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property="og:title" content="Example evaluation of FOCUS Example Dataset D"> -<meta property="og:description" content=""> -<meta name="twitter:card" content="summary"> +<meta property="og:description" content="mkin"> <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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> +<body data-spy="scroll" data-target="#toc"> <div class="container template-article"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> @@ -31,7 +31,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span> </span> </div> @@ -74,7 +74,14 @@ <a href="../news/index.html">News</a> </li> </ul> -<ul class="nav navbar-nav navbar-right"></ul> +<ul class="nav navbar-nav navbar-right"> +<li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul> </div> <!--/.nav-collapse --> </div> @@ -87,12 +94,12 @@ </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> - <h1>Example evaluation of FOCUS Example Dataset D</h1> + <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-11-01</h4> - + <h4 class="date">2020-05-07</h4> + <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.Rmd"><code>vignettes/FOCUS_D.Rmd</code></a></small> <div class="hidden name"><code>FOCUS_D.Rmd</code></div> </div> @@ -100,8 +107,8 @@ <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 at 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" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(mkin, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb1-2" title="2"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(FOCUS_<span class="dv">2006</span>_D)</a></code></pre></div> +<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">mkin</span>, <span class="kw">quietly</span> <span class="kw">=</span> <span class="fl">TRUE</span>) +<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">FOCUS_2006_D</span>)</pre></body></html></div> <pre><code>## name time value ## 1 parent 0 99.46 ## 2 parent 0 102.04 @@ -149,29 +156,29 @@ ## 44 m1 120 33.31</code></pre> <p>Next we specify the degradation model: The parent compound degrades with simple first-order kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.</p> <p>The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p> -<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(SFO_SFO<span class="op">$</span>diffs)</a></code></pre></div> +<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">SFO_SFO</span>$<span class="no">diffs</span>)</pre></body></html></div> <pre><code>## parent ## "d_parent = - k_parent_sink * parent - k_parent_m1 * parent" ## m1 ## "d_m1 = + k_parent_m1 * parent - k_m1_sink * m1"</code></pre> <p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p> -<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">fit <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> -<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with -## value of zero were removed from the data</code></pre> +<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">fit</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/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>)</pre></body></html></div> +<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value +## of zero were removed from the data</code></pre> <p>A plot of the fit including a residual plot for both observed variables is obtained using the <code>plot_sep</code> method for <code>mkinfit</code> objects, which shows separate graphs for all compounds and their residuals.</p> -<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(fit, <span class="dt">lpos =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">fit</span>, <span class="kw">lpos</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</pre></body></html></div> <p><img src="FOCUS_D_files/figure-html/plot-1.png" width="768"></p> <p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p> -<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</a></code></pre></div> +<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(<span class="no">fit</span>)</pre></body></html></div> <p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p> <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p> -<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(fit)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.49.6 -## R version used for fitting: 3.6.1 -## Date of fit: Fri Nov 1 10:10:44 2019 -## Date of summary: Fri Nov 1 10:10:44 2019 +<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">fit</span>)</pre></body></html></div> +<pre><code>## mkin version used for fitting: 0.9.49.11 +## R version used for fitting: 4.0.0 +## Date of fit: Thu May 7 08:59:27 2020 +## Date of summary: Thu May 7 08:59:27 2020 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -179,7 +186,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted using 389 model solutions performed in 1.015 s +## Fitted using 389 model solutions performed in 1.031 s ## ## Error model: Constant variance ## @@ -212,18 +219,18 @@ ## sigma 3.126 0.35850 2.396 3.855 ## ## Parameter correlation: -## parent_0 log_k_parent_sink log_k_parent_m1 -## parent_0 1.000e+00 6.067e-01 -6.372e-02 -## log_k_parent_sink 6.067e-01 1.000e+00 -8.550e-02 -## log_k_parent_m1 -6.372e-02 -8.550e-02 1.000e+00 -## log_k_m1_sink -1.688e-01 -6.252e-01 4.731e-01 -## sigma 1.164e-09 -8.908e-10 1.652e-08 -## log_k_m1_sink sigma -## parent_0 -1.688e-01 1.164e-09 -## log_k_parent_sink -6.252e-01 -8.908e-10 -## log_k_parent_m1 4.731e-01 1.652e-08 -## log_k_m1_sink 1.000e+00 -1.340e-10 -## sigma -1.340e-10 1.000e+00 +## parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +## parent_0 1.000e+00 6.067e-01 -6.372e-02 -1.688e-01 +## log_k_parent_sink 6.067e-01 1.000e+00 -8.550e-02 -6.252e-01 +## log_k_parent_m1 -6.372e-02 -8.550e-02 1.000e+00 4.731e-01 +## log_k_m1_sink -1.688e-01 -6.252e-01 4.731e-01 1.000e+00 +## sigma 5.287e-10 3.306e-09 4.421e-08 -3.319e-10 +## sigma +## parent_0 5.287e-10 +## log_k_parent_sink 3.306e-09 +## log_k_parent_m1 4.421e-08 +## log_k_m1_sink -3.319e-10 +## sigma 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -295,7 +302,7 @@ ## 120 m1 33.31 28.78984 4.520e+00</code></pre> </div> - 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