <span class="kw">summary</span>(m.L1.SFO)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.1 -## Date of fit: Thu Oct 6 08:54:05 2016 -## Date of summary: Thu Oct 6 08:54:05 2016 +## Date of fit: Wed Oct 26 23:18:11 2016 +## Date of summary: Wed Oct 26 23:18:11 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.087 s +## Fitted with method Port using 37 model solutions performed in 0.089 s ## ## Weighting: none ## @@ -138,21 +140,21 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re ## 30 parent 4.0 5.251 -1.2513</code></pre> <p>A plot of the fit is obtained with the plot function for mkinfit objects.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(m.L1.SFO, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - SFO"</span>)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png" width="576"></p> +<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-4-1.png" width="576"></p> <p>The residual plot can be easily obtained by</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/mkinresplot.html">mkinresplot</a></span>(m.L1.SFO, <span class="dt">ylab =</span> <span class="st">"Observed"</span>, <span class="dt">xlab =</span> <span class="st">"Time"</span>)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png" width="576"></p> +<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-5-1.png" width="576"></p> <p>For comparison, the FOMC model is fitted as well, and the <span class="math inline">\(\chi^2\)</span> error level is checked.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L1.FOMC <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, FOCUS_2006_L1_mkin, <span class="dt">quiet=</span><span class="ot">TRUE</span>)</code></pre></div> <pre><code>## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation by method Port did not converge. ## Convergence code is 1</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><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="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> +<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: 0.9.44.9000 ## R version: 3.3.1 -## Date of fit: Thu Oct 6 08:54:06 2016 -## Date of summary: Thu Oct 6 08:54:06 2016 +## Date of fit: Wed Oct 26 23:18:12 2016 +## Date of summary: Wed Oct 26 23:18:12 2016 ## ## ## Warning: Optimisation by method Port did not converge. @@ -164,7 +166,7 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 188 model solutions performed in 0.437 s +## Fitted with method Port using 188 model solutions performed in 0.434 s ## ## Weighting: none ## @@ -219,7 +221,7 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <p>The <span class="math inline">\(\chi^2\)</span> error levels reported in Appendix 3 and Appendix 7 to the FOCUS kinetics report are rounded to integer percentages and partly deviate by one percentage point from the results calculated by mkin. The reason for this is not known. However, mkin gives the same <span class="math inline">\(\chi^2\)</span> error levels as the kinfit package and the calculation routines of the kinfit package have been extensively compared to the results obtained by the KinGUI software, as documented in the kinfit package vignette. KinGUI was the first widely used standard package in this field. Also, the calculation of <span class="math inline">\(\chi^2\)</span> error levels was compared with KinGUII, CAKE and DegKin manager in a project sponsored by the German Umweltbundesamt <span class="citation">(Ranke, n.d.)</span>.</p> </div> <div id="laboratory-data-l2" class="section level1"> -<h1>Laboratory Data L2</h1> +<h1 class="hasAnchor"><html><body><a href="#laboratory-data-l2" class="anchor"> </a></body></html>Laboratory Data L2</h1> <p>The following code defines example dataset L2 from the FOCUS kinetics report, p. 287:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">FOCUS_2006_L2 =<span class="st"> </span><span class="kw">data.frame</span>( <span class="dt">t =</span> <span class="kw">rep</span>(<span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">28</span>), <span class="dt">each =</span> <span class="dv">2</span>), @@ -228,35 +230,35 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <span class="fl">2.6</span>, <span class="fl">1.2</span>, <span class="fl">0.3</span>, <span class="fl">0.6</span>)) FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_2006_L2)</code></pre></div> <div id="sfo-fit-for-l2" class="section level2"> -<h2>SFO fit for L2</h2> +<h2 class="hasAnchor"><html><body><a href="#sfo-fit-for-l2" class="anchor"> </a></body></html>SFO fit for L2</h2> <p>Again, the SFO model is fitted and the result is plotted. The residual plot can be obtained simply by adding the argument <code>show_residuals</code> to the plot command.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L2.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_2006_L2_mkin, <span class="dt">quiet=</span><span class="ot">TRUE</span>) <span class="kw">plot</span>(m.L2.SFO, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L2 - SFO"</span>)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png" width="672"></p> +<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-8-1.png" width="672"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 14% suggests that the model does not fit very well. This is also obvious from the plots of the fit, in which we have included the residual plot.</p> <p>In the FOCUS kinetics report, it is stated that there is no apparent systematic error observed from the residual plot up to the measured DT90 (approximately at day 5), and there is an underestimation beyond that point.</p> <p>We may add that it is difficult to judge the random nature of the residuals just from the three samplings at days 0, 1 and 3. Also, it is not clear <em>a priori</em> why a consistent underestimation after the approximate DT90 should be irrelevant. However, this can be rationalised by the fact that the FOCUS fate models generally only implement SFO kinetics.</p> </div> <div id="fomc-fit-for-l2" class="section level2"> -<h2>FOMC fit for L2</h2> +<h2 class="hasAnchor"><html><body><a href="#fomc-fit-for-l2" class="anchor"> </a></body></html>FOMC fit for L2</h2> <p>For comparison, the FOMC model is fitted as well, and the <span class="math inline">\(\chi^2\)</span> error level is checked.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L2.FOMC <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, FOCUS_2006_L2_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">plot</span>(m.L2.FOMC, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> +<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: 0.9.44.9000 ## R version: 3.3.1 -## Date of fit: Thu Oct 6 08:54:07 2016 -## Date of summary: Thu Oct 6 08:54:07 2016 +## Date of fit: Wed Oct 26 23:18:12 2016 +## Date of summary: Wed Oct 26 23:18:12 2016 ## ## Equations: ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.19 s +## Fitted with method Port using 81 model solutions performed in 0.191 s ## ## Weighting: none ## @@ -309,17 +311,17 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <p>The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is much lower in this case. Therefore, the FOMC model provides a better description of the data, as less experimental error has to be assumed in order to explain the data.</p> </div> <div id="dfop-fit-for-l2" class="section level2"> -<h2>DFOP fit for L2</h2> +<h2 class="hasAnchor"><html><body><a href="#dfop-fit-for-l2" class="anchor"> </a></body></html>DFOP fit for L2</h2> <p>Fitting the four parameter DFOP model further reduces the <span class="math inline">\(\chi^2\)</span> error level.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L2.DFOP <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"DFOP"</span>, FOCUS_2006_L2_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">plot</span>(m.L2.DFOP, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> +<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: 0.9.44.9000 ## R version: 3.3.1 -## Date of fit: Thu Oct 6 08:54:08 2016 -## Date of summary: Thu Oct 6 08:54:08 2016 +## Date of fit: Wed Oct 26 23:18:13 2016 +## Date of summary: Wed Oct 26 23:18:14 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -328,7 +330,7 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.804 s +## Fitted with method Port using 336 model solutions performed in 0.803 s ## ## Weighting: none ## @@ -384,31 +386,31 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re </div> </div> <div id="laboratory-data-l3" class="section level1"> -<h1>Laboratory Data L3</h1> +<h1 class="hasAnchor"><html><body><a href="#laboratory-data-l3" class="anchor"> </a></body></html>Laboratory Data L3</h1> <p>The following code defines example dataset L3 from the FOCUS kinetics report, p. 290.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">FOCUS_2006_L3 =<span class="st"> </span><span class="kw">data.frame</span>( <span class="dt">t =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">30</span>, <span class="dv">60</span>, <span class="dv">91</span>, <span class="dv">120</span>), <span class="dt">parent =</span> <span class="kw">c</span>(<span class="fl">97.8</span>, <span class="dv">60</span>, <span class="dv">51</span>, <span class="dv">43</span>, <span class="dv">35</span>, <span class="dv">22</span>, <span class="dv">15</span>, <span class="dv">12</span>)) FOCUS_2006_L3_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_2006_L3)</code></pre></div> <div id="use-mmkin-to-fit-multiple-models" class="section level2"> -<h2>Use mmkin to fit multiple models</h2> +<h2 class="hasAnchor"><html><body><a href="#use-mmkin-to-fit-multiple-models" class="anchor"> </a></body></html>Use mmkin to fit multiple models</h2> <p>As of mkin version 0.9-39 (June 2015), we can fit several models to one or more datasets in one call to the function <code>mmkin</code>. The datasets have to be passed in a list, in this case a named list holding only the L3 dataset prepared above.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Only use one core here, not to offend the CRAN checks</span> 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_2006_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="/home/jranke/git/mkin/docs/articles/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="672"></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-elements-of-mmkin-objects" class="section level2"> -<h2>Accessing elements of mmkin objects</h2> +<h2 class="hasAnchor"><html><body><a href="#accessing-elements-of-mmkin-objects" class="anchor"> </a></body></html>Accessing elements of mmkin objects</h2> <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: 0.9.44.9000 ## R version: 3.3.1 -## Date of fit: Thu Oct 6 08:54:09 2016 -## Date of summary: Thu Oct 6 08:54:09 2016 +## Date of fit: Wed Oct 26 23:18:15 2016 +## Date of summary: Wed Oct 26 23:18:15 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -417,7 +419,7 @@ 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 0.319 s +## Fitted with method Port using 137 model solutions performed in 0.323 s ## ## Weighting: none ## @@ -484,13 +486,13 @@ 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="/home/jranke/git/mkin/docs/articles/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="672"></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> </div> <div id="laboratory-data-l4" class="section level1"> -<h1>Laboratory Data L4</h1> +<h1 class="hasAnchor"><html><body><a href="#laboratory-data-l4" class="anchor"> </a></body></html>Laboratory Data L4</h1> <p>The following code defines example dataset L4 from the FOCUS kinetics report, p. 293:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">FOCUS_2006_L4 =<span class="st"> </span><span class="kw">data.frame</span>( <span class="dt">t =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">30</span>, <span class="dv">60</span>, <span class="dv">91</span>, <span class="dv">120</span>), @@ -502,20 +504,20 @@ 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_2006_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="/home/jranke/git/mkin/docs/articles/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="672"></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: 0.9.44.9000 ## R version: 3.3.1 -## Date of fit: Thu Oct 6 08:54:10 2016 -## Date of summary: Thu Oct 6 08:54:10 2016 +## Date of fit: Wed Oct 26 23:18:15 2016 +## Date of summary: Wed Oct 26 23:18:16 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.158 s +## Fitted with method Port using 46 model solutions performed in 0.108 s ## ## Weighting: none ## @@ -567,8 +569,8 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <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: 0.9.44.9000 ## R version: 3.3.1 -## Date of fit: Thu Oct 6 08:54:10 2016 -## Date of summary: Thu Oct 6 08:54:10 2016 +## Date of fit: Wed Oct 26 23:18:16 2016 +## Date of summary: Wed Oct 26 23:18:16 2016 ## ## Equations: ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -627,16 +629,17 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## parent 108.9 1644 494.9</code></pre> </div> <div id="references" class="section level1 unnumbered"> -<h1>References</h1> +<h1 class="hasAnchor"><html><body><a href="#references" class="anchor"> </a></body></html>References</h1> <div id="refs" class="references"> <div id="ref-ranke2014"> <p>Ranke, Johannes. n.d. “Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0.” Umweltbundesamt Projektnummer 27452.</p> </div> </div> </div> +</div> </div> - <div class="col-md-3 hidden-xs"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"><li><a href="#laboratory-data-l1">Laboratory Data L1</a></li> @@ -655,7 +658,14 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin </div> - <footer><p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <footer><div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer></div> </body></html> diff --git a/docs/articles/FOCUS_L_cache/html/__packages b/docs/articles/FOCUS_L_cache/html/__packages new file mode 100644 index 00000000..8042c1f3 --- /dev/null +++ b/docs/articles/FOCUS_L_cache/html/__packages @@ -0,0 +1,8 @@ +base +minpack.lm +rootSolve +inline +mkin +knitr +microbenchmark +ggplot2 diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-10_17bd4df3f9dbbfdb646235ad948e7903.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-10_17bd4df3f9dbbfdb646235ad948e7903.RData Binary files differnew file mode 100644 index 00000000..ed0c5a13 --- /dev/null +++ b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-10_17bd4df3f9dbbfdb646235ad948e7903.RData diff --git 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fig.height=6------------------- +Z.2a <- mkinmod(Z0 = mkinsub("SFO", "Z1"), + Z1 = mkinsub("SFO")) +m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.2a) +summary(m.Z.2a, data = FALSE)$bpar + +## ----FOCUS_2006_Z_fits_2, echo=TRUE, fig.height=6------------------- +Z.2a.ff <- mkinmod(Z0 = mkinsub("SFO", "Z1"), + Z1 = mkinsub("SFO"), + use_of_ff = "max") + +m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.2a.ff) +summary(m.Z.2a.ff, data = FALSE)$bpar + +## ----FOCUS_2006_Z_fits_3, echo=TRUE, fig.height=6------------------- +Z.3 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), + Z1 = mkinsub("SFO"), use_of_ff = "max") +m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.3) +summary(m.Z.3, data = FALSE)$bpar + +## ----FOCUS_2006_Z_fits_5, echo=TRUE, fig.height=7------------------- +Z.5 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO"), use_of_ff = "max") +m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.5) + +## ----FOCUS_2006_Z_fits_6, echo=TRUE, fig.height=8------------------- +Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO", "Z3"), + Z3 = mkinsub("SFO"), + use_of_ff = "max") +m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, + parms.ini = m.Z.5$bparms.ode, + quiet = TRUE) +plot_sep(m.Z.FOCUS) +summary(m.Z.FOCUS, data = FALSE)$bpar +endpoints(m.Z.FOCUS) + +## ----FOCUS_2006_Z_fits_7, echo=TRUE, fig.height=8------------------- +Z.mkin.1 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO", "Z3"), + Z3 = mkinsub("SFORB")) +m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.mkin.1) +summary(m.Z.mkin.1, data = FALSE)$cov.unscaled + +## ----FOCUS_2006_Z_fits_9, echo=TRUE, fig.height=8------------------- +Z.mkin.3 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO")) +m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.mkin.3) + +## ----FOCUS_2006_Z_fits_10, echo=TRUE, fig.height=8------------------ +Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO", "Z3"), + Z3 = mkinsub("SFO")) +m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, + parms.ini = m.Z.mkin.3$bparms.ode, + quiet = TRUE) +plot_sep(m.Z.mkin.4) + +## ----FOCUS_2006_Z_fits_11, echo=TRUE, fig.height=8------------------ +Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO", "Z3"), + Z3 = mkinsub("SFORB")) +m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, + parms.ini = m.Z.mkin.4$bparms.ode[1:4], + quiet = TRUE) +plot_sep(m.Z.mkin.5) + +## ----FOCUS_2006_Z_fits_11a, echo=TRUE------------------------------- +m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, + parms.ini = c(m.Z.mkin.5$bparms.ode[1:7], + k_Z3_bound_free = 0), + fixed_parms = "k_Z3_bound_free", + quiet = TRUE) +plot_sep(m.Z.mkin.5a) + +## ----FOCUS_2006_Z_fits_11b, echo=TRUE------------------------------- +mkinparplot(m.Z.mkin.5a) + +## ----FOCUS_2006_Z_fits_11b_endpoints, echo=TRUE--------------------- +endpoints(m.Z.mkin.5a) + diff --git a/docs/articles/FOCUS_Z.Rnw b/docs/articles/FOCUS_Z.Rnw new file mode 100644 index 00000000..5a66db24 --- /dev/null +++ b/docs/articles/FOCUS_Z.Rnw @@ -0,0 +1,274 @@ +%\VignetteIndexEntry{Example evaluation of FOCUS dataset Z} +%\VignetteEngine{knitr::knitr} +\documentclass[12pt,a4paper]{article} +\usepackage{a4wide} +\input{header} +\hypersetup{ + pdftitle = {Example evaluation of FOCUS dataset Z}, + pdfsubject = {Manuscript}, + pdfauthor = {Johannes Ranke}, + colorlinks = {true}, + linkcolor = {blue}, + citecolor = {blue}, + urlcolor = {red}, + hyperindex = {true}, + linktocpage = {true}, +} + +\begin{document} + +<<include=FALSE>>= +require(knitr) +opts_chunk$set(engine='R', tidy = FALSE, cache = TRUE) +options(width=70) +@ + +\title{Example evaluation of FOCUS dataset Z} +\author{\textbf{Johannes Ranke} \\[0.5cm] +%EndAName +Wissenschaftlicher Berater\\ +Kronacher Str. 8, 79639 Grenzach-Wyhlen, Germany\\[0.5cm] +and\\[0.5cm] +University of Bremen\\ +} +\maketitle + +\thispagestyle{empty} \setcounter{page}{0} + +\clearpage + +\tableofcontents + +\textbf{Key words}: Kinetics, FOCUS, nonlinear optimisation + +\section{The data} + +The following code defines the example dataset from Appendix 7 to the FOCUS kinetics +report \citep{FOCUSkinetics2011}, p.350. + +<<FOCUS_2006_Z_data, echo=TRUE, eval=TRUE>>= +require(mkin) +LOD = 0.5 +FOCUS_2006_Z = data.frame( + t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21, + 42, 61, 96, 124), + Z0 = c(100, 81.7, 70.4, 51.1, 41.2, 6.6, 4.6, 3.9, 4.6, 4.3, 6.8, + 2.9, 3.5, 5.3, 4.4, 1.2, 0.7), + Z1 = c(0, 18.3, 29.6, 46.3, 55.1, 65.7, 39.1, 36, 15.3, 5.6, 1.1, + 1.6, 0.6, 0.5 * LOD, NA, NA, NA), + Z2 = c(0, NA, 0.5 * LOD, 2.6, 3.8, 15.3, 37.2, 31.7, 35.6, 14.5, + 0.8, 2.1, 1.9, 0.5 * LOD, NA, NA, NA), + Z3 = c(0, NA, NA, NA, NA, 0.5 * LOD, 9.2, 13.1, 22.3, 28.4, 32.5, + 25.2, 17.2, 4.8, 4.5, 2.8, 4.4)) + +FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z) +@ + +\section{Parent compound and one metabolite} + +The next step is to set up the models used for the kinetic analysis. As the +simultaneous fit of parent and the first metabolite is usually straightforward, +Step 1 (SFO for parent only) is skipped here. We start with the model 2a, +with formation and decline of metabolite Z1 and the pathway from parent +directly to sink included (default in mkin). + +<<FOCUS_2006_Z_fits_1, echo=TRUE, fig.height=6>>= +Z.2a <- mkinmod(Z0 = mkinsub("SFO", "Z1"), + Z1 = mkinsub("SFO")) +m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.2a) +summary(m.Z.2a, data = FALSE)$bpar +@ + +As obvious from the parameter summary (the \texttt{bpar} component of the +summary), the kinetic rate constant from parent compound Z to sink +is negligible. Accordingly, the exact magnitude of the fitted parameter +\texttt{log k\_Z0\_sink} is ill-defined and the covariance matrix is not +returned (not shown, would be visible in the complete summary). +This suggests, in agreement with the analysis in the FOCUS kinetics report, to +simplify the model by removing the pathway to sink. + +A similar result can be obtained when formation fractions are used in the model +formulation: + +<<FOCUS_2006_Z_fits_2, echo=TRUE, fig.height=6>>= +Z.2a.ff <- mkinmod(Z0 = mkinsub("SFO", "Z1"), + Z1 = mkinsub("SFO"), + use_of_ff = "max") + +m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.2a.ff) +summary(m.Z.2a.ff, data = FALSE)$bpar +@ + +Here, the ilr transformed formation fraction fitted in the model takes a very +large value, and the backtransformed formation fraction from parent Z to Z1 is +practically unity. Again, the covariance matrix is not returned as the model is +overparameterised. + +The simplified model is obtained by setting the list component \texttt{sink} to +\texttt{FALSE}.\footnote{If the model formulation without formation fractions +is used, the same effect can be obtained by fixing the parameter \texttt{k\_Z\_sink} +to a value of zero.} + +In the following, we use the parameterisation with formation fractions in order +to be able to compare with the results in the FOCUS guidance, and as it +makes it easier to use parameters obtained in a previous fit when adding a further +metabolite. + +<<FOCUS_2006_Z_fits_3, echo=TRUE, fig.height=6>>= +Z.3 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), + Z1 = mkinsub("SFO"), use_of_ff = "max") +m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.3) +summary(m.Z.3, data = FALSE)$bpar +@ + +As there is only one transformation product for Z0 and no pathway +to sink, the formation fraction is internally fixed to unity. + +\section{Including metabolites Z2 and Z3} + +As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as +well in the next step. While this step appears questionable on the basis of the above results, it +is followed here for the purpose of comparison. Also, in the FOCUS report, it is +assumed that there is additional empirical evidence that Z1 quickly and exclusively +hydrolyses to Z2. + +<<FOCUS_2006_Z_fits_5, echo=TRUE, fig.height=7>>= +Z.5 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO"), use_of_ff = "max") +m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.5) +@ + +Finally, metabolite Z3 is added to the model. We use the optimised +differential equation parameter values from the previous fit in order to +accelerate the optimization. + +<<FOCUS_2006_Z_fits_6, echo=TRUE, fig.height=8>>= +Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO", "Z3"), + Z3 = mkinsub("SFO"), + use_of_ff = "max") +m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, + parms.ini = m.Z.5$bparms.ode, + quiet = TRUE) +plot_sep(m.Z.FOCUS) +summary(m.Z.FOCUS, data = FALSE)$bpar +endpoints(m.Z.FOCUS) +@ + +This fit corresponds to the final result chosen in Appendix 7 of the FOCUS +report. Confidence intervals returned by mkin are based on internally +transformed parameters, however. + +\section{Using the SFORB model for parent and metabolites} + +As the FOCUS report states, there is a certain tailing of the time course of metabolite +Z3. Also, the time course of the parent compound is not fitted very well using the +SFO model, as residues at a certain low level remain. + +Therefore, an additional model is offered here, using the single first-order +reversible binding (SFORB) model for metabolite Z3. As expected, the $\chi^2$ +error level is lower for metabolite Z3 using this model and the graphical +fit for Z3 is improved. However, the covariance matrix is not returned. + +<<FOCUS_2006_Z_fits_7, echo=TRUE, fig.height=8>>= +Z.mkin.1 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO", "Z3"), + Z3 = mkinsub("SFORB")) +m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.mkin.1) +summary(m.Z.mkin.1, data = FALSE)$cov.unscaled +@ + +Therefore, a further stepwise model building is performed starting from the +stage of parent and two metabolites, starting from the assumption that the model +fit for the parent compound can be improved by using the SFORB model. + +<<FOCUS_2006_Z_fits_9, echo=TRUE, fig.height=8>>= +Z.mkin.3 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO")) +m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.mkin.3) +@ + +This results in a much better representation of the behaviour of the parent +compound Z0. + +Finally, Z3 is added as well. These models appear overparameterised (no +covariance matrix returned) if the sink for Z1 is left in the models. + +<<FOCUS_2006_Z_fits_10, echo=TRUE, fig.height=8>>= +Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO", "Z3"), + Z3 = mkinsub("SFO")) +m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, + parms.ini = m.Z.mkin.3$bparms.ode, + quiet = TRUE) +plot_sep(m.Z.mkin.4) +@ + +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. + +<<FOCUS_2006_Z_fits_11, echo=TRUE, fig.height=8>>= +Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO", "Z3"), + Z3 = mkinsub("SFORB")) +m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, + parms.ini = m.Z.mkin.4$bparms.ode[1:4], + quiet = TRUE) +plot_sep(m.Z.mkin.5) +@ + +The summary view of the backtransformed parameters shows that we get no +confidence intervals due to overparameterisation. As the optimized +\texttt{k\_Z3\_bound\_free} is excessively small, it seems reasonable to fix it to +zero. + +<<FOCUS_2006_Z_fits_11a, echo=TRUE>>= +m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, + parms.ini = c(m.Z.mkin.5$bparms.ode[1:7], + k_Z3_bound_free = 0), + fixed_parms = "k_Z3_bound_free", + quiet = TRUE) +plot_sep(m.Z.mkin.5a) +@ + +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 +\texttt{Z.mkin.5a} is proposed as the best-fit model for the dataset from +Appendix 7 of the FOCUS report. + +A graphical representation of the confidence intervals can finally be obtained. + +<<FOCUS_2006_Z_fits_11b, echo=TRUE>>= +mkinparplot(m.Z.mkin.5a) +@ + +The endpoints obtained with this model are + +<<FOCUS_2006_Z_fits_11b_endpoints, echo=TRUE>>= +endpoints(m.Z.mkin.5a) +@ + +It is clear the degradation rate of Z3 towards the end of the experiment +is very low as DT50\_Z3\_b2 (the second Eigenvalue of the system of two differential +equations representing the SFORB system for Z3, corresponding to the slower rate +constant of the DFOP model) is reported to be infinity. However, this appears +to be a feature of the data. + +\bibliographystyle{plainnat} +\bibliography{references} + +\end{document} +% vim: set foldmethod=syntax: diff --git a/docs/articles/FOCUS_Z.aux b/docs/articles/FOCUS_Z.aux new file mode 100644 index 00000000..f997f2d7 --- /dev/null +++ b/docs/articles/FOCUS_Z.aux @@ -0,0 +1,26 @@ +\relax +\providecommand\hyper@newdestlabel[2]{} +\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument} +\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined +\global\let\oldcontentsline\contentsline +\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}} +\global\let\oldnewlabel\newlabel +\gdef\newlabel#1#2{\newlabelxx{#1}#2} +\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}} +\AtEndDocument{\ifx\hyper@anchor\@undefined +\let\contentsline\oldcontentsline +\let\newlabel\oldnewlabel +\fi} +\fi} +\global\let\hyper@last\relax +\gdef\HyperFirstAtBeginDocument#1{#1} +\providecommand\HyField@AuxAddToFields[1]{} +\providecommand\HyField@AuxAddToCoFields[2]{} +\citation{FOCUSkinetics2011} +\@writefile{toc}{\contentsline {section}{\numberline {1}The data}{1}{section.1}} +\@writefile{toc}{\contentsline {section}{\numberline {2}Parent compound and one metabolite}{2}{section.2}} +\@writefile{toc}{\contentsline {section}{\numberline {3}Including metabolites Z2 and Z3}{8}{section.3}} +\@writefile{toc}{\contentsline {section}{\numberline {4}Using the SFORB model for parent and metabolites}{12}{section.4}} +\bibstyle{plainnat} +\bibdata{references} +\bibcite{FOCUSkinetics2011}{{1}{2011}{{FOCUS Work Group on Degradation Kinetics}}{{}}} diff --git a/docs/articles/FOCUS_Z.bbl b/docs/articles/FOCUS_Z.bbl new file mode 100644 index 00000000..451497c8 --- /dev/null +++ b/docs/articles/FOCUS_Z.bbl @@ -0,0 +1,15 @@ +\begin{thebibliography}{1} +\providecommand{\natexlab}[1]{#1} +\providecommand{\url}[1]{\texttt{#1}} +\expandafter\ifx\csname urlstyle\endcsname\relax + \providecommand{\doi}[1]{doi: #1}\else + \providecommand{\doi}{doi: \begingroup \urlstyle{rm}\Url}\fi + +\bibitem[{FOCUS Work Group on Degradation Kinetics}(2011)]{FOCUSkinetics2011} +{FOCUS Work Group on Degradation Kinetics}. +\newblock \emph{Generic guidance for estimating persistence and degradation + kinetics from environmental fate studies on pesticides in EU registration}, + 1.0 edition, November 2011. +\newblock URL \url{http://focus.jrc.ec.europa.eu/dk}. + +\end{thebibliography} diff --git a/docs/articles/FOCUS_Z.blg b/docs/articles/FOCUS_Z.blg new file mode 100644 index 00000000..1da213fb --- /dev/null +++ b/docs/articles/FOCUS_Z.blg @@ -0,0 +1,46 @@ +This is BibTeX, Version 0.99d (TeX Live 2015/dev/Debian) +Capacity: max_strings=35307, hash_size=35307, hash_prime=30011 +The top-level auxiliary file: FOCUS_Z.aux +The style file: plainnat.bst +Database file #1: references.bib +You've used 1 entry, + 2773 wiz_defined-function locations, + 599 strings with 5084 characters, +and the built_in function-call counts, 324 in 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out of 1000 (max. 500000) + 88 words of extra memory for PDF output out of 10000 (max. 10000000) + diff --git a/docs/articles/FOCUS_Z.out b/docs/articles/FOCUS_Z.out new file mode 100644 index 00000000..61a86d0f --- /dev/null +++ b/docs/articles/FOCUS_Z.out @@ -0,0 +1,4 @@ +\BOOKMARK [1][-]{section.1}{The data}{}% 1 +\BOOKMARK [1][-]{section.2}{Parent compound and one metabolite}{}% 2 +\BOOKMARK [1][-]{section.3}{Including metabolites Z2 and Z3}{}% 3 +\BOOKMARK [1][-]{section.4}{Using the SFORB model for parent and metabolites}{}% 4 diff --git a/docs/articles/FOCUS_Z.pdf b/docs/articles/FOCUS_Z.pdf Binary files differnew file mode 100644 index 00000000..bc37c873 --- /dev/null +++ b/docs/articles/FOCUS_Z.pdf diff --git a/docs/articles/FOCUS_Z.tex b/docs/articles/FOCUS_Z.tex new file mode 100644 index 00000000..f1886acd --- /dev/null +++ b/docs/articles/FOCUS_Z.tex @@ -0,0 +1,566 @@ +%\VignetteIndexEntry{Example evaluation of FOCUS dataset Z} +%\VignetteEngine{knitr::knitr} +\documentclass[12pt,a4paper]{article}\usepackage[]{graphicx}\usepackage[]{color} +%% maxwidth is the original width if it is less than linewidth +%% otherwise use linewidth (to make sure the graphics do not exceed the margin) +\makeatletter +\def\maxwidth{ % + \ifdim\Gin@nat@width>\linewidth + \linewidth + \else + \Gin@nat@width + \fi +} +\makeatother + +\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345} +\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}% +\newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}% +\newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}% +\newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}% +\newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}% +\newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}% +\newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}% +\newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}% +\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}% +\let\hlipl\hlkwb + +\usepackage{framed} +\makeatletter +\newenvironment{kframe}{% + \def\at@end@of@kframe{}% + \ifinner\ifhmode% + \def\at@end@of@kframe{\end{minipage}}% + \begin{minipage}{\columnwidth}% + \fi\fi% + \def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep + \colorbox{shadecolor}{##1}\hskip-\fboxsep + % There is no \\@totalrightmargin, so: + \hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}% + \MakeFramed {\advance\hsize-\width + \@totalleftmargin\z@ \linewidth\hsize + \@setminipage}}% + {\par\unskip\endMakeFramed% + \at@end@of@kframe} +\makeatother + +\definecolor{shadecolor}{rgb}{.97, .97, .97} +\definecolor{messagecolor}{rgb}{0, 0, 0} +\definecolor{warningcolor}{rgb}{1, 0, 1} +\definecolor{errorcolor}{rgb}{1, 0, 0} +\newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX + +\usepackage{alltt} +\usepackage{a4wide} +\input{header} +\hypersetup{ + pdftitle = {Example evaluation of FOCUS dataset Z}, + pdfsubject = {Manuscript}, + pdfauthor = {Johannes Ranke}, + colorlinks = {true}, + linkcolor = {blue}, + citecolor = {blue}, + urlcolor = {red}, + hyperindex = {true}, + linktocpage = {true}, +} +\IfFileExists{upquote.sty}{\usepackage{upquote}}{} +\begin{document} + + + +\title{Example evaluation of FOCUS dataset Z} +\author{\textbf{Johannes Ranke} \\[0.5cm] +%EndAName +Wissenschaftlicher Berater\\ +Kronacher Str. 8, 79639 Grenzach-Wyhlen, Germany\\[0.5cm] +and\\[0.5cm] +University of Bremen\\ +} +\maketitle + +\thispagestyle{empty} \setcounter{page}{0} + +\clearpage + +\tableofcontents + +\textbf{Key words}: Kinetics, FOCUS, nonlinear optimisation + +\section{The data} + +The following code defines the example dataset from Appendix 7 to the FOCUS kinetics +report \citep{FOCUSkinetics2011}, p.350. + +\begin{knitrout} +\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} +\begin{alltt} +\hlkwd{require}\hlstd{(mkin)} +\end{alltt} + + +{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: mkin}} + +{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: minpack.lm}} + +{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: rootSolve}} + +{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: inline}} + +{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: methods}} + +{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: parallel}}\begin{alltt} +\hlstd{LOD} \hlkwb{=} \hlnum{0.5} +\hlstd{FOCUS_2006_Z} \hlkwb{=} \hlkwd{data.frame}\hlstd{(} + \hlkwc{t} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,} \hlnum{0.04}\hlstd{,} \hlnum{0.125}\hlstd{,} \hlnum{0.29}\hlstd{,} \hlnum{0.54}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{2}\hlstd{,} \hlnum{3}\hlstd{,} \hlnum{4}\hlstd{,} \hlnum{7}\hlstd{,} \hlnum{10}\hlstd{,} \hlnum{14}\hlstd{,} \hlnum{21}\hlstd{,} + \hlnum{42}\hlstd{,} \hlnum{61}\hlstd{,} \hlnum{96}\hlstd{,} \hlnum{124}\hlstd{),} + \hlkwc{Z0} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{100}\hlstd{,} \hlnum{81.7}\hlstd{,} \hlnum{70.4}\hlstd{,} \hlnum{51.1}\hlstd{,} \hlnum{41.2}\hlstd{,} \hlnum{6.6}\hlstd{,} \hlnum{4.6}\hlstd{,} \hlnum{3.9}\hlstd{,} \hlnum{4.6}\hlstd{,} \hlnum{4.3}\hlstd{,} \hlnum{6.8}\hlstd{,} + \hlnum{2.9}\hlstd{,} \hlnum{3.5}\hlstd{,} \hlnum{5.3}\hlstd{,} \hlnum{4.4}\hlstd{,} \hlnum{1.2}\hlstd{,} \hlnum{0.7}\hlstd{),} + \hlkwc{Z1} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,} \hlnum{18.3}\hlstd{,} \hlnum{29.6}\hlstd{,} \hlnum{46.3}\hlstd{,} \hlnum{55.1}\hlstd{,} \hlnum{65.7}\hlstd{,} \hlnum{39.1}\hlstd{,} \hlnum{36}\hlstd{,} \hlnum{15.3}\hlstd{,} \hlnum{5.6}\hlstd{,} \hlnum{1.1}\hlstd{,} + \hlnum{1.6}\hlstd{,} \hlnum{0.6}\hlstd{,} \hlnum{0.5} \hlopt{*} \hlstd{LOD,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{),} + \hlkwc{Z2} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{0.5} \hlopt{*} \hlstd{LOD,} \hlnum{2.6}\hlstd{,} \hlnum{3.8}\hlstd{,} \hlnum{15.3}\hlstd{,} \hlnum{37.2}\hlstd{,} \hlnum{31.7}\hlstd{,} \hlnum{35.6}\hlstd{,} \hlnum{14.5}\hlstd{,} + \hlnum{0.8}\hlstd{,} \hlnum{2.1}\hlstd{,} \hlnum{1.9}\hlstd{,} \hlnum{0.5} \hlopt{*} \hlstd{LOD,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{),} + \hlkwc{Z3} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{0.5} \hlopt{*} \hlstd{LOD,} \hlnum{9.2}\hlstd{,} \hlnum{13.1}\hlstd{,} \hlnum{22.3}\hlstd{,} \hlnum{28.4}\hlstd{,} \hlnum{32.5}\hlstd{,} + \hlnum{25.2}\hlstd{,} \hlnum{17.2}\hlstd{,} \hlnum{4.8}\hlstd{,} \hlnum{4.5}\hlstd{,} \hlnum{2.8}\hlstd{,} \hlnum{4.4}\hlstd{))} + +\hlstd{FOCUS_2006_Z_mkin} \hlkwb{<-} \hlkwd{mkin_wide_to_long}\hlstd{(FOCUS_2006_Z)} +\end{alltt} +\end{kframe} +\end{knitrout} + +\section{Parent compound and one metabolite} + +The next step is to set up the models used for the kinetic analysis. As the +simultaneous fit of parent and the first metabolite is usually straightforward, +Step 1 (SFO for parent only) is skipped here. We start with the model 2a, +with formation and decline of metabolite Z1 and the pathway from parent +directly to sink included (default in mkin). + +\begin{knitrout} +\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} +\begin{alltt} +\hlstd{Z.2a} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{),} + \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{))} +\end{alltt} +\begin{verbatim} +## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +\end{verbatim} + + +{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt} +\hlstd{m.Z.2a} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.2a, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)} +\hlkwd{plot_sep}\hlstd{(m.Z.2a)} +\end{alltt} +\end{kframe} +\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_1-1} +\begin{kframe}\begin{alltt} +\hlkwd{summary}\hlstd{(m.Z.2a,} \hlkwc{data} \hlstd{=} \hlnum{FALSE}\hlstd{)}\hlopt{$}\hlstd{bpar} +\end{alltt} +\begin{verbatim} +## Estimate se_notrans t value Pr(>t) +## Z0_0 9.701488e+01 3.55313691 2.730401e+01 1.679214e-21 +## k_Z0_sink 1.281376e-11 0.22689470 5.647447e-11 5.000000e-01 +## k_Z0_Z1 2.236006e+00 0.16507604 1.354531e+01 7.396594e-14 +## k_Z1_sink 4.821248e-01 0.06585369 7.321150e+00 3.552015e-08 +## Lower Upper +## Z0_0 91.4058170 102.6239462 +## k_Z0_sink 0.0000000 Inf +## k_Z0_Z1 1.8419826 2.7143172 +## k_Z1_sink 0.4005856 0.5802613 +\end{verbatim} +\end{kframe} +\end{knitrout} + +As obvious from the parameter summary (the \texttt{bpar} component of the +summary), the kinetic rate constant from parent compound Z to sink +is negligible. Accordingly, the exact magnitude of the fitted parameter +\texttt{log k\_Z0\_sink} is ill-defined and the covariance matrix is not +returned (not shown, would be visible in the complete summary). +This suggests, in agreement with the analysis in the FOCUS kinetics report, to +simplify the model by removing the pathway to sink. + +A similar result can be obtained when formation fractions are used in the model +formulation: + +\begin{knitrout} +\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} +\begin{alltt} +\hlstd{Z.2a.ff} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{),} + \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{),} + \hlkwc{use_of_ff} \hlstd{=} \hlstr{"max"}\hlstd{)} +\end{alltt} +\begin{verbatim} +## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +\end{verbatim} + + +{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt} +\hlstd{m.Z.2a.ff} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.2a.ff, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)} +\hlkwd{plot_sep}\hlstd{(m.Z.2a.ff)} +\end{alltt} +\end{kframe} +\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_2-1} +\begin{kframe}\begin{alltt} +\hlkwd{summary}\hlstd{(m.Z.2a.ff,} \hlkwc{data} \hlstd{=} \hlnum{FALSE}\hlstd{)}\hlopt{$}\hlstd{bpar} +\end{alltt} +\begin{verbatim} +## Estimate se_notrans t value Pr(>t) Lower +## Z0_0 97.0148812 3.55314944 27.303912 1.679369e-21 91.3287912 +## k_Z0 2.2360064 0.21684747 10.311425 3.661846e-11 1.8052909 +## k_Z1 0.4821248 0.06585372 7.321147 3.552045e-08 0.3996826 +## f_Z0_to_Z1 1.0000000 0.10147342 9.854798 9.707056e-11 0.0000000 +## Upper +## Z0_0 102.7009713 +## k_Z0 2.7694843 +## k_Z1 0.5815722 +## f_Z0_to_Z1 1.0000000 +\end{verbatim} +\end{kframe} +\end{knitrout} + +Here, the ilr transformed formation fraction fitted in the model takes a very +large value, and the backtransformed formation fraction from parent Z to Z1 is +practically unity. Again, the covariance matrix is not returned as the model is +overparameterised. + +The simplified model is obtained by setting the list component \texttt{sink} to +\texttt{FALSE}.\footnote{If the model formulation without formation fractions +is used, the same effect can be obtained by fixing the parameter \texttt{k\_Z\_sink} +to a value of zero.} + +In the following, we use the parameterisation with formation fractions in order +to be able to compare with the results in the FOCUS guidance, and as it +makes it easier to use parameters obtained in a previous fit when adding a further +metabolite. + +\begin{knitrout} +\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} +\begin{alltt} +\hlstd{Z.3} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),} + \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{),} \hlkwc{use_of_ff} \hlstd{=} \hlstr{"max"}\hlstd{)} +\end{alltt} +\begin{verbatim} +## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +\end{verbatim} + + +{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt} +\hlstd{m.Z.3} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.3, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)} +\hlkwd{plot_sep}\hlstd{(m.Z.3)} +\end{alltt} +\end{kframe} +\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_3-1} +\begin{kframe}\begin{alltt} +\hlkwd{summary}\hlstd{(m.Z.3,} \hlkwc{data} \hlstd{=} \hlnum{FALSE}\hlstd{)}\hlopt{$}\hlstd{bpar} +\end{alltt} +\begin{verbatim} +## Estimate se_notrans t value Pr(>t) Lower +## Z0_0 97.0148815 2.68177093 36.17568 2.363587e-25 91.5215237 +## k_Z0 2.2360064 0.14686110 15.22531 2.246514e-15 1.9545310 +## k_Z1 0.4821248 0.04268712 11.29439 3.068581e-12 0.4021552 +## Upper +## Z0_0 102.5082392 +## k_Z0 2.5580177 +## k_Z1 0.5779966 +\end{verbatim} +\end{kframe} +\end{knitrout} + +As there is only one transformation product for Z0 and no pathway +to sink, the formation fraction is internally fixed to unity. + +\section{Including metabolites Z2 and Z3} + +As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as +well in the next step. While this step appears questionable on the basis of the above results, it +is followed here for the purpose of comparison. Also, in the FOCUS report, it is +assumed that there is additional empirical evidence that Z1 quickly and exclusively +hydrolyses to Z2. + +\begin{knitrout} +\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} +\begin{alltt} +\hlstd{Z.5} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),} + \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),} + \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{),} \hlkwc{use_of_ff} \hlstd{=} \hlstr{"max"}\hlstd{)} +\end{alltt} +\begin{verbatim} +## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +\end{verbatim} + + +{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt} +\hlstd{m.Z.5} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.5, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)} +\hlkwd{plot_sep}\hlstd{(m.Z.5)} +\end{alltt} +\end{kframe} +\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_5-1} + +\end{knitrout} + +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. + +\begin{knitrout} +\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} +\begin{alltt} +\hlstd{Z.FOCUS} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),} + \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),} + \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z3"}\hlstd{),} + \hlkwc{Z3} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{),} + \hlkwc{use_of_ff} \hlstd{=} \hlstr{"max"}\hlstd{)} +\end{alltt} +\begin{verbatim} +## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +\end{verbatim} + + +{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt} +\hlstd{m.Z.FOCUS} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.FOCUS, FOCUS_2006_Z_mkin,} + \hlkwc{parms.ini} \hlstd{= m.Z.5}\hlopt{$}\hlstd{bparms.ode,} + \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)} +\hlkwd{plot_sep}\hlstd{(m.Z.FOCUS)} +\end{alltt} +\end{kframe} +\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_6-1} +\begin{kframe}\begin{alltt} +\hlkwd{summary}\hlstd{(m.Z.FOCUS,} \hlkwc{data} \hlstd{=} \hlnum{FALSE}\hlstd{)}\hlopt{$}\hlstd{bpar} +\end{alltt} +\begin{verbatim} +## Estimate se_notrans t value Pr(>t) Lower +## Z0_0 96.83849566 2.05886133 47.034977 5.583742e-44 92.70517559 +## k_Z0 2.21540897 0.11813046 18.753919 7.744034e-25 1.99051134 +## k_Z1 0.47829896 0.02928763 16.331089 3.333376e-22 0.42297603 +## k_Z2 0.45161653 0.04421268 10.214638 3.110936e-14 0.37103495 +## k_Z3 0.05869343 0.01429485 4.105914 7.285393e-05 0.03599566 +## f_Z2_to_Z3 0.47150952 0.05705233 8.264510 2.809889e-11 0.36038193 +## Upper +## Z0_0 100.97181573 +## k_Z0 2.46571661 +## k_Z1 0.54085782 +## k_Z2 0.54969886 +## k_Z3 0.09570371 +## f_Z2_to_Z3 0.58553462 +\end{verbatim} +\begin{alltt} +\hlkwd{endpoints}\hlstd{(m.Z.FOCUS)} +\end{alltt} +\begin{verbatim} +## $ff +## Z2_Z3 Z2_sink +## 0.4715095 0.5284905 +## +## $SFORB +## logical(0) +## +## $distimes +## DT50 DT90 +## Z0 0.3128755 1.039350 +## Z1 1.4491923 4.814113 +## Z2 1.5348136 5.098540 +## Z3 11.8096217 39.230714 +\end{verbatim} +\end{kframe} +\end{knitrout} + +This fit corresponds to the final result chosen in Appendix 7 of the FOCUS +report. Confidence intervals returned by mkin are based on internally +transformed parameters, however. + +\section{Using the SFORB model for parent and metabolites} + +As the FOCUS report states, there is a certain tailing of the time course of metabolite +Z3. Also, the time course of the parent compound is not fitted very well using the +SFO model, as residues at a certain low level remain. + +Therefore, an additional model is offered here, using the single first-order +reversible binding (SFORB) model for metabolite Z3. As expected, the $\chi^2$ +error level is lower for metabolite Z3 using this model and the graphical +fit for Z3 is improved. However, the covariance matrix is not returned. + +\begin{knitrout} +\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} +\begin{alltt} +\hlstd{Z.mkin.1} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),} + \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),} + \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z3"}\hlstd{),} + \hlkwc{Z3} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFORB"}\hlstd{))} +\end{alltt} +\begin{verbatim} +## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +\end{verbatim} + + +{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt} +\hlstd{m.Z.mkin.1} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.mkin.1, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)} +\hlkwd{plot_sep}\hlstd{(m.Z.mkin.1)} +\end{alltt} +\end{kframe} +\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_7-1} +\begin{kframe}\begin{alltt} +\hlkwd{summary}\hlstd{(m.Z.mkin.1,} \hlkwc{data} \hlstd{=} \hlnum{FALSE}\hlstd{)}\hlopt{$}\hlstd{cov.unscaled} +\end{alltt} +\begin{verbatim} +## NULL +\end{verbatim} +\end{kframe} +\end{knitrout} + +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. + +\begin{knitrout} +\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} +\begin{alltt} +\hlstd{Z.mkin.3} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFORB"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),} + \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),} + \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{))} +\end{alltt} +\begin{verbatim} +## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +\end{verbatim} + + +{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt} +\hlstd{m.Z.mkin.3} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.mkin.3, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)} +\hlkwd{plot_sep}\hlstd{(m.Z.mkin.3)} +\end{alltt} +\end{kframe} +\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_9-1} + +\end{knitrout} + +This results in a much better representation of the behaviour of the parent +compound Z0. + +Finally, Z3 is added as well. These models appear overparameterised (no +covariance matrix returned) if the sink for Z1 is left in the models. + +\begin{knitrout} +\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} +\begin{alltt} +\hlstd{Z.mkin.4} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFORB"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),} + \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),} + \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z3"}\hlstd{),} + \hlkwc{Z3} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{))} +\end{alltt} +\begin{verbatim} +## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +\end{verbatim} + + +{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt} +\hlstd{m.Z.mkin.4} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.mkin.4, FOCUS_2006_Z_mkin,} + \hlkwc{parms.ini} \hlstd{= m.Z.mkin.3}\hlopt{$}\hlstd{bparms.ode,} + \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)} +\hlkwd{plot_sep}\hlstd{(m.Z.mkin.4)} +\end{alltt} +\end{kframe} +\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_10-1} + +\end{knitrout} + +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. + +\begin{knitrout} +\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} +\begin{alltt} +\hlstd{Z.mkin.5} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFORB"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),} + \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),} + \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z3"}\hlstd{),} + \hlkwc{Z3} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFORB"}\hlstd{))} +\end{alltt} +\begin{verbatim} +## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +\end{verbatim} + + +{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt} +\hlstd{m.Z.mkin.5} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.mkin.5, FOCUS_2006_Z_mkin,} + \hlkwc{parms.ini} \hlstd{= m.Z.mkin.4}\hlopt{$}\hlstd{bparms.ode[}\hlnum{1}\hlopt{:}\hlnum{4}\hlstd{],} + \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)} +\hlkwd{plot_sep}\hlstd{(m.Z.mkin.5)} +\end{alltt} +\end{kframe} +\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_11-1} + +\end{knitrout} + +The summary view of the backtransformed parameters shows that we get no +confidence intervals due to overparameterisation. As the optimized +\texttt{k\_Z3\_bound\_free} is excessively small, it seems reasonable to fix it to +zero. + +\begin{knitrout} +\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} +\begin{alltt} +\hlstd{m.Z.mkin.5a} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.mkin.5, FOCUS_2006_Z_mkin,} + \hlkwc{parms.ini} \hlstd{=} \hlkwd{c}\hlstd{(m.Z.mkin.5}\hlopt{$}\hlstd{bparms.ode[}\hlnum{1}\hlopt{:}\hlnum{7}\hlstd{],} + \hlkwc{k_Z3_bound_free} \hlstd{=} \hlnum{0}\hlstd{),} + \hlkwc{fixed_parms} \hlstd{=} \hlstr{"k_Z3_bound_free"}\hlstd{,} + \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)} +\hlkwd{plot_sep}\hlstd{(m.Z.mkin.5a)} +\end{alltt} +\end{kframe} +\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_11a-1} + +\end{knitrout} + +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 +\texttt{Z.mkin.5a} is proposed as the best-fit model for the dataset from +Appendix 7 of the FOCUS report. + +A graphical representation of the confidence intervals can finally be obtained. + +\begin{knitrout} +\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} +\begin{alltt} +\hlkwd{mkinparplot}\hlstd{(m.Z.mkin.5a)} +\end{alltt} +\end{kframe} +\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_11b-1} + +\end{knitrout} + +The endpoints obtained with this model are + +\begin{knitrout} +\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} +\begin{alltt} +\hlkwd{endpoints}\hlstd{(m.Z.mkin.5a)} +\end{alltt} +\begin{verbatim} +## $ff +## Z0_free_Z1 Z1_Z2 Z2_sink Z2_Z3_free Z3_free_sink +## 1.0000000 1.0000000 0.4634431 0.5365569 1.0000000 +## +## $SFORB +## Z0_b1 Z0_b2 Z3_b1 Z3_b2 +## 2.447138640 0.007512589 0.080007099 0.000000000 +## +## $distimes +## DT50 DT90 DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2 +## Z0 0.3042972 1.184811 0.283248 92.26476 NA NA +## Z1 1.5147787 5.031986 NA NA NA NA +## Z2 1.6413857 5.452565 NA NA NA NA +## Z3 NA NA NA NA 8.663571 Inf +\end{verbatim} +\end{kframe} +\end{knitrout} + +It is clear the degradation rate of Z3 towards the end of the experiment +is very low as DT50\_Z3\_b2 (the second Eigenvalue of the system of two differential +equations representing the SFORB system for Z3, corresponding to the slower rate +constant of the DFOP model) is reported to be infinity. However, this appears +to be a feature of the data. + +\bibliographystyle{plainnat} +\bibliography{references} + +\end{document} +% vim: set foldmethod=syntax: diff --git a/docs/articles/FOCUS_Z.toc b/docs/articles/FOCUS_Z.toc new file mode 100644 index 00000000..ebb3b24a --- /dev/null +++ b/docs/articles/FOCUS_Z.toc @@ -0,0 +1,4 @@ +\contentsline {section}{\numberline {1}The data}{1}{section.1} +\contentsline {section}{\numberline {2}Parent compound and one metabolite}{2}{section.2} +\contentsline {section}{\numberline {3}Including metabolites Z2 and Z3}{8}{section.3} +\contentsline {section}{\numberline {4}Using the SFORB model for parent and metabolites}{12}{section.4} diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_10_ad34939f1c4da097e64c6add505f564d.RData b/docs/articles/cache/FOCUS_2006_Z_fits_10_ad34939f1c4da097e64c6add505f564d.RData Binary files differnew file mode 100644 index 00000000..53e2a7d5 --- /dev/null +++ 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100644 index 00000000..72bad839 --- /dev/null +++ b/docs/articles/cache/__packages @@ -0,0 +1,6 @@ +base +knitr +minpack.lm +rootSolve +inline +mkin diff --git a/docs/articles/compiled_models.R b/docs/articles/compiled_models.R new file mode 100644 index 00000000..4f544b0d --- /dev/null +++ b/docs/articles/compiled_models.R @@ -0,0 +1,42 @@ +## ----benchmark_SFO_SFO, fig.height = 3----------------------------------- +library("microbenchmark") +library("ggplot2") +mb.1 <- microbenchmark( + "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D, + solution_type = "deSolve", + use_compiled = FALSE, quiet = TRUE), + "Eigenvalue based" = mkinfit(SFO_SFO, FOCUS_2006_D, + solution_type = "eigen", quiet = TRUE), + "deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_2006_D, + solution_type = "deSolve", quiet = TRUE), + times = 3, control = list(warmup = 0)) + +smb.1 <- summary(mb.1) +print(mb.1) +autoplot(mb.1) + +## ------------------------------------------------------------------------ +rownames(smb.1) <- smb.1$expr +smb.1["median"]/smb.1["deSolve, compiled", "median"] + +## ----benchmark_FOMC_SFO, fig.height = 3---------------------------------- +FOMC_SFO <- mkinmod( + parent = mkinsub("FOMC", "m1"), + m1 = mkinsub( "SFO")) + +mb.2 <- microbenchmark( + "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, + use_compiled = FALSE, quiet = TRUE), + "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE), + times = 3, control = list(warmup = 0)) +smb.2 <- summary(mb.2) +print(mb.2) +smb.2["median"]/smb.2["deSolve, compiled", "median"] +autoplot(mb.2) + +## ----sessionInfo, echo = FALSE------------------------------------------- +cat(capture.output(sessionInfo())[1:3], sep = "\n") +if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { + cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]])) +} + diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index d2e1d87d..e02b9cf3 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -1,10 +1,10 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" 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src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body> - <div class="container"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container template-vignette"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -30,6 +30,7 @@ </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header><div class="row"> <div class="col-md-9"> @@ -37,13 +38,14 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-10-06</h4> + <h4 class="date">2016-10-26</h4> </div> +<div class="contents"> <div id="benchmark-for-a-model-that-can-also-be-solved-with-eigenvalues" class="section level2"> -<h2>Benchmark for a model that can also be solved with Eigenvalues</h2> +<h2 class="hasAnchor"><html><body><a href="#benchmark-for-a-model-that-can-also-be-solved-with-eigenvalues" class="anchor"> </a></body></html>Benchmark for a model that can also be solved with Eigenvalues</h2> <p>This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The <code><a href="../reference/mkinmod.html">mkinmod()</a></code> function checks for presence of the gcc compiler using</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">Sys.which</span>(<span class="st">"gcc"</span>)</code></pre></div> <pre><code>## gcc @@ -73,25 +75,25 @@ mb<span class="fl">.1</span> <-<span class="st"> </span><span class="kw">micr <span class="kw">print</span>(mb<span class="fl">.1</span>)</code></pre></div> <pre><code>## Unit: milliseconds ## expr min lq mean median uq -## deSolve, not compiled 6365.2773 6407.1609 6467.4083 6449.0446 6518.4738 -## Eigenvalue based 872.0339 912.6754 926.7178 953.3169 954.0597 -## deSolve, compiled 730.1252 740.7149 751.8881 751.3045 762.7695 +## deSolve, not compiled 6298.7342 6308.6792 6343.9668 6318.6243 6366.5831 +## Eigenvalue based 871.7379 880.7757 903.5267 889.8135 919.4211 +## deSolve, compiled 724.9025 730.6729 732.9837 736.4432 737.0243 ## max neval cld -## 6587.9031 3 b -## 954.8026 3 a -## 774.2345 3 a</code></pre> +## 6414.5420 3 c +## 949.0287 3 b +## 737.6054 3 a</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.1</span>)</code></pre></div> <p><img src="compiled_models_files/figure-html/benchmark_SFO_SFO-1.png" width="672"></p> <p>We see that using the compiled model is by a factor of 8.6 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rownames</span>(smb<span class="fl">.1</span>) <-<span class="st"> </span>smb<span class="fl">.1</span>$expr smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="fl">.1</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div> <pre><code>## median -## deSolve, not compiled 8.583796 -## Eigenvalue based 1.268882 +## deSolve, not compiled 8.579920 +## Eigenvalue based 1.208258 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> -<h2>Benchmark for a model that can not be solved with Eigenvalues</h2> +<h2 class="hasAnchor"><html><body><a href="#benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="anchor"> </a></body></html>Benchmark for a model that can not be solved with Eigenvalues</h2> <p>This evaluation is also taken from the example section of mkinfit.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>( <span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>), @@ -108,28 +110,29 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span> <-<span class="st"> </span><span class="kw">summary</span>(mb<span class="fl">.2</span>) <span class="kw">print</span>(mb<span class="fl">.2</span>)</code></pre></div> <pre><code>## Unit: seconds -## expr min lq mean median uq -## deSolve, not compiled 13.464194 13.498471 13.52712 13.532748 13.558577 -## deSolve, compiled 1.328628 1.342168 1.35224 1.355707 1.364046 +## expr min lq mean median uq +## deSolve, not compiled 13.265212 13.330161 13.412053 13.395109 13.485473 +## deSolve, compiled 1.322466 1.326851 1.364827 1.331236 1.386007 ## max neval cld -## 13.584407 3 b -## 1.372385 3 a</code></pre> +## 13.575837 3 b +## 1.440779 3 a</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span>[<span class="st">"median"</span>]/smb<span class="fl">.2</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div> <pre><code>## median ## 1 NA ## 2 NA</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.2</span>)</code></pre></div> <p><img src="compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png" width="672"></p> -<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>Here we get a performance benefit of a factor of 10.1 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.44.9000 on</p> <pre><code>## R version 3.3.1 (2016-06-21) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 8 (jessie)</code></pre> <pre><code>## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</code></pre> </div> +</div> </div> - <div class="col-md-3 hidden-xs"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"><li><a href="#benchmark-for-a-model-that-can-also-be-solved-with-eigenvalues">Benchmark for a model that can also be solved with Eigenvalues</a></li> @@ -140,7 +143,14 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" </div> - <footer><p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <footer><div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer></div> </body></html> diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png Binary files differindex 54420d5b..bba259d6 100644 --- a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png +++ b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png Binary files differindex af90245e..6b732075 100644 --- a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png +++ 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+\usepackage{latexsym} +\usepackage{amsmath} +\usepackage{amssymb} +\usepackage{graphicx} +\usepackage{parskip} +\usepackage[round]{natbib} +\usepackage{amstext} +\usepackage{hyperref} + +\newcommand{\Rpackage}[1]{{\normalfont\fontseries{b}\selectfont #1}} +\newcommand{\Robject}[1]{\texttt{#1}} +\newcommand{\Rclass}[1]{\textit{#1}} +\newcommand{\Rcmd}[1]{\texttt{#1}} + +\newcommand{\RR}{\textsf{R}} + +\RequirePackage[T1]{fontenc} +\RequirePackage{graphicx,ae,fancyvrb} +\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} +\usepackage{relsize} diff --git a/docs/articles/index.html b/docs/articles/index.html index 4ed79733..9994716d 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Articles. mkin</title> +<title>Articles • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container 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Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/articles/mkin.R b/docs/articles/mkin.R new file mode 100644 index 00000000..175bd33b --- /dev/null +++ b/docs/articles/mkin.R @@ -0,0 +1,22 @@ +## ---- echo = TRUE, cache = TRUE, fig = TRUE, fig.width = 8, fig.height = 7---- +require(mkin) +m_SFO_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"), + M1 = mkinsub("SFO", "M2"), + M2 = mkinsub("SFO"), + use_of_ff = "max", quiet = TRUE) + +sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) + +d_SFO_SFO_SFO <- mkinpredict(m_SFO_SFO_SFO, + c(k_parent = 0.03, + f_parent_to_M1 = 0.5, k_M1 = log(2)/100, + f_M1_to_M2 = 0.9, k_M2 = log(2)/50), + c(parent = 100, M1 = 0, M2 = 0), + sampling_times) + +d_SFO_SFO_SFO_err <- add_err(d_SFO_SFO_SFO, function(x) 3, n = 1, seed = 123456789 ) + +f_SFO_SFO_SFO <- mkinfit(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[1]], quiet = TRUE) + +plot_sep(f_SFO_SFO_SFO, lpos = c("topright", "bottomright", "bottomright")) + diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index c1b38794..74d8ccca 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -1,10 +1,10 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>mkin - 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" 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"><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html><head><meta http-equiv="Content-Type" content="text/html; 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For the evaluation of pesticide degradation experiments, detailed guidance has been developed, based on nonlinear optimisation. The <code>R</code> add-on package <code>mkin</code> <span class="citation">(Ranke 2016)</span> implements fitting some of the models recommended in this guidance from within R and calculates some statistical measures for data series within one or more compartments, for parent and metabolites.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">require</span>(mkin) m_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>), @@ -66,10 +68,10 @@ d_SFO_SFO_SFO_err <-<span class="st"> </span><span class="kw"><a href="../ref f_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[<span class="dv">1</span>]], <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(f_SFO_SFO_SFO, <span class="dt">lpos =</span> <span class="kw">c</span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> +<p><img src="mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> </div> <div id="background" class="section level1"> -<h1>Background</h1> +<h1 class="hasAnchor"><html><body><a href="#background" class="anchor"> </a></body></html>Background</h1> <p>Many approaches are possible regarding the evaluation of chemical degradation data.</p> <p>The now deprecated <code>kinfit</code> package <span class="citation">(Ranke 2015)</span> in <code>R</code> <span class="citation">(R Development Core Team 2016)</span> implements the approach recommended in the kinetics report provided by the FOrum for Co-ordination of pesticide fate models and their USe <span class="citation">(FOCUS Work Group on Degradation Kinetics 2006; 2014)</span> for simple data series for one parent compound in one compartment.</p> <p>The <code>mkin</code> package <span class="citation">(Ranke 2016)</span> extends this approach to data series with transformation products, commonly termed metabolites, and to more than one compartment. It is also possible to include back reactions, so equilibrium reactions and equilibrium partitioning can be specified, although this oftentimes leads to an overparameterisation of the model.</p> @@ -79,39 +81,39 @@ f_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../referen <p>Also, <code>mkin</code> introduced using analytical solutions for parent only kinetics for improved optimization speed. Later, Eigenvalue based solutions were introduced to <code>mkin</code> for the case of linear differential equations (<em>i.e.</em> where the FOMC or DFOP models were not used for the parent compound), greatly improving the optimization speed for these cases.</p> <p>The possibility to specify back-reactions and a biphasic model (SFORB) for metabolites were present in <code>mkin</code> from the very beginning.</p> <div id="derived-software-tools" class="section level2"> -<h2>Derived software tools</h2> +<h2 class="hasAnchor"><html><body><a href="#derived-software-tools" class="anchor"> </a></body></html>Derived software tools</h2> <p>Soon after the publication of <code>mkin</code>, two derived tools were published, namely KinGUII (available from Bayer Crop Science) and CAKE (commissioned to Tessella by Syngenta), which added a graphical user interface (GUI), and added fitting by iteratively reweighted least squares (IRLS) and characterisation of likely parameter distributions by Markov Chain Monte Carlo (MCMC) sampling.</p> <p>CAKE focuses on a smooth use experience, sacrificing some flexibility in the model definition, originally allowing only two primary metabolites in parallel. The current version 3.2 of CAKE release in March 2016 uses a basic scheme for up to six metabolites in a flexible arrangement, but does not support back-reactions (non-instantaneous equilibria) or biphasic kinetics for metabolites.</p> <p>KinGUI offers an even more flexible widget for specifying complex kinetic models. Back-reactions (non-instanteneous equilibria) were supported early on, but until 2014, only simple first-order models could be specified for transformation products. Starting with KinGUII version 2.1, biphasic modelling of metabolites was also available in KinGUII.</p> <p>A further graphical user interface (GUI) that has recently been brought to a decent degree of maturity is the browser based GUI named <code>gmkin</code>. Please see its <a href="http://kinfit.r-forge.r-project.org/gmkin_static">documentation page</a> and <a href="http://kinfit.r-forge.r-project.org/gmkin_static/vignettes/gmkin_manual.html">manual</a> for further information.</p> </div> <div id="recent-developments" class="section level2"> -<h2>Recent developments</h2> +<h2 class="hasAnchor"><html><body><a href="#recent-developments" class="anchor"> </a></body></html>Recent developments</h2> <p>Currently (June 2016), the main features available in <code>mkin</code> which are not present in KinGUII or CAKE, are the speed increase by using compiled code when a compiler is present, parallel model fitting on multicore machines using the <code>mmkin</code> function, and the estimation of parameter confidence intervals based on transformed parameters. These are explained in more detail below.</p> </div> </div> <div id="internal-parameter-transformations" class="section level1"> -<h1>Internal parameter transformations</h1> +<h1 class="hasAnchor"><html><body><a href="#internal-parameter-transformations" class="anchor"> </a></body></html>Internal parameter transformations</h1> <p>For rate constants, the log transformation is used, as proposed by Bates and Watts <span class="citation">(1988, 77, 149)</span>. Approximate intervals are constructed for the transformed rate constants <span class="citation">(compare Bates and Watts 1988, 135)</span>, <em>i.e.</em> for their logarithms. Confidence intervals for the rate constants are then obtained using the appropriate backtransformation using the exponential function.</p> <p>In the first version of <code>mkin</code> allowing for specifying models using formation fractions, a home-made reparameterisation was used in order to ensure that the sum of formation fractions would not exceed unity.</p> <p>This method is still used in the current version of KinGUII (v2.1 from April 2014), with a modification that allows for fixing the pathway to sink to zero. CAKE uses penalties in the objective function in order to enforce this constraint.</p> <p>In 2012, an alternative reparameterisation of the formation fractions was proposed together with René Lehmann <span class="citation">(Ranke and Lehmann 2012)</span>, based on isometric logratio transformation (ILR). The aim was to improve the validity of the linear approximation of the objective function during the parameter estimation procedure as well as in the subsequent calculation of parameter confidence intervals.</p> <div id="confidence-intervals-based-on-transformed-parameters" class="section level2"> -<h2>Confidence intervals based on transformed parameters</h2> +<h2 class="hasAnchor"><html><body><a href="#confidence-intervals-based-on-transformed-parameters" class="anchor"> </a></body></html>Confidence intervals based on transformed parameters</h2> <p>In the first attempt at providing improved parameter confidence intervals introduced to <code>mkin</code> in 2013, confidence intervals obtained from FME on the transformed parameters were simply all backtransformed one by one to yield asymetric confidence intervals for the backtransformed parameters.</p> <p>However, while there is a 1:1 relation between the rate constants in the model and the transformed parameters fitted in the model, the parameters obtained by the isometric logratio transformation are calculated from the set of formation fractions that quantify the paths to each of the compounds formed from a specific parent compound, and no such 1:1 relation exists.</p> <p>Therefore, parameter confidence intervals for formation fractions obtained with this method only appear valid for the case of a single transformation product, where only one formation fraction is to be estimated, directly corresponding to one component of the ilr transformed parameter.</p> <p>The confidence intervals obtained by backtransformation for the cases where a 1:1 relation between transformed and original parameter exist are considered by the author of this vignette to be more accurate than those obtained using a re-estimation of the Hessian matrix after backtransformation, as implemented in the FME package.</p> </div> <div id="parameter-t-test-based-on-untransformed-parameters" class="section level2"> -<h2>Parameter t-test based on untransformed parameters</h2> +<h2 class="hasAnchor"><html><body><a href="#parameter-t-test-based-on-untransformed-parameters" class="anchor"> </a></body></html>Parameter t-test based on untransformed parameters</h2> <p>The standard output of many nonlinear regression software packages includes the results from a test for significant difference from zero for all parameters. Such a test is also recommended to check the validity of rate constants in the FOCUS guidance <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 96ff)</span>.</p> <p>It has been argued that the precondition for this test, <em>i.e.</em> normal distribution of the estimator for the parameters, is not fulfilled in the case of nonlinear regression <span class="citation">(Ranke and Lehmann 2015)</span>. However, this test is commonly used by industry, consultants and national authorities in order to decide on the reliability of parameter estimates, based on the FOCUS guidance mentioned above. Therefore, the results of this one-sided t-test are included in the summary output from <code>mkin</code>.</p> <p>As it is not reasonable to test for significant difference of the transformed parameters (<em>e.g.</em> <span class="math inline">\(log(k)\)</span>) from zero, the t-test is calculated based on the model definition before parameter transformation, <em>i.e.</em> in a similar way as in packages that do not apply such an internal parameter transformation. A note is included in the <code>mkin</code> output, pointing to the fact that the t-test is based on the unjustified assumption of normal distribution of the parameter estimators.</p> </div> </div> <div id="references" class="section level1"> -<h1>References</h1> +<h1 class="hasAnchor"><html><body><a href="#references" class="anchor"> </a></body></html>References</h1> <!-- vim: set foldmethod=syntax: --> <div id="refs" class="references"> <div id="ref-bates1988"> @@ -146,9 +148,10 @@ 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"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"><li><a href="#abstract">Abstract</a></li> @@ -165,7 +168,14 @@ f_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../referen </div> - <footer><p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <footer><div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer></div> </body></html> diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages new file mode 100644 index 00000000..c8b1e877 --- /dev/null +++ b/docs/articles/mkin_cache/html/__packages @@ -0,0 +1,8 @@ +base +knitr +minpack.lm +rootSolve +inline +mkin +microbenchmark +ggplot2 diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.RData Binary files differnew file mode 100644 index 00000000..8fd3567d --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.RData diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdb Binary files differnew file mode 100644 index 00000000..7f4d6c92 --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdb diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdx Binary files differnew file mode 100644 index 00000000..7f5f16b7 --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdx diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png Binary files differnew file mode 100644 index 00000000..d34e3805 --- /dev/null +++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png diff --git a/docs/articles/mkin_vignettes.css b/docs/articles/mkin_vignettes.css new file mode 100644 index 00000000..3bd91ab1 --- /dev/null +++ b/docs/articles/mkin_vignettes.css @@ -0,0 +1,16 @@ +/* Thanks to Steve Powell for http://rpubs.com/stevepowell99/floating-css */ +#TOC { + position: fixed; + left: 0; + top: 0; + width: 200px; + height: 100%; + overflow:auto; +} + +body { + max-width: 800px; + margin: auto; + margin-left:210px; + line-height: 20px; +} diff --git a/docs/articles/references.bib b/docs/articles/references.bib new file mode 100644 index 00000000..da51602f --- /dev/null +++ b/docs/articles/references.bib @@ -0,0 +1,112 @@ +% This file was originally created with JabRef 2.7b. +% Encoding: ISO8859_1 + +@BOOK{bates1988, + title = {Nonlinear regression and its applications}, + publisher = {Wiley-Interscience}, + year = {1988}, + author = {D. Bates and D. Watts} +} + +@MANUAL{FOCUSkinetics2011, + title = {Generic guidance for estimating persistence and degradation kinetics + from environmental fate studies on pesticides in EU registration}, + author = {{FOCUS Work Group on Degradation Kinetics}}, + edition = {1.0}, + month = {November}, + year = {2011}, + file = {FOCUS kinetics 2011 Generic guidance:/home/ranke/dok/orgs/focus/FOCUSkineticsvc_1_0_Nov23.pdf:PDF}, + url = {http://focus.jrc.ec.europa.eu/dk} +} + +@MANUAL{FOCUSkinetics2014, + title = {Generic guidance for estimating persistence and degradation kinetics + from environmental fate studies on pesticides in EU registration}, + author = {{FOCUS Work Group on Degradation Kinetics}}, + edition = {1.1}, + month = {December}, + year = {2014}, + file = {FOCUS kinetics 2011 Generic guidance:/home/ranke/dok/orgs/focus/FOCUSkineticsvc_1_0_Nov23.pdf:PDF}, + url = {http://focus.jrc.ec.europa.eu/dk} +} + +@MANUAL{FOCUS2006, + title = {Guidance Document on Estimating Persistence and Degradation Kinetics + from Environmental Fate Studies on Pesticides in EU Registration. + Report of the FOCUS Work Group on Degradation Kinetics}, + author = {{FOCUS Work Group on Degradation Kinetics}}, + year = {2006}, + note = {EC Document Reference Sanco/10058/2005 version 2.0}, + url = {http://focus.jrc.ec.europa.eu/dk} +} + +@MANUAL{rcore2016, + title = {\textsf{R}: A Language and Environment for Statistical Computing}, + author = {{R Development Core Team}}, + organization = {R Foundation for Statistical Computing}, + address = {Vienna, Austria}, + year = {2016}, + note = {{ISBN} 3-900051-07-0}, + url = {http://www.R-project.org} +} + +@MANUAL{pkg:kinfit, + title = {`kinfit`: {R}outines for fitting simple kinetic models to chemical + degradation data}, + author = {J. Ranke}, + year = {2015}, + url = {http://CRAN.R-project.org/package=kinfit} +} + +@MANUAL{pkg:mkin, + title = {`mkin`: {K}inetic evaluation of chemical degradation data}, + author = {J. Ranke}, + year = {2016}, + url = {http://CRAN.R-project.org/package=mkin} +} + +@Inproceedings{ schaefer2007, + title = {{KinGUI}: a new kinetic software tool for evaluations according to {FOCUS} degradation kinetics}, + author = {D. Sch\"{a}fer and B. Mikolasch and P. Rainbird and B. Harvey}, + booktitle = {Proceedings of the XIII Symposium Pesticide Chemistry}, + editor = {Del Re A. A. M. and Capri E. and Fragoulis G. and Trevisan M.}, + year = {2007}, + address = {Piacenza}, + pages = {916--923} +} + +@ARTICLE{soetaert2010, + author = {Karline Soetaert and Thomas Petzoldt}, + title = {Inverse Modelling, Sensitivity and Monte Carlo Analysis in {R} Using + Package {FME}}, + journal = {Journal of Statistical Software}, + year = {2010}, + volume = {33}, + pages = {1--28}, + number = {3}, + url = {http://www.jstatsoft.org/v33/i03/} +} + +@Inproceedings{ ranke2012, + title = {Parameter reliability in kinetic evaluation of environmental metabolism data - Assessment and the influence of model specification}, + author = {J. Ranke and R. Lehmann}, + booktitle = {SETAC World 20-24 May}, + year = {2012}, + address = {Berlin} +} +@Inproceedings{ ranke2015, + title = {To t-test or not to t-test, that is the question}, + author = {J. Ranke and R. Lehmann}, + booktitle = {XV Symposium on Pesticide Chemistry 2-4 September 2015}, + year = {2015}, + address = {Piacenza}, + url = {http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf} +} +@Techreport{ranke2014, + title = {{Prüfung und Validierung von Modellierungssoftware als Alternative zu + ModelMaker 4.0}}, + author = {J. Ranke}, + year = 2014, + institution = {Umweltbundesamt}, + volume = {Projektnummer 27452} +} diff --git a/docs/index.html b/docs/index.html index 0ae09340..180fe5f9 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1,43 +1,10 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Home. 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" 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"> - - -<!-- pkgdown --> -<link href="pkgdown.css" rel="stylesheet"> -<script src="pkgdown.js"></script> - -<!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> - -<!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><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" 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"><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - </head> - - <body> - <div class="container"> - <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> +<![endif]--></head><body> + <div class="container template-home"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -48,46 +15,54 @@ <a class="navbar-brand" href="index.html">mkin</a> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="index.html">Home</a> </li> <li> <a href="reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> + </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> </a> </li> - </ul> - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + - </header> + </header><div class="row"> + <div class="contents col-md-9"> + <div id="mkin" class="section level1"> +<div class="page-header"><h1 class="hasAnchor"><a href="#mkin" class="anchor"> </a>mkin</h1></div> - <div class="row"> - <div class="col-md-9"> - -<h1 id="mkin">mkin</h1> -<p><a href="http://cran.r-project.org/package=mkin"><img src="http://www.r-pkg.org/badges/version/mkin"></a></p> <p>The R package <strong>mkin</strong> provides calculation routines for the analysis of chemical degradation data, including <b>m</b>ulticompartment <b>kin</b>etics as needed for modelling the formation and decline of transformation products, or if several compartments are involved.</p> -<h2 id="installation">Installation</h2> +<div id="installation" class="section level2"> +<h2 class="hasAnchor"> +<a href="#installation" class="anchor"> </a>Installation</h2> <p>You can install the latest released version from <a href="http://cran.r-project.org/package=mkin">CRAN</a> from within R:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">install.packages</span>(<span class="st">"mkin"</span>)</code></pre></div> -<h2 id="background">Background</h2> +</div> +<div id="background" class="section level2"> +<h2 class="hasAnchor"> +<a href="#background" class="anchor"> </a>Background</h2> <p>In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance and helpful tools have been developed as detailed in ‘Credits and historical remarks’ below.</p> -<h2 id="usage">Usage</h2> +</div> +<div id="usage" class="section level2"> +<h2 class="hasAnchor"> +<a href="#usage" class="anchor"> </a>Usage</h2> <p>For a start, have a look a the code examples provided for <a href="http://kinfit.r-forge.r-project.org/mkin_static/plot.mkinfit.html"><code>plot.mkinfit</code></a> and <a href="http://kinfit.r-forge.r-project.org/mkin_static/plot.mmkin.html"><code>plot.mmkin</code></a>, and at the package vignettes <a href="http://kinfit.r-forge.r-project.org/mkin_static/vignettes/FOCUS_L.html"><code>FOCUS L</code></a> and <a href="http://kinfit.r-forge.r-project.org/mkin_static/vignettes/FOCUS_D.html"><code>FOCUS D</code></a>.</p> -<h2 id="documentation">Documentation</h2> +</div> +<div id="documentation" class="section level2"> +<h2 class="hasAnchor"> +<a href="#documentation" class="anchor"> </a>Documentation</h2> <p>The <a href="http://kinfit.r-forge.r-project.org/mkin_static">HTML documentation</a> is maintained at the R-Forge project site.</p> -<h2 id="features">Features</h2> -<ul> -<li>Highly flexible model specification using <a href="http://kinfit.r-forge.r-project.org/mkin_static/mkinmod.html"><code>mkinmod</code></a>, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.</li> +</div> +<div id="features" class="section level2"> +<h2 class="hasAnchor"> +<a href="#features" class="anchor"> </a>Features</h2> +<ul><li>Highly flexible model specification using <a href="http://kinfit.r-forge.r-project.org/mkin_static/mkinmod.html"><code>mkinmod</code></a>, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.</li> <li>As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example <a href="http://kinfit.r-forge.r-project.org/mkin_static/plot.mmkin.html"><code>plot.mmkin</code></a>.</li> <li>Model solution (forward modelling) in the function <a href="http://kinfit.r-forge.r-project.org/mkin_static/mkinpredict.html"><code>mkinpredict</code></a> is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the <code>deSolve</code> package (default is <code>lsoda</code>).</li> <li>If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see<br><a href="http://kinfit.r-forge.r-project.org/mkin_static/vignettes/compiled_models.html">vignette <code>compiled_models</code></a>. The autogeneration of C code was inspired by the <a href="https://github.com/karlines/ccSolve"><code>ccSolve</code></a> package. Thanks to Karline Soetaert for her work on that.</li> @@ -98,12 +73,20 @@ <li>The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.</li> <li>Iteratively reweighted least squares fitting is implemented in a similar way as in KinGUII and CAKE (see below). Simply add the argument <code>reweight = "obs"</code> to your call to <code>mkinfit</code> and a separate variance componenent for each of the observed variables will be optimised in a second stage after the primary optimisation algorithm has converged.</li> <li>When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite.</li> -</ul> -<h2 id="gui">GUI</h2> +</ul></div> +<div id="gui" class="section level2"> +<h2 class="hasAnchor"> +<a href="#gui" class="anchor"> </a>GUI</h2> <p>There is a graphical user interface that I consider useful for real work. Please refer to its <a href="http://kinfit.r-forge.r-project.org/gmkin_static">documentation page</a> for installation instructions and a manual.</p> -<h2 id="news">News</h2> +</div> +<div id="news" class="section level2"> +<h2 class="hasAnchor"> +<a href="#news" class="anchor"> </a>News</h2> <p>Yes, there is a ChangeLog, for the latest <a href="http://cran.r-project.org/web/packages/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> -<h2 id="credits-and-historical-remarks">Credits and historical remarks</h2> +</div> +<div id="credits-and-historical-remarks" class="section level2"> +<h2 class="hasAnchor"> +<a href="#credits-and-historical-remarks" class="anchor"> </a>Credits and historical remarks</h2> <p><code>mkin</code> would not be possible without the underlying software stack consisting of R and the packages <a href="http://cran.r-project.org/package=deSolve">deSolve</a> and <a href="http://cran.r-project.org/package=FME">FME</a>, to say the least.</p> <p>It could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). <code>mkin</code> greatly profits from and largely follows the work done by the <a href="http://focus.jrc.ec.europa.eu/dk">FOCUS Degradation Kinetics Workgroup</a>, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.</p> <p>Also, it was inspired by the first version of KinGUI developed by BayerCropScience, which is based on the MatLab runtime environment.</p> @@ -112,16 +95,41 @@ <p>In 2011, Bayer Crop Science started to distribute an R based successor to KinGUI named KinGUII whose R code is based on <code>mkin</code>, but which added, amongst other refinements, a closed source graphical user interface (GUI), iteratively reweighted least squares (IRLS) optimisation of the variance for each of the observed variables, and Markov Chain Monte Carlo (MCMC) simulation functionality, similar to what is available e.g. in the <code>FME</code> package.</p> <p>Somewhat in parallel, Syngenta has sponsored the development of an <code>mkin</code> and KinGUII based GUI application called CAKE, which also adds IRLS and MCMC, is more limited in the model formulation, but puts more weight on usability. CAKE is available for download from the <a href="http://projects.tessella.com/cake">CAKE website</a>, where you can also find a zip archive of the R scripts derived from <code>mkin</code>, published under the GPL license.</p> <p>Finally, there is <a href="http://github.com/zhenglei-gao/KineticEval">KineticEval</a>, which contains a further development of the scripts used for KinGUII, so the different tools will hopefully be able to learn from each other in the future as well.</p> -<h2 id="development">Development</h2> +</div> +<div id="development" class="section level2"> +<h2 class="hasAnchor"> +<a href="#development" class="anchor"> </a>Development</h2> <p>Contributions are welcome! Your <a href="https://help.github.com/articles/fork-a-repo">mkin fork</a> is just a mouse click away… The master branch on github should always be in good shape, I implement new features in separate branches now. If you prefer subversion, project members for the <a href="http://r-forge.r-project.org/R/?group_id=615">r-forge project</a> are welcome as well. Generally, the source code of the latest CRAN version should be available there. You can also browse the source code at <a href="http://cgit.jrwb.de/mkin">cgit.jrwb.de/mkin</a>.</p> - +</div> +</div> </div> + + <div class="col-md-3" id="sidebar"> + <h2>Links</h2><ul class="list-unstyled"><li>Download from CRAN at <a href="https://cran.r-project.org/package=mkin">https://cran.r-project.org/package=mkin</a></li> +<li>Browse source code at <a href="http://kinfit.r-forge.r-project.org/mkin_static%0A%20%20%20%20%20http://github.com/jranke/mkin">http://kinfit.r-forge.r-project.org/mkin_static + http://github.com/jranke/mkin</a></li> +<li>Report a bug at <a href="http://github.com/jranke/mkin/issues">http://github.com/jranke/mkin/issues</a></li> +</ul><h2>Authors</h2><ul class="list-unstyled"><li>Johannes Ranke<br><small class="roles">Author, maintainer, copyright holder</small></li> +<li>Katrin Lindenberger<br><small class="roles">Contributor</small></li> +<li>René Lehmann<br><small class="roles">Contributor</small></li> +<li>Eurofins Regulatory AG<br><small class="roles">Copyright holder</small></li> +</ul><h2>License</h2> +<p>GPL</p> + + <html><body><h2>Dev status</h2><ul class="list-unstyled"><li><a href="http://cran.r-project.org/package=mkin"> + <img src="http://www.r-pkg.org/badges/version/mkin"></a></li> +</ul></body></html></div> +</div> + + + <footer><div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> </div> - <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. 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SVG Version: 6.00 Build 0) --> +<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px" + viewBox="0 0 20 20" style="enable-background:new 0 0 20 20;" xml:space="preserve"> +<style type="text/css"> + .st0{fill:#75AADB;} +</style> +<path class="st0" d="M4,11.3h1.3v1.3H4c-2,0-4-2.3-4-4.7s2.1-4.7,4-4.7h5.3c1.9,0,4,2.3,4,4.7c0,1.9-1.2,3.6-2.7,4.3v-1.5 + C11.4,10.2,12,9.1,12,8c0-1.7-1.4-3.3-2.7-3.3H4C2.7,4.7,1.3,6.3,1.3,8S2.7,11.3,4,11.3z M16,7.3h-1.3v1.3H16c1.3,0,2.7,1.6,2.7,3.3 + s-1.4,3.3-2.7,3.3h-5.3C9.4,15.3,8,13.7,8,12c0-1.1,0.6-2.2,1.3-2.8V7.7C7.9,8.4,6.7,10.1,6.7,12c0,2.4,2.1,4.7,4,4.7H16 + c1.9,0,4-2.3,4-4.7S18,7.3,16,7.3z"/> +</svg> diff --git a/docs/news/index.html b/docs/news/index.html index 4e321474..b30b400f 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -6,14 +6,13 @@ <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>All news • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-news"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,30 +67,43 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> <div class="row"> + <div class="col-md-9"> - <div id="mkin-0.9.45" class="section level1"> -<h1>mkin 0.9.45</h1> + <div class="page-header"> + <h1>Change log <small>All releases</small></h1> + </div> + + <div class="contents"> + <div id="mkin-0-9-45" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-45" class="anchor"> </a>mkin 0.9.45</h1> <div id="minor-changes" class="section level2"> -<h2>Minor changes</h2> +<h2 class="hasAnchor"> +<a href="#minor-changes" class="anchor"> </a>Minor changes</h2> <ul><li> <code>plot.mkinfit</code>: Plotting does not fail any more when the compiled model is not available, e.g. because it was removed from the temporary directory. In this case, the uncompiled model is now used for plotting</li> </ul></div> </div> - <div id="mkin-0.9.44-2016-06-29" class="section level1"> -<h1>mkin 0.9.44 (2016-06-29)</h1> + <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> <div id="bug-fixes" class="section level2"> -<h2>Bug fixes</h2> +<h2 class="hasAnchor"> +<a href="#bug-fixes" class="anchor"> </a>Bug fixes</h2> <ul><li>The test <code>test_FOMC_ill-defined</code> failed on several architectures, so the test is now skipped</li> </ul></div> </div> - <div id="mkin-0.9.43-2016-06-28" class="section level1"> -<h1>mkin 0.9.43 (2016-06-28)</h1> + <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> <div id="major-changes" class="section level2"> -<h2>Major changes</h2> +<h2 class="hasAnchor"> +<a href="#major-changes" class="anchor"> </a>Major changes</h2> <ul><li><p>The title was changed to <code>Kinetic evaluations of chemical degradation data</code></p></li> <li><p><code>plot.mkinfit</code>: Add the possibility to show fits (and residual plots if requested) separately for the observed variables</p></li> <li><p><code>plot.mkinfit</code>: Add the possibility to show the chi2 error levels in the plot, similar to the way they are shown in <code>plot.mmkin</code></p></li> @@ -99,7 +112,8 @@ <li><p>The function <code>add_err</code> was added to the package, making it easy to generate simulated data using an error model based on the normal distribution</p></li> </ul></div> <div id="minor-changes-1" class="section level2"> -<h2>Minor changes</h2> +<h2 class="hasAnchor"> +<a href="#minor-changes-1" class="anchor"> </a>Minor changes</h2> <ul><li><p>Remove an outdated reference to the inline package in the <code>compiled_models</code> vignette</p></li> <li><p><code>mkinfit</code>: Do not error out in cases where the fit converges, but the Jacobian for the untransformed model cost can not be estimated. Give a warning instead and return NA for the t-test results.</p></li> <li><p><code>summary.mkinfit</code>: Give a warning message when the covariance matrix can not be obtained.</p></li> @@ -108,155 +122,187 @@ <li><p><code>mkinfit</code>: Return the <code>err</code> values used on weighted fits as a column named <code>err</code>. Also include these inverse weights when the column <code>value</code> in the observed data is used, which is returned as <code>observed</code> in the data component of the mkinfit object.</p></li> </ul></div> <div id="bug-fixes-1" class="section level2"> -<h2>Bug fixes</h2> +<h2 class="hasAnchor"> +<a href="#bug-fixes-1" class="anchor"> </a>Bug fixes</h2> <ul><li><p><code>endpoints</code>: When the name of a substance degrading to a metabolite (e.g. a parent compound) used in the model formulation ended in the letter <code>f</code>, some rate parameters could be listed as formation fractions with mixed up names. These would also appear in the summary.</p></li> <li><p><code>mkinfit</code>: Check for all observed variables when checking if the user tried to fix formation fractions when fitting them using ilr transformation.</p></li> <li><p><code>plot.mmkin</code>: Set the plot margins correctly, also in the case of a single fit to be plotted, so the main title is placed in a reasonable way.</p></li> <li><p><code>plot.mkinfit</code>: Correct default values for <code>col_obs</code>, <code>pch_obs</code> and <code>lty_obs</code> for the case that <code>obs_vars</code> is specified.</p></li> </ul></div> </div> - <div id="mkin-0.9.42-2016-03-25" class="section level1"> -<h1>mkin 0.9.42 (2016-03-25)</h1> + <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> <div id="major-changes-1" class="section level2"> -<h2>Major changes</h2> +<h2 class="hasAnchor"> +<a href="#major-changes-1" class="anchor"> </a>Major changes</h2> <ul><li>Add the argument <code>from_max_mean</code> to <code>mkinfit</code>, for fitting only the decline from the maximum observed value for models with a single observed variable</li> </ul></div> <div id="minor-changes-2" class="section level2"> -<h2>Minor changes</h2> +<h2 class="hasAnchor"> +<a href="#minor-changes-2" class="anchor"> </a>Minor changes</h2> <ul><li><p>Add plots to <code>compiled_models</code> vignette</p></li> <li><p>Give an explanatory error message when mkinmod fails due to a missing definition of a target variable</p></li> <li><p><code><a href="../reference/print.mkinmod.html">print.mkinmod()</a></code>: Improve formatting when printing mkinmod model definitions</p></li> </ul></div> </div> - <div id="mkin-0.9-41-2015-11-09" class="section level1"> -<h1>mkin 0.9-41 (2015-11-09)</h1> + <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> <div id="minor-changes-3" class="section level2"> -<h2>Minor changes</h2> +<h2 class="hasAnchor"> +<a href="#minor-changes-3" class="anchor"> </a>Minor changes</h2> <ul><li><p>Add an R6 class <code>mkinds</code> representing datasets with a printing method</p></li> <li><p>Add a printing method for mkinmod objects</p></li> <li><p>Make it possible to specify arbitrary strings as names for the compounds in <code>mkinmod</code>, and show them in the plot</p></li> <li><p>Use an index.r file to group help topics in static documentation</p></li> </ul></div> <div id="bug-fixes-2" class="section level2"> -<h2>Bug fixes</h2> +<h2 class="hasAnchor"> +<a href="#bug-fixes-2" class="anchor"> </a>Bug fixes</h2> <ul><li> <code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36</li> </ul></div> </div> - <div id="mkin-0.9-40-2015-07-21" class="section level1"> -<h1>mkin 0.9-40 (2015-07-21)</h1> + <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> <div id="bug-fixes-3" class="section level2"> -<h2>Bug fixes</h2> +<h2 class="hasAnchor"> +<a href="#bug-fixes-3" class="anchor"> </a>Bug fixes</h2> <ul><li> <code><a href="../reference/endpoints.html">endpoints()</a></code>: For DFOP and SFORB models, where <code>optimize()</code> is used, make use of the fact that the DT50 must be between DT50_k1 and DT50_k2 (DFOP) or DT50_b1 and DT50_b2 (SFORB), as <code>optimize()</code> sometimes did not find the minimum. Likewise for finding DT90 values. Also fit on the log scale to make the function more efficient.</li> </ul></div> <div id="internal-changes" class="section level2"> -<h2>Internal changes</h2> +<h2 class="hasAnchor"> +<a href="#internal-changes" class="anchor"> </a>Internal changes</h2> <ul><li> <code>DESCRIPTION</code>, <code>NAMESPACE</code>, <code>R/*.R</code>: Import (from) stats, graphics and methods packages, and qualify some function calls for non-base packages installed with R to avoid NOTES made by R CMD check –as-cran with upcoming R versions.</li> </ul></div> </div> - <div id="mkin-0.9-39-2015-06-26" class="section level1"> -<h1>mkin 0.9-39 (2015-06-26)</h1> + <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> <div id="major-changes-2" class="section level2"> -<h2>Major changes</h2> +<h2 class="hasAnchor"> +<a href="#major-changes-2" class="anchor"> </a>Major changes</h2> <ul><li><p>New function <code><a href="../reference/mmkin.html">mmkin()</a></code>: This function takes a character vector of model shorthand names, or alternatively a list of mkinmod models, as well as a list of dataset as main arguments. It returns a matrix of mkinfit objects, with a row for each model and a column for each dataset. A subsetting method with single brackets is available. Fitting the models in parallel using the <code>parallel</code> package is supported.</p></li> <li><p>New function <code><a href="../reference/plot.mmkin.html">plot.mmkin()</a></code>: Plots single-row or single-column <code>mmkin</code> objects including residual plots.</p></li> </ul></div> <div id="bug-fixes-4" class="section level2"> -<h2>Bug fixes</h2> +<h2 class="hasAnchor"> +<a href="#bug-fixes-4" class="anchor"> </a>Bug fixes</h2> <ul><li> <code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Fix the x axis scaling for rate constants and formation fractions that got confused by the introduction of the t-values of transformed parameters.</li> </ul></div> </div> - <div id="mkin-0.9-38-2015-06-24" class="section level1"> -<h1>mkin 0.9-38 (2015-06-24)</h1> + <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> <div id="minor-changes-4" class="section level2"> -<h2>Minor changes</h2> +<h2 class="hasAnchor"> +<a href="#minor-changes-4" class="anchor"> </a>Minor changes</h2> <ul><li><p><code>vignettes/compiled_models.html</code>: Show the performance improvement factor actually obtained when building the vignette, as well as mkin version, some system info and the CPU model used for building the vignette.</p></li> <li><p><code>GNUMakefile</code>,<code>vignettes/*</code>: Clean up vignette generation and include table of contents in HTML vignettes.</p></li> </ul></div> <div id="bug-fixes-5" class="section level2"> -<h2>Bug fixes</h2> +<h2 class="hasAnchor"> +<a href="#bug-fixes-5" class="anchor"> </a>Bug fixes</h2> <ul><li> <code><a href="../reference/mkinmod.html">mkinmod()</a></code>: When generating the C code for the derivatives, only declare the time variable when it is needed and remove the ‘-W-no-unused-variable’ compiler flag as the C compiler used in the CRAN checks on Solaris does not know it.</li> </ul></div> </div> - <div id="mkin-0.9-36-2015-06-21" class="section level1"> -<h1>mkin 0.9-36 (2015-06-21)</h1> + <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> <div id="major-changes-3" class="section level2"> -<h2>Major changes</h2> +<h2 class="hasAnchor"> +<a href="#major-changes-3" class="anchor"> </a>Major changes</h2> <ul><li><p><code><a href="../reference/summary.mkinfit.html">summary.mkinfit()</a></code>: A one-sided t-test for significant difference of untransformed parameters from zero is now always shown, based on the assumption of normal distribution for estimators of all untransformed parameters. Use with caution, as this assumption is unrealistic e.g. for rate constants in these nonlinear kinetic models.</p></li> <li><p>If a compiler (gcc) is installed, use a version of the differential equation model compiled from C code, which is a huge performance boost for models where only the deSolve method works.</p></li> <li><p><code><a href="../reference/mkinmod.html">mkinmod()</a></code>: Create a list component $cf (of class CFuncList) in the list returned by mkinmod, if a version can be compiled from autogenerated C code (see above).</p></li> <li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: Set the default <code>solution_type</code> to <code>deSolve</code> when a compiled version of the model is present, except when an analytical solution is possible.</p></li> </ul></div> <div id="minor-changes-5" class="section level2"> -<h2>Minor changes</h2> +<h2 class="hasAnchor"> +<a href="#minor-changes-5" class="anchor"> </a>Minor changes</h2> <ul><li>Added a simple showcase vignette with an evaluation of FOCUS example dataset D</li> </ul></div> </div> - <div id="mkin-0.9-35-2015-05-15" class="section level1"> -<h1>mkin 0.9-35 (2015-05-15)</h1> + <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> <div id="major-changes-4" class="section level2"> -<h2>Major changes</h2> +<h2 class="hasAnchor"> +<a href="#major-changes-4" class="anchor"> </a>Major changes</h2> <ul><li>Switch from RUnit to testthat for testing</li> </ul></div> <div id="bug-fixes-6" class="section level2"> -<h2>Bug fixes</h2> +<h2 class="hasAnchor"> +<a href="#bug-fixes-6" class="anchor"> </a>Bug fixes</h2> <ul><li><p><code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit</p></li> <li><p><code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Fix printing the summary for the case that the number of iterations is not available</p></li> <li><p>NAMESPACE: export S3 methods plot.mkinfit, summary.mkinfit and print.summary.mkinfit to satisfy R CMD check on R-devel</p></li> <li><p><code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Avoid warning in R CMD check about undeclared global variable <code>Lower</code></p></li> </ul></div> <div id="new-features" class="section level2"> -<h2>New features</h2> +<h2 class="hasAnchor"> +<a href="#new-features" class="anchor"> </a>New features</h2> <ul><li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: Report successful termination when quiet = FALSE. This is helpful for more difficult problems fitted with reweight.method = obs, as no progress is often indicated during the reweighting.</p></li> <li><p>A first test using results established in the expertise written for the German Federal Environmental Agency (UBA) was added.</p></li> <li><p>Add synthetic datasets generated for expertise written for the German Federal Environmental Agency UBA</p></li> <li><p>Add tests based on these datasets</p></li> </ul></div> </div> - <div id="mkin-0.9-34-2014-11-22" class="section level1"> -<h1>mkin 0.9-34 (2014-11-22)</h1> + <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> <div id="new-features-1" class="section level2"> -<h2>New features</h2> +<h2 class="hasAnchor"> +<a href="#new-features-1" class="anchor"> </a>New features</h2> <ul><li><p>Add the convenience function <code><a href="../reference/mkinsub.html">mkinsub()</a></code> for creating the lists used in <code><a href="../reference/mkinmod.html">mkinmod()</a></code></p></li> <li><p>Add the possibility to fit indeterminate order rate equation (IORE) models using an analytical solution (parent only) or a numeric solution. Paths from IORE compounds to metabolites are supported when using formation fractions (use_of_ff = ‘max’). Note that the numerical solution (method.ode = ‘deSolve’) of the IORE differential equations sometimes fails due to numerical problems.</p></li> <li><p>Switch to using the Port algorithm (using a model/trust region approach) per default. While needing more iterations than the Levenberg-Marquardt algorithm previously used per default, it is less sensitive to starting parameters.</p></li> </ul></div> <div id="minor-changes-6" class="section level2"> -<h2>Minor changes</h2> +<h2 class="hasAnchor"> +<a href="#minor-changes-6" class="anchor"> </a>Minor changes</h2> <ul><li><p>The formatting of differential equations in the summary was further improved</p></li> <li><p>Always include 0 on y axis when plotting during the fit</p></li> </ul></div> </div> - <div id="mkin-0.9-33-2014-10-22" class="section level1"> -<h1>mkin 0.9-33 (2014-10-22)</h1> + <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> <div id="new-features-2" class="section level2"> -<h2>New features</h2> +<h2 class="hasAnchor"> +<a href="#new-features-2" class="anchor"> </a>New features</h2> <ul><li><p>The initial value (state.ini) for the observed variable with the highest observed residue is set to 100 in case it has no time zero observation and <code>state.ini = "auto"</code></p></li> <li><p>A basic unit test for <code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code> was written</p></li> </ul></div> <div id="bug-fixes-7" class="section level2"> -<h2>Bug fixes</h2> +<h2 class="hasAnchor"> +<a href="#bug-fixes-7" class="anchor"> </a>Bug fixes</h2> <ul><li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: The internally fitted parameter for <code>g</code> was named <code>g_ilr</code> even when <code>transform_fractions=FALSE</code></p></li> <li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: The initial value (state.ini) for the parent compound was not set when the parent was not the (only) variable with the highest value in the observed data.</p></li> <li><p><code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code>: When checking for degrees of freedom for metabolites, check if their time zero value is fixed instead of checking if the observed value is zero. This ensures correct calculation of degrees of freedom also in cases where the metabolite residue at time zero is greater zero.</p></li> <li><p><code><a href="../reference/plot.mkinfit.html">plot.mkinfit()</a></code>: Avoid a warning message about only using the first component of ylim that occurred when ylim was specified explicitly</p></li> </ul></div> <div id="minor-changes-7" class="section level2"> -<h2>Minor changes</h2> +<h2 class="hasAnchor"> +<a href="#minor-changes-7" class="anchor"> </a>Minor changes</h2> <ul><li><p>The formatting of differential equations in the summary was improved by wrapping overly long lines</p></li> <li><p>The FOCUS_Z vignette was rebuilt with the above improvement and using a width of 70 to avoid output outside of the grey area</p></li> <li><p><code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Avoid a warning that occurred when gmkin showed summaries ofinitial fits without iterations</p></li> <li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: Avoid a warning that occurred when summarising a fit that was performed with maxitmodFit = 0 as done in gmkin for configuring new fits.</p></li> </ul></div> </div> - <div id="mkin-0.9-32-2014-07-24" class="section level1"> -<h1>mkin 0.9-32 (2014-07-24)</h1> + <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> <div id="new-features-3" class="section level2"> -<h2>New features</h2> +<h2 class="hasAnchor"> +<a href="#new-features-3" class="anchor"> </a>New features</h2> <ul><li><p>The number of degrees of freedom is difficult to define in the case of ilr transformation of formation fractions. Now for each source compartment the number of ilr parameters (=number of optimised parameters) is divided by the number of pathways to metabolites (=number of affected data series) which leads to fractional degrees of freedom in some cases.</p></li> <li><p>The default for the initial value for the first state value is now taken from the mean of the observations at time zero, if available.</p></li> <li><p>The kinetic model can alternatively be specified with a shorthand name for parent only degradation models, e.g. <code>SFO</code>, or <code>DFOP</code>.</p></li> @@ -265,7 +311,8 @@ <li><p>mkinfit gives a warning when the fit does not converge (does not apply to SANN method). This warning is included in the summary.</p></li> </ul></div> <div id="bug-fixes-8" class="section level2"> -<h2>Bug fixes</h2> +<h2 class="hasAnchor"> +<a href="#bug-fixes-8" class="anchor"> </a>Bug fixes</h2> <ul><li><p>Avoid plotting an artifical 0 residual at time zero in <code>mkinresplot</code></p></li> <li><p>In the determination of the degrees of freedom in <code>mkinerrmin</code>, formation fractions were accounted for multiple times in the case of parallel formation of metabolites. See the new feature described above for the solution.</p></li> <li><p><code>transform_rates=FALSE</code> in <code>mkinfit</code> now also works for FOMC and HS models.</p></li> @@ -273,32 +320,39 @@ <li><p>No warning was given when the fit did not converge when a method other than the default Levenberg-Marquardt method <code>Marq</code> was used.</p></li> </ul></div> <div id="minor-changes-8" class="section level2"> -<h2>Minor changes</h2> +<h2 class="hasAnchor"> +<a href="#minor-changes-8" class="anchor"> </a>Minor changes</h2> <ul><li><p>Vignettes were rebuilt to reflect the changes in the summary method.</p></li> <li><p>Algorithm <code>Pseudo</code> was excluded because it needs user-defined parameter limits which are not supported.</p></li> <li><p>Algorithm <code>Newton</code> was excluded because of its different way to specify the maximum number of iterations and because it does not appear to provide additional benefits.</p></li> </ul></div> </div> - <div id="mkin-0.9-31-2014-07-14" class="section level1"> -<h1>mkin 0.9-31 (2014-07-14)</h1> + <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> <div id="bug-fixes-9" class="section level2"> -<h2>Bug fixes</h2> +<h2 class="hasAnchor"> +<a href="#bug-fixes-9" class="anchor"> </a>Bug fixes</h2> <ul><li>The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in <code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code> used by the summary function.</li> </ul></div> </div> - <div id="mkin-0.9-30-2014-07-11" class="section level1"> -<h1>mkin 0.9-30 (2014-07-11)</h1> + <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> <div id="new-features-4" class="section level2"> -<h2>New features</h2> +<h2 class="hasAnchor"> +<a href="#new-features-4" class="anchor"> </a>New features</h2> <ul><li>It is now possible to use formation fractions in combination with turning off the sink in <code><a href="../reference/mkinmod.html">mkinmod()</a></code>.</li> </ul></div> <div id="major-changes-5" class="section level2"> -<h2>Major changes</h2> +<h2 class="hasAnchor"> +<a href="#major-changes-5" class="anchor"> </a>Major changes</h2> <ul><li><p>The original and the transformed parameters now have different names (e.g. <code>k_parent</code> and <code>log_k_parent</code>. They also differ in how many they are when we have formation fractions but no pathway to sink.</p></li> <li><p>The order of some of the information blocks in <code>print.summary.mkinfit.R()</code> has been ordered in a more logical way.</p></li> </ul></div> <div id="minor-changes-9" class="section level2"> -<h2>Minor changes</h2> +<h2 class="hasAnchor"> +<a href="#minor-changes-9" class="anchor"> </a>Minor changes</h2> <ul><li><p>The vignette FOCUS_Z has been simplified to use formation fractions with turning off the sink, and slightly amended to use the new versions of DT50 values calculated since mkin 0.9-29.</p></li> <li><p>All vignettes have been rebuilt so they reflect all changes.</p></li> <li><p>The ChangeLog was renamed to NEWS.md and the entries were converted to markdown syntax compatible with the <code>tools::news()</code> function built into R.</p></li> @@ -307,20 +361,23 @@ <li><p>Some more checks were introduced to <code><a href="../reference/mkinfit.html">mkinfit()</a></code>, leading to warnings or stopping execution if unsupported combinations of methods and parameters are requested.</p></li> </ul></div> </div> - <div id="mkin-0.9-29-2014-06-27" class="section level1"> -<h1>mkin 0.9-29 (2014-06-27)</h1> + <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> <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> <li><p>R/endpoints.R, man/endpoints.Rd: Calculate additional (pseudo)-DT50 values for FOMC, DFOP, HS and SFORB. Avoid calculation of formation fractions from rate constants when they are directly fitted</p></li> </ul></div> - <div id="mkin-0.9-28-2014-05-20" class="section level1"> -<h1>mkin 0.9-28 (2014-05-20)</h1> + <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> <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> <li><p>Correct ‘isotropic’ into ‘isometric’ for the ilr transformation</p></li> </ul></div> - <div id="mkin-0.9-27-2014-05-10" class="section level1"> -<h1>mkin 0.9-27 (2014-05-10)</h1> + <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> <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> <li><p>Remove files belonging to the GUI</p></li> @@ -339,14 +396,16 @@ <li><p>Change the format of the workspace files of gmkin so they can be distributed and documented in the package</p></li> <li><p>Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin</p></li> </ul></div> - <div id="mkin-0.9-24-2013-11-06" class="section level1"> -<h1>mkin 0.9-24 (2013-11-06)</h1> + <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> <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> <li><p>Backtransform fixed ODE parameters for the summary</p></li> </ul></div> - <div id="mkin-0.9-22-2013-10-26" class="section level1"> -<h1>mkin 0.9-22 (2013-10-26)</h1> + <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> <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> <li><p>Do not use <code>plot=TRUE</code> in <code><a href="../reference/mkinfit.html">mkinfit()</a></code> example</p></li> @@ -360,32 +419,33 @@ <li><p>Do not use 0 values at time zero for chi2 error level calculations. This is the way it is done in KinGUII and it makes sense. It does impact the chi2 error levels in the output. Generally they seem to be lower for metabolites now, presumably because the mean of the observed values is higher</p></li> </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"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#mkin-0.9.45">0.9.45</a></li> - <li><a href="#mkin-0.9.44-2016-06-29">0.9.44</a></li> - <li><a href="#mkin-0.9.43-2016-06-28">0.9.43</a></li> - <li><a href="#mkin-0.9.42-2016-03-25">0.9.42</a></li> - <li><a href="#mkin-0.9-41-2015-11-09">0.9</a></li> - <li><a href="#mkin-0.9-40-2015-07-21">0.9</a></li> - <li><a href="#mkin-0.9-39-2015-06-26">0.9</a></li> - <li><a href="#mkin-0.9-38-2015-06-24">0.9</a></li> - <li><a href="#mkin-0.9-36-2015-06-21">0.9</a></li> - <li><a href="#mkin-0.9-35-2015-05-15">0.9</a></li> - <li><a href="#mkin-0.9-34-2014-11-22">0.9</a></li> - <li><a href="#mkin-0.9-33-2014-10-22">0.9</a></li> - <li><a href="#mkin-0.9-32-2014-07-24">0.9</a></li> - <li><a href="#mkin-0.9-31-2014-07-14">0.9</a></li> - <li><a href="#mkin-0.9-30-2014-07-11">0.9</a></li> - <li><a href="#mkin-0.9-29-2014-06-27">0.9</a></li> - <li><a href="#mkin-0.9-28-2014-05-20">0.9</a></li> - <li><a href="#mkin-0.9-27-2014-05-10">0.9</a></li> - <li><a href="#mkin-0.9-24-2013-11-06">0.9</a></li> - <li><a href="#mkin-0.9-22-2013-10-26">0.9</a></li> + <li><a href="#mkin-0-9-45">0.9.45</a></li> + <li><a href="#mkin-0-9-44-2016-06-29">0.9.44</a></li> + <li><a href="#mkin-0-9-43-2016-06-28">0.9.43</a></li> + <li><a href="#mkin-0-9-42-2016-03-25">0.9.42</a></li> + <li><a href="#mkin-0-9-41-2015-11-09">0.9-41</a></li> + <li><a href="#mkin-0-9-40-2015-07-21">0.9-40</a></li> + <li><a href="#mkin-0-9-39-2015-06-26">0.9-39</a></li> + <li><a href="#mkin-0-9-38-2015-06-24">0.9-38</a></li> + <li><a href="#mkin-0-9-36-2015-06-21">0.9-36</a></li> + <li><a href="#mkin-0-9-35-2015-05-15">0.9-35</a></li> + <li><a href="#mkin-0-9-34-2014-11-22">0.9-34</a></li> + <li><a href="#mkin-0-9-33-2014-10-22">0.9-33</a></li> + <li><a href="#mkin-0-9-32-2014-07-24">0.9-32</a></li> + <li><a href="#mkin-0-9-31-2014-07-14">0.9-31</a></li> + <li><a href="#mkin-0-9-30-2014-07-11">0.9-30</a></li> + <li><a href="#mkin-0-9-29-2014-06-27">0.9-29</a></li> + <li><a href="#mkin-0-9-28-2014-05-20">0.9-28</a></li> + <li><a href="#mkin-0-9-27-2014-05-10">0.9-27</a></li> + <li><a href="#mkin-0-9-24-2013-11-06">0.9-24</a></li> + <li><a href="#mkin-0-9-22-2013-10-26">0.9-22</a></li> </ul> </div> </div> @@ -393,7 +453,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 2edd2759..ec6cc73b 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -1,52 +1,103 @@ -body { - position: relative; +/* Sticker footer */ +body > .container { + display: flex; + padding-top: 60px; + min-height: calc(100vh); + flex-direction: column; } -.icon img { - float: right; - border: 1px solid #ccc; +body > .container .row { + flex: 1; } -.index .internal {display: none;} -ul.index li {margin-bottom: 0.5em; clear: both;} footer { margin-top: 45px; padding: 35px 0 36px; border-top: 1px solid #e5e5e5; + color: #666; + display: flex; +} +footer p { + margin-bottom: 0; +} +footer div { + flex: 1; +} +footer .pkgdown { + text-align: right; } footer p { margin-bottom: 0; - 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- $('#tocnav').affix({ - offset: { - top: $('#tocnav').offset().top - 80 - } - }); + $("#sidebar").stick_in_parent({offset_top: 40}); $('body').scrollspy({ - target: '#tocnav', - offset: 80 + target: '#sidebar', + offset: 60 }); }); diff --git a/docs/reference/DFOP.solution-2.png b/docs/reference/DFOP.solution-2.png Binary files differnew file mode 100644 index 00000000..91efcebb --- /dev/null +++ b/docs/reference/DFOP.solution-2.png diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 3422c206..5c90809c 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>DFOP.solution. mkin</title> +<title> + — DFOP.solution • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>Function describing decline from a defined starting value using the sum of two exponential decline functions.</p> @@ -84,7 +86,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>t</dt> <dd> Time. </dd> @@ -100,31 +102,49 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> - - <p>The value of the response variable at time <code>t</code>.</p> - </div> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <div class="References"> - <h2>References</h2> + <p>The value of the response variable at time <code>t</code>.</p> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">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><img src='unknown-2.png' alt='' width='540' height='400' /></pre> + + <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><img src='DFOP.solution-2.png' alt='' width='540' height='400' /></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index b513fac1..ee86854a 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>[.mmkin. mkin</title> +<title>Subsetting method for mmkin objects — [.mmkin • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,15 +67,16 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1>Subsetting method for mmkin objects</h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Subsetting method for mmkin objects</h1> + </div> -<div class="row"> - <div class="col-md-9"> <p>Subsetting method for mmkin objects.</p> @@ -83,10 +84,10 @@ <pre># S3 method for mmkin [(x, i, j, ..., drop = FALSE)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>x</dt> - <dd>An <code>mmkin object</code></dd> + <dd>An <code><a href='mmkin.html'>mmkin</a> object</code></dd> <dt>i</dt> <dd>Row index selecting the fits for specific models</dd> <dt>j</dt> @@ -98,15 +99,17 @@ a list of mkinfit objects or a single mkinfit object.</dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>An object of class <code>mmkin</code>.</p> - </div> + <p>An object of class <code><a href='mmkin.html'>mmkin</a></code>.</p> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'> <span class='co'># Only use one core, to pass R CMD check --as-cran</span> - <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='fu'>c</span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>), <span class='fu'>list</span>(<span class='kw'>B</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), + <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'>"SFO"</span>, <span class='st'>"FOMC"</span>), <span class='fu'>list</span>(<span class='kw'>B</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</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='no'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#> dataset #> model B C @@ -192,7 +195,7 @@ #> #> $time #> user system elapsed -#> 0.252 0.000 0.253 +#> 0.268 0.000 0.264 #> #> $mkinmod #> <mkinmod> model generated with @@ -378,7 +381,7 @@ #> } #> return(mC) #> } -#> <environment: 0x3e9c368> +#> <environment: 0x49c37f0> #> #> $cost_notrans #> function (P) @@ -400,7 +403,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x3e9c368> +#> <environment: 0x49c37f0> #> #> $hessian_notrans #> parent_0 alpha beta @@ -466,7 +469,7 @@ #> 99.66619 #> #> $date -#> [1] "Thu Oct 6 10:47:28 2016" +#> [1] "Wed Oct 26 23:16:41 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" @@ -547,7 +550,7 @@ #> #> $time #> user system elapsed -#> 0.064 0.000 0.067 +#> 0.072 0.004 0.074 #> #> $mkinmod #> <mkinmod> model generated with @@ -734,7 +737,7 @@ #> } #> return(mC) #> } -#> <environment: 0x3c1a660> +#> <environment: 0x4ae0880> #> #> $cost_notrans #> function (P) @@ -756,7 +759,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x3c1a660> +#> <environment: 0x4ae0880> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -819,7 +822,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Oct 6 10:47:28 2016" +#> [1] "Wed Oct 26 23:16:41 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" @@ -896,7 +899,7 @@ #> #> $time #> user system elapsed -#> 0.064 0.000 0.067 +#> 0.072 0.004 0.074 #> #> $mkinmod #> <mkinmod> model generated with @@ -1083,7 +1086,7 @@ #> } #> return(mC) #> } -#> <environment: 0x3c1a660> +#> <environment: 0x4ae0880> #> #> $cost_notrans #> function (P) @@ -1105,7 +1108,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x3c1a660> +#> <environment: 0x4ae0880> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1168,14 +1171,23 @@ #> 99.17407 #> #> $date -#> [1] "Thu Oct 6 10:47:28 2016" +#> [1] "Wed Oct 26 23:16:41 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" #> #> </div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -1184,7 +1196,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> 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 5c0faa43..61871ba9 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>FOCUS_2006_DFOP_ref_A_to_B. mkin</title> +<title> + — FOCUS_2006_DFOP_ref_A_to_B • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -87,10 +89,9 @@ in this fit.</p> <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span>)</pre> - <div class="Format"> - <h2>Format</h2> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>A data frame containing the following variables. + <p>A data frame containing the following variables. <dl class='dl-horizontal'> <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd> <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd> @@ -101,27 +102,45 @@ in this fit.</p> <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd> <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd> </dl></p> - </div> - - <div class="Source"> - <h2>Source</h2> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span>)</div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> 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 89faecbf..4fdb5f45 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>FOCUS_2006_FOMC_ref_A_to_F. mkin</title> +<title> + — FOCUS_2006_FOMC_ref_A_to_F • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -87,10 +89,9 @@ in this fit.</p> <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span>)</pre> - <div class="Format"> - <h2>Format</h2> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>A data frame containing the following variables. + <p>A data frame containing the following variables. <dl class='dl-horizontal'> <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd> <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd> @@ -100,27 +101,45 @@ in this fit.</p> <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd> <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd> </dl></p> - </div> - - <div class="Source"> - <h2>Source</h2> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span>)</div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> 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 2dfafec6..d9e43f4a 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>FOCUS_2006_HS_ref_A_to_F. mkin</title> +<title> + — FOCUS_2006_HS_ref_A_to_F • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -87,10 +89,9 @@ in this fit.</p> <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_HS_ref_A_to_F</span>)</pre> - <div class="Format"> - <h2>Format</h2> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>A data frame containing the following variables. + <p>A data frame containing the following variables. <dl class='dl-horizontal'> <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd> <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd> @@ -101,27 +102,45 @@ in this fit.</p> <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd> <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd> </dl></p> - </div> - - <div class="Source"> - <h2>Source</h2> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_HS_ref_A_to_F</span>)</div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> 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 ed3a4aff..68475b64 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>FOCUS_2006_SFO_ref_A_to_F. mkin</title> +<title> + — FOCUS_2006_SFO_ref_A_to_F • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -87,10 +89,9 @@ in this fit.</p> <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_SFO_ref_A_to_F</span>)</pre> - <div class="Format"> - <h2>Format</h2> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>A data frame containing the following variables. + <p>A data frame containing the following variables. <dl class='dl-horizontal'> <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd> <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd> @@ -99,27 +100,45 @@ in this fit.</p> <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd> <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd> </dl></p> - </div> - - <div class="Source"> - <h2>Source</h2> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_SFO_ref_A_to_F</span>)</div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index c1eacbd8..6221f53f 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>FOCUS_2006_datasets. mkin</title> +<title> + — FOCUS_2006_datasets • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,44 +68,45 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>Data taken from FOCUS (2006), p. 258.</p> <pre><span class='no'>FOCUS_2006_datasets</span></pre> - <div class="Format"> - <h2>Format</h2> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>6 datasets with observations on the following variables. + <p>6 datasets with observations on the following variables. <dl class='dl-horizontal'> <dt><code>name</code></dt><dd>a factor containing the name of the observed variable</dd> <dt><code>time</code></dt><dd>a numeric vector containing time points</dd> <dt><code>value</code></dt><dd>a numeric vector containing concentrations in percent of applied radioactivity</dd> </dl></p> - </div> - - <div class="Source"> - <h2>Source</h2> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='no'>FOCUS_2006_C</span></div><div class='output co'>#> name time value #> 1 parent 0 85.1 #> 2 parent 1 57.9 @@ -117,12 +119,29 @@ #> 9 parent 119 0.6 #> </div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/FOMC.solution-2.png b/docs/reference/FOMC.solution-2.png Binary files differnew file mode 100644 index 00000000..0efe8f07 --- /dev/null +++ b/docs/reference/FOMC.solution-2.png diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 912cf414..99d95fcb 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>FOMC.solution. mkin</title> +<title> First-Order Multi-Compartment kinetics — FOMC.solution • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,15 +67,16 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> First-Order Multi-Compartment kinetics </h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> First-Order Multi-Compartment kinetics </h1> + </div> -<div class="row"> - <div class="col-md-9"> <p>Function describing exponential decline from a defined starting value, with a decreasing rate constant.</p> @@ -87,7 +88,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>t</dt> <dd> Time. </dd> @@ -103,43 +104,61 @@ </dd> </dl> - <div class="Note"> - <h2>Note</h2> + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>The solution of the FOMC kinetic model reduces to the - <code>SFO.solution</code> for large values of <code>alpha</code> and + <p>The solution of the FOMC kinetic model reduces to the + <code><a href='SFO.solution.html'>SFO.solution</a></code> for large values of <code>alpha</code> and <code>beta</code> with \(k = \frac{\beta}{\alpha}\).</p> - </div> - - <div class="Value"> - <h2>Value</h2> - - <p>The value of the response variable at time <code>t</code>.</p> - </div> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <div class="References"> - <h2>References</h2> + <p>The value of the response variable at time <code>t</code>.</p> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <p>Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A + <p>Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A new model based on spatial variability. <em>Environmental Science and Technology</em> <b>24</b>, 1032-1038</p> - </div> - <h2 id="examples">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><img src='unknown-2.png' alt='' width='540' height='400' /></pre> + + <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><img src='FOMC.solution-2.png' alt='' width='540' height='400' /></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#note">Note</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/HS.solution-2.png b/docs/reference/HS.solution-2.png Binary files differnew file mode 100644 index 00000000..0bdb37a9 --- /dev/null +++ b/docs/reference/HS.solution-2.png diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 994f8373..06c6e3c1 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>HS.solution. mkin</title> +<title> Hockey-Stick kinetics — HS.solution • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,15 +67,16 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> Hockey-Stick kinetics </h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> Hockey-Stick kinetics </h1> + </div> -<div class="row"> - <div class="col-md-9"> <p>Function describing two exponential decline functions with a break point between them.</p> @@ -83,7 +84,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>t</dt> <dd> Time. </dd> @@ -99,31 +100,49 @@ according to <code>k2</code>. </dd> </dl> - <div class="Value"> - <h2>Value</h2> - - <p>The value of the response variable at time <code>t</code>.</p> - </div> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <div class="References"> - <h2>References</h2> + <p>The value of the response variable at time <code>t</code>.</p> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">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><img src='unknown-2.png' alt='' width='540' height='400' /></pre> + + <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><img src='HS.solution-2.png' alt='' width='540' height='400' /></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/IORE.solution-2.png b/docs/reference/IORE.solution-2.png Binary files differnew file mode 100644 index 00000000..df268b64 --- /dev/null +++ b/docs/reference/IORE.solution-2.png diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 06f5c1ad..58546489 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>IORE.solution. mkin</title> +<title> Indeterminate order rate equation kinetics — IORE.solution • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,15 +67,16 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> Indeterminate order rate equation kinetics </h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> Indeterminate order rate equation kinetics </h1> + </div> -<div class="row"> - <div class="col-md-9"> <p>Function describing exponential decline from a defined starting value, with a concentration dependent rate constant.</p> @@ -83,7 +84,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>t</dt> <dd> Time. </dd> @@ -95,53 +96,71 @@ <dd> Exponent describing the nonlinearity of the rate equation </dd> </dl> - <div class="Note"> - <h2>Note</h2> + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>The solution of the IORE kinetic model reduces to the - <code>SFO.solution</code> if N = 1. + <p>The solution of the IORE kinetic model reduces to the + <code><a href='SFO.solution.html'>SFO.solution</a></code> if N = 1. The parameters of the IORE model can be transformed to equivalent parameters of the FOMC mode - see the NAFTA guidance for details.</p> - </div> - - <div class="Value"> - <h2>Value</h2> - - <p>The value of the response variable at time <code>t</code>.</p> - </div> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <div class="References"> - <h2>References</h2> + <p>The value of the response variable at time <code>t</code>.</p> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for + <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> - </div> - <h2 id="examples">Examples</h2> + + <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><img src='unknown-2.png' alt='' width='540' height='400' /><div class='input'> <span class='no'>fit.fomc</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='no'>fit.iore</span> <span class='kw'><-</span> <span class='fu'>mkinfit</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'>mkinfit</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>) + <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><img src='IORE.solution-2.png' alt='' width='540' height='400' /><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>) <span class='fu'>print</span>(<span class='fu'>data.frame</span>(<span class='fu'>coef</span>(<span class='no'>fit.fomc</span>), <span class='fu'>coef</span>(<span class='no'>fit.iore</span>), <span class='fu'>coef</span>(<span class='no'>fit.iore.deS</span>), <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'>paste</span>(<span class='st'>"model par"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)))</div><div class='output co'>#> coef.fit.fomc. coef.fit.iore. coef.fit.iore.deS. #> model par 1 85.87489063 85.874891 85.874890 #> model par 2 0.05192238 -4.826631 -4.826631 #> model par 3 0.65096665 1.949403 1.949403 -#> </div><div class='input'> <span class='fu'>print</span>(<span class='fu'>rbind</span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'>endpoints</span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'>endpoints</span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>, - <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'>endpoints</span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>))</div><div class='output co'>#> DT50 DT90 DT50back +#> </div><div class='input'> <span class='fu'>print</span>(<span class='fu'>rbind</span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>, + <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>))</div><div class='output co'>#> DT50 DT90 DT50back #> fomc 1.785233 15.1479 4.559973 #> iore 1.785233 15.1479 4.559973 #> iore.deS 1.785233 15.1479 4.559973 #> </div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#note">Note</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 9cf069d7..b2d5526e 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>SFO.solution. mkin</title> +<title> Single First-Order kinetics — SFO.solution • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,22 +67,23 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> Single First-Order kinetics </h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> Single First-Order kinetics </h1> + </div> -<div class="row"> - <div class="col-md-9"> <p>Function describing exponential decline from a defined starting value.</p> <pre><span class='fu'>SFO.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>t</dt> <dd> Time. </dd> @@ -92,31 +93,49 @@ <dd> Kinetic constant. </dd> </dl> - <div class="Value"> - <h2>Value</h2> - - <p>The value of the response variable at time <code>t</code>.</p> - </div> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <div class="References"> - <h2>References</h2> + <p>The value of the response variable at time <code>t</code>.</p> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFO.solution(x, 100, 3), 0, 2)</span></div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 57959f26..135edb51 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>SFORB.solution. mkin</title> +<title> Single First-Order Reversible Binding kinetics — SFORB.solution • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,15 +67,16 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> Single First-Order Reversible Binding kinetics </h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> Single First-Order Reversible Binding kinetics </h1> + </div> -<div class="row"> - <div class="col-md-9"> <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 @@ -86,7 +87,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>t</dt> <dd> Time. </dd> @@ -100,32 +101,50 @@ <dd> Kinetic constant describing degradation of the free fraction. </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>The value of the response variable, which is the sum of free and bound + <p>The value of the response variable, which is the sum of free and bound fractions at time <code>t</code>.</p> - </div> - - <div class="References"> - <h2>References</h2> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)</span></div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/add_err-4.png b/docs/reference/add_err-4.png Binary files differnew file mode 100644 index 00000000..f3d04134 --- /dev/null +++ b/docs/reference/add_err-4.png diff --git a/docs/reference/add_err-6.png b/docs/reference/add_err-6.png Binary files differnew file mode 100644 index 00000000..05b27247 --- /dev/null +++ b/docs/reference/add_err-6.png diff --git a/docs/reference/add_err-8.png b/docs/reference/add_err-8.png Binary files differnew file mode 100644 index 00000000..b0182d2a --- /dev/null +++ b/docs/reference/add_err-8.png diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index cbc925ca..9020a486 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>add_err. mkin</title> +<title> + — add_err • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,19 +68,20 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>Normally distributed errors are added to data predicted for a specific - degradation model using <code>mkinpredict</code>. The variance of the error + 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> @@ -87,11 +89,11 @@ <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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>prediction</dt> <dd> - A prediction from a kinetic model as produced by <code>mkinpredict</code>. + A prediction from a kinetic model as produced by <code><a href='mkinpredict.html'>mkinpredict</a></code>. </dd> <dt>sdfunc</dt> <dd> @@ -123,31 +125,31 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A list of datasets compatible with <code>mmkin</code>, i.e. + <p>A list of datasets compatible with <code><a href='mmkin.html'>mmkin</a></code>, i.e. the components of the list are datasets compatible with - <code>mkinfit</code>.</p> - </div> - - <div class="References"> - <h2>References</h2> + <code><a href='mkinfit.html'>mkinfit</a></code>.</p> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <p>Ranke J and Lehmann R (2015) To t-test or not to t-test, that is the question. XV Symposium on Pesticide Chemistry 2-4 September 2015, Piacenza, Italy + <p>Ranke J and Lehmann R (2015) To t-test or not to t-test, that is the question. XV Symposium on Pesticide Chemistry 2-4 September 2015, Piacenza, Italy http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='co'># The kinetic model</span> -<span class='no'>m_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"M1"</span>), - <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> +<span class='no'>m_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'>M1</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'># Generate a prediction for a specific set of parameters</span> <span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>) <span class='co'># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span> <span class='co'># from 2015</span> -<span class='no'>d_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinpredict</span>(<span class='no'>m_SFO_SFO</span>, +<span class='no'>d_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fu'>log</span>(<span class='fl'>2</span>)/<span class='fl'>1000</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>), @@ -165,21 +167,32 @@ <span class='co'># Be quiet and use the faster Levenberg-Marquardt algorithm, as the datasets</span> <span class='co'># are easy and examples are run often. Use only one core not to offend CRAN</span> <span class='co'># checks</span> -<span class='no'>f_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='fu'>list</span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>m_SFO_SFO</span>), +<span class='no'>f_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>list</span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>m_SFO_SFO</span>), <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><img src='unknown-4.png' alt='' width='540' height='400' /><div class='input'> +<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>)</div><img src='add_err-4.png' alt='' width='540' height='400' /><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><img src='unknown-6.png' alt='' width='540' height='400' /><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><img src='add_err-6.png' alt='' width='540' height='400' /><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><img src='unknown-8.png' alt='' width='540' height='400' /><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><img src='add_err-8.png' alt='' width='540' height='400' /><div class='input'> </div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -188,7 +201,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 8ceb39d9..89e9cf52 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>endpoints. mkin</title> +<title> + — endpoints • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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, @@ -86,27 +88,34 @@ with the advantage that the SFORB model can also be used for metabolites.</p> <pre><span class='fu'>endpoints</span>(<span class='no'>fit</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>fit</dt> <dd> - An object of class <code>mkinfit</code>. + An object of class <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> </dl> - <div class="Note"> - <h2>Note</h2> + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>The function is used internally by <code>summary.mkinfit</code>.</p> - </div> + <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>A list with the components mentioned above.</p> + - <div class="Value"> - <h2>Value</h2> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#note">Note</a></li> + + <li><a href="#value">Value</a></li> + </ul> - <p>A list with the components mentioned above.</p> - </div> - </div> - <div class="col-md-3"> <h2>Author</h2> Johannes Ranke @@ -115,7 +124,14 @@ with the advantage that the SFORB model can also be used for metabolites.</p> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 1d9a9e66..793d893c 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>geometric_mean. mkin</title> +<title> Calculate the geometric mean — geometric_mean • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,22 +67,23 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> Calculate the geometric mean </h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> Calculate the geometric mean </h1> + </div> -<div class="row"> - <div class="col-md-9"> <p>Function calculating the geometric mean of numeric vectors</p> <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>x</dt> <dd> A numeric vector </dd> @@ -90,24 +91,42 @@ <dd> Should NA values be ignored </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>The geometric mean.</p> - </div> + <p>The geometric mean.</p> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] 3 #> </div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>))</div><div class='output co'>#> [1] NA #> </div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>), <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> [1] 1.732051 #> </div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 355cbb78..d249101d 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>ilr. mkin</title> +<title> + — ilr • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>This implementation is a special case of the class of isometric log-ratio transformations.</p> @@ -84,7 +86,7 @@ <pre><span class='fu'>ilr</span>(<span class='no'>x</span>) <span class='fu'>invilr</span>(<span class='no'>x</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>x</dt> <dd> @@ -93,26 +95,24 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>The result of the forward or backward transformation. The returned components always + <p>The result of the forward or backward transformation. The returned components always sum to 1 for the case of the inverse log-ratio transformation.</p> - </div> - - <div class="References"> - <h2>References</h2> - - <p>Peter Filzmoser, Karel Hron (2008) Outlier Detection for Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> - </div> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <div class="See also"> - <h2>See also</h2> + <p>Peter Filzmoser, Karel Hron (2008) Outlier Detection for Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> + + <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> + <p>Another implementation can be found in R package <code>robCompositions</code>.</p> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='co'># Order matters</span> <span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.1</span>, <span class='fl'>1</span>, <span class='fl'>10</span>))</div><div class='output co'>#> [1] -1.628174 -2.820079 #> </div><div class='input'><span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>10</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>))</div><div class='output co'>#> [1] 1.628174 2.820079 @@ -135,7 +135,20 @@ #> </div><div class='input'><span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'>sum</span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>]))) <span class='co'># Gives c(0.1, 0.3, 0.5)</span></div><div class='output co'>#> [1] 0.1 0.3 0.5 #> </div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#references">References</a></li> + + <li><a href="#see-also">See also</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> René Lehmann and Johannes Ranke @@ -144,7 +157,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/index.html b/docs/reference/index.html index 869f61dd..60d11171 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Function reference. mkin</title> +<title>Function reference • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-index"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,43 +67,61 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1>Function reference <small>version 0.9.44.9000</small></h1> -</div> - -<div class="row"> + <div class="row"> <div class="col-md-9"> - <div class="section "> - <h2>Main functions</h2> + <div class="page-header"> + <h1>Function reference</h1> + <h4>version 0.9.44.9000</h4> + </div> + + <div class="contents"> + <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> - <dl class="dl-horizontal"> - <dt><a href="mkinfit.html">mkinfit</a></dt> - <dd> -</dd> - <dt><a href="mkinmod.html">mkinmod</a></dt> - <dd> -</dd> - <dt><a href="mmkin.html">mmkin</a></dt> - <dd> -</dd> - </dl> - </div> - <div class="section "> - <h2>Show results</h2> + <p><a href="mkinfit.html"> +</a></p> + <ul> + <li><code><a href="mkinfit.html">mkinfit</a></code></li> + </ul> + <p><a href="mkinmod.html"> +</a></p> + <ul> + <li><code><a href="mkinmod.html">mkinmod</a></code></li> + </ul> + <p><a href="mmkin.html"> +</a></p> + <ul> + <li><code><a href="mmkin.html">mmkin</a></code></li> + </ul> + <h2 id="section-show-results" class="hasAnchor"><a href="#section-show-results" class="anchor"></a>Show results</h2> <p class="section-desc"></p> - <dl class="dl-horizontal"> - </dl> + </div> </div> + + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#section-main-functions">Main functions</a></li> + <li><a href="#section-show-results">Show results</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 63635f9a..7a96be3b 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mccall81_245T. mkin</title> +<title> + — mccall81_245T • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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 @@ -85,31 +87,31 @@ <pre><span class='no'>mccall81_245T</span></pre> - <div class="Format"> - <h2>Format</h2> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>A dataframe containing the following variables. + <p>A dataframe containing the following variables. <dl class='dl-horizontal'> <dt><code>name</code></dt><dd>the name of the compound observed. Note that T245 is used as an acronym for 2,4,5-T. T245 is a legitimate object name in R, which is necessary for specifying models using - <code>mkinmod</code>.</dd> + <code><a href='mkinmod.html'>mkinmod</a></code>.</dd> <dt><code>time</code></dt><dd>a numeric vector containing sampling times in days after treatment</dd> <dt><code>value</code></dt><dd>a numeric vector containing concentrations in percent of applied radioactivity</dd> <dt><code>soil</code></dt><dd>a factor containing the name of the soil</dd> </dl></p> - </div> - - <div class="Source"> - <h2>Source</h2> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 + <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 <a href = 'http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p> - </div> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>), + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> + <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>), <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>), <span class='kw'>anisole</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'>## Not run: ------------------------------------</span> <span class='co'># fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span> @@ -117,13 +119,13 @@ <span class='co'># </span> <span class='co'>## ---------------------------------------------</span> <span class='co'># No covariance matrix and k_phenol_sink is really small, therefore fix it to zero</span> - <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO_SFO</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='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</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'>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: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Thu Oct 6 10:47:34 2016 -#> Date of summary: Thu Oct 6 10:47:34 2016 +#> Date of fit: Wed Oct 26 23:16:47 2016 +#> Date of summary: Wed Oct 26 23:16:47 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -133,7 +135,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.492 s +#> Fitted with method Port using 246 model solutions performed in 1.487 s #> #> Weighting: none #> @@ -216,12 +218,29 @@ #> anisole 103.784 344.763 #> </div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 5b1a8353..d8b616c2 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkin_long_to_wide. mkin</title> +<title> + — mkin_long_to_wide • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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 @@ -85,7 +87,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>long_data</dt> <dd> @@ -103,13 +105,15 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>Dataframe in wide format.</p> - </div> + <p>Dataframe in wide format.</p> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='fu'>mkin_long_to_wide</span>(<span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#> time parent m1 #> 1 0 99.46 0.00 #> 2 0 102.04 0.00 @@ -135,7 +139,16 @@ #> 22 120 NA 33.31 #> </div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -144,7 +157,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 2a70ebbe..31207861 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkin_wide_to_long. mkin</title> +<title> + — mkin_wide_to_long • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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> @@ -84,7 +86,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>wide_data</dt> <dd> @@ -97,13 +99,15 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>Dataframe in long format as needed for <code>modCost</code>.</p> - </div> + <p>Dataframe in long format as needed for <code>modCost</code>.</p> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='no'>wide</span> <span class='kw'><-</span> <span class='fu'>data.frame</span>(<span class='kw'>t</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>2</span>,<span class='fl'>3</span>), <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>4</span>,<span class='fl'>7</span>), <span class='kw'>y</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>3</span>,<span class='fl'>4</span>,<span class='fl'>5</span>)) <span class='fu'>mkin_wide_to_long</span>(<span class='no'>wide</span>)</div><div class='output co'>#> name time value #> 1 x 1 1 @@ -114,7 +118,16 @@ #> 6 y 3 5 #> </div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -123,7 +136,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 0b4341aa..45cc315f 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinds. mkin</title> +<title>A dataset class for mkin — mkinds • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,52 +67,70 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1>A dataset class for mkin</h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>A dataset class for mkin</h1> + </div> -<div class="row"> - <div class="col-md-9"> <p>A dataset class for mkin</p> <pre><span class='no'>mkinds</span></pre> - <div class="Format"> - <h2>Format</h2> - - <p>An <code>R6Class</code> generator object.</p> - </div> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <div class="Fields"> - <h2>Fields</h2> + <p>An <code>R6Class</code> generator object.</p> + + <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2> - <p></p> - <p><dl class='dl-horizontal'> + <p></p> + <p><dl class='dl-horizontal'> <dt><code>title</code></dt><dd>A full title for the dataset</dd></p> - <p><dt><code>sampling</code></dt><dd>times The sampling times</dd></p> - <p><dt><code>time_unit</code></dt><dd>The time unit</dd></p> - <p><dt><code>observed</code></dt><dd>Names of the observed compounds</dd></p> - <p><dt><code>unit</code></dt><dd>The unit of the observations</dd></p> - <p><dt><code>replicates</code></dt><dd>The number of replicates</dd></p> - <p><dt><code>data</code></dt><dd>A dataframe with at least the columns name, time and value + <p><dt><code>sampling</code></dt><dd>times The sampling times</dd></p> + <p><dt><code>time_unit</code></dt><dd>The time unit</dd></p> + <p><dt><code>observed</code></dt><dd>Names of the observed compounds</dd></p> + <p><dt><code>unit</code></dt><dd>The unit of the observations</dd></p> + <p><dt><code>replicates</code></dt><dd>The number of replicates</dd></p> + <p><dt><code>data</code></dt><dd>A dataframe with at least the columns name, time and value in order to be compatible with mkinfit</dd> </dl></p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='no'>mds</span> <span class='kw'><-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>)</div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#fields">Fields</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index cd9faf1a..2e1833da 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinerrmin. mkin</title> +<title> + — mkinerrmin • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>This function uses <code>optimize</code> in order to iteratively find the smallest relative error still resulting in passing the chi-squared test @@ -85,11 +87,11 @@ as defined in the FOCUS kinetics report from 2006.</p> <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>fit</dt> <dd> - an object of class <code>mkinfit</code>. + an object of class <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> <dt>alpha</dt> <dd> @@ -97,52 +99,70 @@ as defined in the FOCUS kinetics report from 2006.</p> </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A dataframe with the following components:</p> - <p>The dataframe has one row for the total dataset and one further row for + <p>A dataframe with the following components:</p> + <p>The dataframe has one row for the total dataset and one further row for each observed state variable in the model.</p> - </div> - - <div class="Details"> - <h2>Details</h2> - - <p>This function is used internally by <code>summary.mkinfit</code>.</p> - </div> + + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - <div class="References"> - <h2>References</h2> + <p>This function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> + <pre class="examples"><div class='input'><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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), <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>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> -<span class='no'>fit_FOCUS_D</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'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='no'>fit_FOCUS_D</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'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_D</span>), <span class='fl'>4</span>)</div><div class='output co'>#> err.min n.optim df #> All data 0.0640 4 15 #> parent 0.0646 2 7 #> m1 0.0469 2 8 -#> </div><div class='input'><span class='no'>fit_FOCUS_E</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +#> </div><div class='input'><span class='no'>fit_FOCUS_E</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_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_E</span>), <span class='fl'>4</span>)</div><div class='output co'>#> err.min n.optim df #> All data 0.1544 4 13 #> parent 0.1659 2 7 #> m1 0.1095 2 6 #> </div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#details">Details</a></li> + + <li><a href="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 7acbbe5a..3c9bd05c 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinfit. mkin</title> +<title> + — mkinfit • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>This function uses the Flexible Modelling Environment package <code>FME</code> to create a function calculating the model cost, i.e. the @@ -86,7 +88,7 @@ Per default, parameters in the kinetic models are internally transformed in order to better satisfy the assumption of a normal distribution of their estimators. In each step of the optimsation, the kinetic model is solved using the - function <code>mkinpredict</code>. The variance of the residuals for each + function <code><a href='mkinpredict.html'>mkinpredict</a></code>. The variance of the residuals for each observed variable can optionally be iteratively reweighted until convergence using the argument <code>reweight.method = "obs"</code>.</p> @@ -111,11 +113,11 @@ <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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>mkinmod</dt> <dd> - A list of class <code>mkinmod</code>, containing the kinetic model to be + A list of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the kinetic model to be fitted to the data, or one of the shorthand names ("SFO", "FOMC", "DFOP", "HS", "SFORB"). If a shorthand name is given, a parent only degradation model is generated for the variable with the highest value in @@ -151,7 +153,7 @@ A named vector of initial values for the state variables of the model. In case the observed variables are represented by more than one model variable, the names will differ from the names of the observed variables - (see <code>map</code> component of <code>mkinmod</code>). The default is to set + (see <code>map</code> component of <code><a href='mkinmod.html'>mkinmod</a></code>). The default is to set the initial value of the first model variable to the mean of the time zero values for the variable with the maximum observed value, and all others to 0. If this variable has no time zero observations, its initial value is set to 100. @@ -187,18 +189,18 @@ otherwise "eigen" if the model can be expressed using eigenvalues and eigenvectors, and finally "deSolve" for the remaining models (time dependence of degradation rates and metabolites). This argument is passed - on to the helper function <code>mkinpredict</code>. + on to the helper function <code><a href='mkinpredict.html'>mkinpredict</a></code>. </dd> <dt>method.ode</dt> <dd> - The solution method passed via <code>mkinpredict</code> to + The solution method passed via <code><a href='mkinpredict.html'>mkinpredict</a></code> to <code>ode</code> in case the solution type is "deSolve". The default "lsoda" is performant, but sometimes fails to converge. </dd> <dt>use_compiled</dt> <dd> - If set to <code>FALSE</code>, no compiled version of the <code>mkinmod</code> - model is used, in the calls to <code>mkinpredict</code> even if + If set to <code>FALSE</code>, no compiled version of the <code><a href='mkinmod.html'>mkinmod</a></code> + model is used, in the calls to <code><a href='mkinpredict.html'>mkinpredict</a></code> even if a compiled verion is present. </dd> <dt>method.modFit</dt> @@ -251,7 +253,7 @@ to do transformations. If TRUE, the g parameter of the DFOP and HS models are also transformed, as they can also be seen as compositional data. The transformation used for these transformations is the - <code>ilr</code> transformation. + <code><a href='ilr.html'>ilr</a></code> transformation. </dd> <dt>plot</dt> <dd> @@ -290,7 +292,7 @@ <dt>n.outtimes</dt> <dd> The length of the dataseries that is produced by the model prediction - function <code>mkinpredict</code>. This impacts the accuracy of + function <code><a href='mkinpredict.html'>mkinpredict</a></code>. This impacts the accuracy of the numerical solver if that is used (see <code>solution_type</code> argument. The default value is 100. </dd> @@ -324,54 +326,50 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> - - <p>A list with "mkinfit" and "modFit" in the class attribute. - A summary can be obtained by <code>summary.mkinfit</code>.</p> - </div> - - <div class="See also"> - <h2>See also</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>Plotting methods <code>plot.mkinfit</code> and - <code>mkinparplot</code>.</p> - <p>Fitting of several models to several datasets in a single call to - <code>mmkin</code>.</p> - </div> + <p>A list with "mkinfit" and "modFit" in the class attribute. + A summary can be obtained by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> + + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <div class="Note"> - <h2>Note</h2> + <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> + + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>The implementation of iteratively reweighted least squares is inspired by the + <p>The implementation of iteratively reweighted least squares is inspired by the work of the KinGUII team at Bayer Crop Science (Walter Schmitt and Zhenglei Gao). A similar implemention can also be found in CAKE 2.0, which is the other GUI derivative of mkin, sponsored by Syngenta.</p> - </div> - - <div class="Note"> - <h2>Note</h2> + + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>When using the "IORE" submodel for metabolites, fitting with + <p>When using the "IORE" submodel for metabolites, fitting with "transform_rates = TRUE" (the default) often leads to failures of the numerical ODE solver. In this situation it may help to switch off the internal rate transformation.</p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <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: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Thu Oct 6 10:47:36 2016 -#> Date of summary: Thu Oct 6 10:47:36 2016 +#> Date of fit: Wed Oct 26 23:16:49 2016 +#> Date of summary: Wed Oct 26 23:16:49 2016 #> #> Equations: #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.152 s +#> Fitted with method Port using 64 model solutions performed in 0.148 s #> #> Weighting: none #> @@ -436,15 +434,15 @@ #> </div><div class='input'> <span class='co'># One parent compound, one metabolite, both single first order.</span> <span class='co'># Use mkinsub for convenience in model formulation. Pathway to sink included per default.</span> -<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( - <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</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'>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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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 -#> 1.240 1.280 0.973 +#> 1.224 1.196 0.913 #> </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'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff +#> </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 #> @@ -514,7 +512,22 @@ <span class='co'># summary(f.w.man.irls)</span> <span class='co'>## ---------------------------------------------</span></div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#see-also">See also</a></li> + + <li><a href="#note">Note</a></li> + + <li><a href="#note">Note</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -523,7 +536,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 9dd8fca0..53c87e92 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinmod. mkin</title> +<title> + — mkinmod • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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 @@ -89,7 +91,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>...</dt> <dd> @@ -131,41 +133,39 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A list of class <code>mkinmod</code> for use with <code>mkinfit</code>, containing</p> - </div> - - <div class="Note"> - <h2>Note</h2> + <p>A list of class <code>mkinmod</code> for use with <code><a href='mkinfit.html'>mkinfit</a></code>, containing</p> + + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>The IORE submodel is not well tested (yet). When using this model for metabolites, + <p>The IORE submodel is not well tested (yet). When using this model for metabolites, you may want to read the second note in the help page to - <code>mkinfit</code>.</p> - </div> - - <div class="References"> - <h2>References</h2> + <code><a href='mkinfit.html'>mkinfit</a></code>.</p> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for + <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='co'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span> <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)) <span class='co'># One parent compound, one metabolite, both single first order</span> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( - <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> + <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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'>## Not run: ------------------------------------</span> <span class='co'># # The above model used to be specified like this, before the advent of mkinsub()</span> <span class='co'># SFO_SFO <- mkinmod(</span> @@ -189,7 +189,20 @@ <span class='co'># quiet = TRUE)</span> <span class='co'>## ---------------------------------------------</span></div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#note">Note</a></li> + + <li><a href="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -198,7 +211,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinparplot-4.png b/docs/reference/mkinparplot-4.png Binary files differnew file mode 100644 index 00000000..77eafd95 --- /dev/null +++ b/docs/reference/mkinparplot-4.png diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index f2fae22d..6d4f2cfd 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinparplot. mkin</title> +<title> + — mkinparplot • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,45 +68,57 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>This function plots the confidence intervals for the parameters - fitted using <code>mkinfit</code>.</p> + fitted using <code><a href='mkinfit.html'>mkinfit</a></code>.</p> <pre><span class='fu'>mkinparplot</span>(<span class='no'>object</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>object</dt> <dd> - A fit represented in an <code>mkinfit</code> object. + A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object. </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> - </div> + <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + + <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'>T245</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</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><img src='unknown-4.png' alt='' width='540' height='400' /></pre> + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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><img src='mkinparplot-4.png' alt='' width='540' height='400' /></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -114,7 +127,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 51ca3992..925a6683 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinplot. mkin</title> +<title> + — mkinplot • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,41 +68,49 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> - <p>Deprecated function. It now only calls the plot method <code>plot.mkinfit</code>.</p> + <p>Deprecated function. It now only calls the plot method <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p> <pre><span class='fu'>mkinplot</span>(<span class='no'>fit</span>, <span class='no'>...</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>fit</dt> <dd> - an object of class <code>mkinfit</code>. + an object of class <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> <dt>&#8230;</dt> <dd> - further arguments passed to <code>plot.mkinfit</code>. + further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>. </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The function is called for its side effect.</p> + + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + </ul> - <p>The function is called for its side effect.</p> - </div> - </div> - <div class="col-md-3"> <h2>Author</h2> Johannes Ranke @@ -110,7 +119,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 5b7cdb32..cf04c6b6 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinpredict. mkin</title> +<title> + — mkinpredict • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,19 +68,20 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>This function produces a time series for all the observed variables in a - kinetic model as specified by <code>mkinmod</code>, using a specific set of + 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> @@ -87,11 +89,11 @@ <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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>mkinmod</dt> <dd> - A kinetic model as produced by <code>mkinmod</code>. + A kinetic model as produced by <code><a href='mkinmod.html'>mkinmod</a></code>. </dd> <dt>odeparms</dt> <dd> @@ -125,7 +127,7 @@ </dd> <dt>use_compiled</dt> <dd> - If set to <code>FALSE</code>, no compiled version of the <code>mkinmod</code> + If set to <code>FALSE</code>, no compiled version of the <code><a href='mkinmod.html'>mkinmod</a></code> model is used, even if is present. </dd> <dt>atol</dt> @@ -149,14 +151,16 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A matrix in the same format as the output of <code>ode</code>.</p> - </div> + <p>A matrix in the same format as the output of <code>ode</code>.</p> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)) + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> + <pre class="examples"><div class='input'> <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)) <span class='co'># Compare solution types</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)</div><div class='output co'>#> time degradinol @@ -277,31 +281,40 @@ #> 2001 20 0.2478752 #> </div><div class='input'> <span class='co'># Check compiled model versions - they are faster than the eigenvalue based solutions!</span> - <span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), <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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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'>"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 -#> 0.008 0.020 0.004 +#> 0.008 0.024 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 -#> 0.016 0.004 0.003 +#> 0.000 0.020 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 -#> 0.032 0.000 0.034 +#> 0.036 0.000 0.035 #> </div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -310,7 +323,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinresplot-4.png b/docs/reference/mkinresplot-4.png Binary files differnew file mode 100644 index 00000000..7dbd7522 --- /dev/null +++ b/docs/reference/mkinresplot-4.png diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index fb9ab40d..f16dee5d 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinresplot. mkin</title> +<title> + — mkinresplot • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,20 +68,21 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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>plot.mkinfit</code> + 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> @@ -90,11 +92,11 @@ <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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>object</dt> <dd> - A fit represented in an <code>mkinfit</code> object. + A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object. </dd> <dt>obs_vars</dt> <dd> @@ -132,24 +134,35 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> - - <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> - </div> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <div class="See also"> - <h2>See also</h2> + <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> + + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p><code>mkinplot</code>, for a way to plot the data and the fitted lines of the + <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 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</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><img src='unknown-4.png' alt='' width='540' height='400' /></pre> + + <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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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><img src='mkinresplot-4.png' alt='' width='540' height='400' /></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#see-also">See also</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -158,7 +171,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 6b079c40..2432e981 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinsub. mkin</title> +<title> + — mkinsub • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,29 +68,30 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>This is a convenience function to set up the lists used as arguments for - <code>mkinmod</code>.</p> + <code><a href='mkinmod.html'>mkinmod</a></code>.</p> <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>submodel</dt> <dd> Character vector of length one to specify the submodel type. See - <code>mkinmod</code> for the list of allowed submodel names. + <code><a href='mkinmod.html'>mkinmod</a></code> for the list of allowed submodel names. </dd> <dt>to</dt> <dd> @@ -110,27 +112,38 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A list for use with <code>mkinmod</code>.</p> - </div> + <p>A list for use with <code><a href='mkinmod.html'>mkinmod</a></code>.</p> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order.</span> -<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), <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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'># The same model using mkinsub</span> -<span class='no'>SFO_SFO.2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( +<span class='no'>SFO_SFO.2</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'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'># Now supplying full names</span> -<span class='no'>SFO_SFO.2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( +<span class='no'>SFO_SFO.2</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'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Test compound"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -139,7 +152,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 5b624893..0ad3321c 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mmkin. mkin</title> +<title> + — mmkin • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,36 +68,37 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> - <p>This function calls <code>mkinfit</code> on all combinations of models and datasets + <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> <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>models</dt> <dd> Either a character vector of shorthand names ("SFO", "FOMC", "DFOP", - "HS", "SFORB"), or an optionally named list of <code>mkinmod</code> + "HS", "SFORB"), or an optionally named list of <code><a href='mkinmod.html'>mkinmod</a></code> objects. </dd> <dt>datasets</dt> <dd> An optionally named list of datasets suitable as observed data for - <code>mkinfit</code>. + <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> <dt>cores</dt> <dd> @@ -110,24 +112,24 @@ </dd> <dt>&#8230;</dt> <dd> - Further arguments that will be passed to <code>mkinfit</code>. + Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A matrix of <code>mkinfit</code> objects that can be indexed using the model + <p>A matrix of <code><a href='mkinfit.html'>mkinfit</a></code> objects that can be indexed using the model and dataset names as row and column indices.</p> - </div> - - <div class="See also"> - <h2>See also</h2> + + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p><code>[.mmkin</code> for subsetting, <code>plot.mmkin</code> for plotting.</p> - </div> + <p><code><a href='[.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for plotting.</p> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span> <span class='co'># m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),</span> <span class='co'># M1 = mkinsub("SFO", "M2"),</span> @@ -161,7 +163,18 @@ <span class='co'># plot(fits.0[1, 1])</span> <span class='co'>## ---------------------------------------------</span></div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#see-also">See also</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -170,7 +183,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/plot.mkinfit-10.png b/docs/reference/plot.mkinfit-10.png Binary files differnew file mode 100644 index 00000000..09bb687c --- /dev/null +++ b/docs/reference/plot.mkinfit-10.png diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png Binary files differnew file mode 100644 index 00000000..1e90d789 --- /dev/null +++ b/docs/reference/plot.mkinfit-4.png diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png Binary files differnew file mode 100644 index 00000000..1dfbbe4c --- /dev/null +++ b/docs/reference/plot.mkinfit-6.png diff --git a/docs/reference/plot.mkinfit-8.png b/docs/reference/plot.mkinfit-8.png Binary files differnew file mode 100644 index 00000000..e4ab674a --- /dev/null +++ b/docs/reference/plot.mkinfit-8.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 94aebf63..631ea429 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>plot.mkinfit. mkin</title> +<title> + — plot.mkinfit • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,19 +68,20 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>Solves the differential equations with the optimised and fixed parameters - from a previous successful call to <code>mkinfit</code> and plots + from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots the observed data together with the solution of the fitted model.</p> @@ -98,7 +100,7 @@ plot(x, fit = x, show_errmin = FALSE, errmin_digits = 3, …) plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>x</dt> <dd> @@ -106,7 +108,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … </dd> <dt>fit</dt> <dd> - An object of class <code>mkinfit</code>. + An object of class <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> <dt>obs_vars</dt> <dd> @@ -194,27 +196,38 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>The function is called for its side effect.</p> - </div> + <p>The function is called for its side effect.</p> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order, path from</span> <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'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</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'>mkinsub</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><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'>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><img src='unknown-4.png' alt='' width='540' height='400' /><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><img src='unknown-6.png' alt='' width='540' height='400' /><div class='input'> +<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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /><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><img src='plot.mkinfit-6.png' alt='' width='540' height='400' /><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><img src='unknown-8.png' alt='' width='540' height='400' /><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><img src='plot.mkinfit-8.png' alt='' width='540' height='400' /><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><img src='unknown-10.png' alt='' width='540' height='400' /><div class='input'> + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='plot.mkinfit-10.png' alt='' width='540' height='400' /><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> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -223,7 +236,14 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png Binary files differnew file mode 100644 index 00000000..a26e413f --- /dev/null +++ b/docs/reference/plot.mmkin-2.png diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png Binary files differnew file mode 100644 index 00000000..f23ed172 --- /dev/null +++ b/docs/reference/plot.mmkin-4.png diff --git a/docs/reference/plot.mmkin-6.png b/docs/reference/plot.mmkin-6.png Binary files differnew file mode 100644 index 00000000..dc24d92f --- /dev/null +++ b/docs/reference/plot.mmkin-6.png diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 358da679..44ae760f 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>plot.mmkin. mkin</title> +<title> + — plot.mmkin • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,18 +68,19 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> - <p>When x is a row selected from an mmkin object (<code>[.mmkin</code>), the same model + <p>When x is a row selected from an mmkin object (<code><a href='[.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 to the same dataset is shown.</p> @@ -87,11 +89,11 @@ <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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>x</dt> <dd> - An object of class <code>mmkin</code>, with either one row or one column. + An object of class <code><a href='mmkin.html'>mmkin</a></code>, with either one row or one column. </dd> <dt>main</dt> <dd> @@ -119,27 +121,38 @@ </dd> <dt>&#8230;</dt> <dd> - Further arguments passed to <code>plot.mkinfit</code> and <code>mkinresplot</code>. + Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinresplot.html'>mkinresplot</a></code>. </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>The function is called for its side effect.</p> - </div> + <p>The function is called for its side effect.</p> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'> <span class='co'># Only use one core not to offend CRAN checks, use Levenberg-Marquardt for speed</span> - <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'>mmkin</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='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='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><img src='unknown-2.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><img src='unknown-4.png' alt='' width='540' height='400' /><div class='input'> + <span class='fu'>plot</span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><img src='plot.mmkin-2.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><img src='plot.mmkin-4.png' alt='' width='540' height='400' /><div class='input'> <span class='co'># We can also plot a single fit, if we like the way 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 staticdocs, 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><img src='unknown-6.png' alt='' width='540' height='400' /></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><img src='plot.mmkin-6.png' alt='' width='540' height='400' /></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -148,7 +161,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index dea5f75c..c4bc08d5 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>print.mkinds. mkin</title> +<title> + — print.mkinds • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>Print mkinds objects.</p> @@ -84,24 +86,38 @@ <pre><span class='co'># S3 method for mkinds</span> <span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>x</dt> <dd> - An <code>mkinds</code> object. + An <code><a href='mkinds.html'>mkinds</a></code> object. </dd> <dt>&#8230;</dt> <dd> Not used. </dd> </dl> - </div> - <div class="col-md-3"> + + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 38663f8f..edc9cde7 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>print.mkinmod. mkin</title> +<title> + — print.mkinmod • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>Print mkinmod objects in a way that the user finds his way to get to its components.</p> @@ -84,24 +86,38 @@ <pre><span class='co'># S3 method for mkinmod</span> <span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>x</dt> <dd> - An <code>mkinmod</code> object. + An <code><a href='mkinmod.html'>mkinmod</a></code> object. </dd> <dt>&#8230;</dt> <dd> Not used. </dd> </dl> - </div> - <div class="col-md-3"> + + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 12776c74..1cd71697 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>schaefer07_complex_case. mkin</title> +<title> + — schaefer07_complex_case • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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). @@ -85,10 +87,9 @@ <pre><span class='fu'>data</span>(<span class='no'>schaefer07_complex_case</span>)</pre> - <div class="Format"> - <h2>Format</h2> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>The data set is a data frame with 8 observations on the following 6 variables. + <p>The data set is a data frame with 8 observations on the following 6 variables. <dl class='dl-horizontal'> <dt><code>time</code></dt><dd>a numeric vector</dd> <dt><code>parent</code></dt><dd>a numeric vector</dd> @@ -97,33 +98,51 @@ <dt><code>C1</code></dt><dd>a numeric vector</dd> <dt><code>A2</code></dt><dd>a numeric vector</dd> </dl></p> - <p>The results are a data frame with 14 results for different parameter values</p> - </div> - - <div class="References"> - <h2>References</h2> + <p>The results are a data frame with 14 results for different parameter values</p> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <p>Schäfer D, Mikolasch B, Rainbird P and Harvey B (2007). KinGUI: a new kinetic + <p>Schäfer D, Mikolasch B, Rainbird P and Harvey B (2007). KinGUI: a new kinetic software tool for evaluations according to FOCUS degradation kinetics. In: Del Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.</p> - </div> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class='no'>data</span> <span class='kw'><-</span> <span class='fu'>mkin_wide_to_long</span>(<span class='no'>schaefer07_complex_case</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>) -<span class='no'>model</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> + <pre class="examples"><div class='input'><span class='no'>data</span> <span class='kw'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>schaefer07_complex_case</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>) +<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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"A1"</span>, <span class='st'>"B1"</span>, <span class='st'>"C1"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>), <span class='kw'>B1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>C1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'>## Not run: mkinfit(model, data, plot=TRUE)</span></div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index acbf36dc..1e1a0e2f 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>summary.mkinfit. mkin</title> +<title> + — summary.mkinfit • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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 @@ -89,11 +91,11 @@ <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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>object</dt> <dd> - an object of class <code>mkinfit</code>. + an object of class <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> <dt>x</dt> <dd> @@ -121,36 +123,36 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>The summary function returns a list derived from + <p>The summary function returns a list derived from <code>summary.modFit</code>, with components, among others</p> - <p>The print method is called for its side effect, i.e. printing the summary.</p> - </div> - - <div class="References"> - <h2>References</h2> + <p>The print method is called for its side effect, i.e. printing the summary.</p> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'>mkinfit</span>(<span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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: 0.9.44.9000 + + <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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Thu Oct 6 10:47:44 2016 -#> Date of summary: Thu Oct 6 10:47:44 2016 +#> Date of fit: Wed Oct 26 23:16:57 2016 +#> Date of summary: Wed Oct 26 23:16:57 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.079 s +#> Fitted with method Port using 35 model solutions performed in 0.089 s #> #> Weighting: none #> @@ -212,7 +214,18 @@ #> 118 parent 0.39 1.351 -0.9613 #> </div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -221,7 +234,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 04550199..b45c07fc 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>synthetic_data_for_UBA_2014. mkin</title> +<title> + — synthetic_data_for_UBA_2014 • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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 @@ -99,28 +101,28 @@ <pre><span class='no'>synthetic_data_for_UBA_2014</span></pre> - <div class="Format"> - <h2>Format</h2> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>A list containing datasets in the form internally used by the 'gmkin' package. + <p>A list containing datasets in the form internally used by the 'gmkin' package. The list has twelfe components. Each of the components is one dataset that has, among others, the following components <dl class='dl-horizontal'> <dt><code>title</code></dt><dd>The name of the dataset, e.g. <code>SFO_lin_a</code></dd> - <dt><code>data</code></dt><dd>A data frame with the data in the form expected by <code>mkinfit</code></dd> + <dt><code>data</code></dt><dd>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></dd> </dl></p> - </div> - - <div class="Source"> - <h2>Source</h2> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative + <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> - <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for + <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span> <span class='co'># m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),</span> <span class='co'># M1 = list(type = "SFO", to = "M2"),</span> @@ -144,12 +146,29 @@ <span class='co'># mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data)</span> <span class='co'>## ---------------------------------------------</span></div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 66253bba..a07be0a0 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>transform_odeparms. mkin</title> +<title> + — transform_odeparms • 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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<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 --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,27 +68,28 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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 constants and other paramters that can only take on positive values, a simple log transformation is used. For compositional parameters, such as the formations fractions that should always sum up to 1 and can not be - negative, the <code>ilr</code> transformation is used.</p> + negative, the <code><a href='ilr.html'>ilr</a></code> transformation is used.</p> <p>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>mkinfit</code>.</p> + This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit</a></code>.</p> <pre><span class='fu'>transform_odeparms</span>(<span class='no'>parms</span>, <span class='no'>mkinmod</span>, @@ -95,7 +97,7 @@ <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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>parms</dt> <dd> @@ -107,9 +109,9 @@ </dd> <dt>mkinmod</dt> <dd> - The kinetic model of class <code>mkinmod</code>, containing the names of + The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the names of the model variables that are needed for grouping the formation fractions - before <code>ilr</code> transformation, the parameter names and + before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter names and the information if the pathway to sink is included in the model. </dd> <dt>transform_rates</dt> @@ -128,27 +130,29 @@ assumption of normal distribution of the estimator. The default (TRUE) is to do transformations. The g parameter of the DFOP and HS models are also transformed, as they can also be seen as compositional data. The - transformation used for these transformations is the <code>ilr</code> + transformation used for these transformations is the <code><a href='ilr.html'>ilr</a></code> transformation. </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A vector of transformed or backtransformed parameters with the same names + <p>A vector of transformed or backtransformed parameters with the same names as the original parameters.</p> - </div> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> + <pre class="examples"><div class='input'><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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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'>mkinfit</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='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: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Thu Oct 6 10:47:45 2016 -#> Date of summary: Thu Oct 6 10:47:45 2016 +#> Date of fit: Wed Oct 26 23:16:59 2016 +#> Date of summary: Wed Oct 26 23:16:59 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -156,7 +160,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.638 s +#> Fitted with method Port using 153 model solutions performed in 0.721 s #> #> Weighting: none #> @@ -259,7 +263,16 @@ <span class='co'># summary(fit.ff.2, data = FALSE)</span> <span class='co'>## ---------------------------------------------</span></div></pre> </div> - <div class="col-md-3"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -268,7 +281,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> |
