aboutsummaryrefslogtreecommitdiff
path: root/docs/articles/web_only/FOCUS_Z.html
diff options
context:
space:
mode:
Diffstat (limited to 'docs/articles/web_only/FOCUS_Z.html')
-rw-r--r--docs/articles/web_only/FOCUS_Z.html285
1 files changed, 140 insertions, 145 deletions
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 14234785..0c34d77d 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -6,19 +6,19 @@
<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 dataset Z • mkin</title>
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous">
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous">
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../../pkgdown.css" rel="stylesheet">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../../bootstrap-toc.css">
+<script src="../../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../../pkgdown.css" rel="stylesheet">
<script src="../../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS dataset Z">
-<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">0.9.50.2</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 dataset Z</h1>
+ <h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-11-01</h4>
-
+ <h4 class="date">2020-05-12</h4>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/FOCUS_Z.Rmd"><code>vignettes/web_only/FOCUS_Z.Rmd</code></a></small>
<div class="hidden name"><code>FOCUS_Z.Rmd</code></div>
</div>
@@ -104,71 +111,71 @@
<h1 class="hasAnchor">
<a href="#the-data" class="anchor"></a>The data</h1>
<p>The following code defines the example dataset from Appendix 7 to the FOCUS kinetics report <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 354)</span>.</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(mkin, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a>
-<a class="sourceLine" id="cb1-2" title="2">LOD =<span class="st"> </span><span class="fl">0.5</span></a>
-<a class="sourceLine" id="cb1-3" title="3">FOCUS_<span class="dv">2006</span>_Z =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(</a>
-<a class="sourceLine" id="cb1-4" title="4"> <span class="dt">t =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">3</span>, <span class="dv">4</span>, <span class="dv">7</span>, <span class="dv">10</span>, <span class="dv">14</span>, <span class="dv">21</span>,</a>
-<a class="sourceLine" id="cb1-5" title="5"> <span class="dv">42</span>, <span class="dv">61</span>, <span class="dv">96</span>, <span class="dv">124</span>),</a>
-<a class="sourceLine" id="cb1-6" title="6"> <span class="dt">Z0 =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,</a>
-<a class="sourceLine" id="cb1-7" title="7"> <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span>),</a>
-<a class="sourceLine" id="cb1-8" title="8"> <span class="dt">Z1 =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="dv">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,</a>
-<a class="sourceLine" id="cb1-9" title="9"> <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>),</a>
-<a class="sourceLine" id="cb1-10" title="10"> <span class="dt">Z2 =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,</a>
-<a class="sourceLine" id="cb1-11" title="11"> <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>),</a>
-<a class="sourceLine" id="cb1-12" title="12"> <span class="dt">Z3 =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,</a>
-<a class="sourceLine" id="cb1-13" title="13"> <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span>))</a>
-<a class="sourceLine" id="cb1-14" title="14"></a>
-<a class="sourceLine" id="cb1-15" title="15">FOCUS_<span class="dv">2006</span>_Z_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_Z)</a></code></pre></div>
+<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="no">LOD</span> <span class="kw">=</span> <span class="fl">0.5</span>
+<span class="no">FOCUS_2006_Z</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(
+ <span class="kw">t</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">21</span>,
+ <span class="fl">42</span>, <span class="fl">61</span>, <span class="fl">96</span>, <span class="fl">124</span>),
+ <span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,
+ <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span>),
+ <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="fl">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,
+ <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> * <span class="no">LOD</span>, <span class="fl">NA</span>, <span class="fl">NA</span>, <span class="fl">NA</span>),
+ <span class="kw">Z2</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0</span>, <span class="fl">NA</span>, <span class="fl">0.5</span> * <span class="no">LOD</span>, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,
+ <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> * <span class="no">LOD</span>, <span class="fl">NA</span>, <span class="fl">NA</span>, <span class="fl">NA</span>),
+ <span class="kw">Z3</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0</span>, <span class="fl">NA</span>, <span class="fl">NA</span>, <span class="fl">NA</span>, <span class="fl">NA</span>, <span class="fl">0.5</span> * <span class="no">LOD</span>, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,
+ <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span>))
+
+<span class="no">FOCUS_2006_Z_mkin</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(<span class="no">FOCUS_2006_Z</span>)</pre></body></html></div>
</div>
<div id="parent-and-one-metabolite" class="section level1">
<h1 class="hasAnchor">
<a href="#parent-and-one-metabolite" class="anchor"></a>Parent and one metabolite</h1>
<p>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).</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">Z<span class="fl">.2</span>a &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),</a>
-<a class="sourceLine" id="cb2-2" title="2"> <span class="dt">Z1 =</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="cb2"><html><body><pre class="r"><span class="no">Z.2a</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),
+ <span class="kw">Z1</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="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">m.Z<span class="fl">.2</span>a &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
-<pre><code>## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations
-## with value of zero were removed from the data</code></pre>
-<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a)</a></code></pre></div>
+<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="no">m.Z.2a</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.2a</span>, <span class="no">FOCUS_2006_Z_mkin</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
+<pre><code>## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
+## value of zero were removed from the data</code></pre>
+<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.2a</span>)</pre></body></html></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p>
-<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
-<pre><code>## Estimate se_notrans t value Pr(&gt;t) Lower Upper
-## Z0_0 9.7015e+01 3.393176 2.8591e+01 6.4352e-21 91.66556 102.3642
-## k_Z0_sink 7.2231e-10 0.225254 3.2067e-09 5.0000e-01 0.00000 Inf
-## k_Z0_Z1 2.2360e+00 0.159134 1.4051e+01 1.1369e-13 1.95303 2.5600
-## k_Z1_sink 4.8212e-01 0.065454 7.3658e+00 5.1186e-08 0.40341 0.5762
-## sigma 4.8041e+00 0.637618 7.5345e+00 3.4431e-08 3.52677 6.0815</code></pre>
+<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.Z.2a</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)$<span class="no">bpar</span></pre></body></html></div>
+<pre><code>## Estimate se_notrans t value Pr(&gt;t) Lower Upper
+## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642
+## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600
+## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762
+## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000
+## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</code></pre>
<p>As obvious from the parameter summary (the component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.</p>
<p>A similar result can be obtained when formation fractions are used in the model formulation:</p>
-<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">Z<span class="fl">.2</span>a.ff &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),</a>
-<a class="sourceLine" id="cb9-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a>
-<a class="sourceLine" id="cb9-3" title="3"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="no">Z.2a.ff</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),
+ <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/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>)</pre></body></html></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1">m.Z<span class="fl">.2</span>a.ff &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a.ff, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
-<pre><code>## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations
-## with value of zero were removed from the data</code></pre>
-<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a.ff)</a></code></pre></div>
+<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="no">m.Z.2a.ff</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.2a.ff</span>, <span class="no">FOCUS_2006_Z_mkin</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
+<pre><code>## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
+## value of zero were removed from the data</code></pre>
+<div class="sourceCode" id="cb13"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.2a.ff</span>)</pre></body></html></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></p>
-<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.Z<span class="fl">.2</span>a.ff, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
+<div class="sourceCode" id="cb14"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.Z.2a.ff</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)$<span class="no">bpar</span></pre></body></html></div>
<pre><code>## Estimate se_notrans t value Pr(&gt;t) Lower Upper
## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642
## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600
-## k_Z1 0.48212 0.063265 7.6207 2.8155e-08 0.40341 0.5762
+## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762
## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000
## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</code></pre>
<p>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. Here, the covariance matrix used for the calculation of confidence intervals is not returned as the model is overparameterised.</p>
<p>A simplified model is obtained by removing the pathway to the sink. </p>
<p>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.</p>
-<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1">Z<span class="fl">.3</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb16-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb16"><html><body><pre class="r"><span class="no">Z.3</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>),
+ <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/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>)</pre></body></html></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1">m.Z<span class="fl">.3</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb18"><html><body><pre class="r"><span class="no">m.Z.3</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.3</span>, <span class="no">FOCUS_2006_Z_mkin</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
<pre><code>## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
## value of zero were removed from the data</code></pre>
-<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.3</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb20"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.3</span>)</pre></body></html></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p>
-<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.Z<span class="fl">.3</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
+<div class="sourceCode" id="cb21"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.Z.3</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)$<span class="no">bpar</span></pre></body></html></div>
<pre><code>## Estimate se_notrans t value Pr(&gt;t) Lower Upper
## Z0_0 97.01488 2.597342 37.352 2.0106e-24 91.67597 102.3538
## k_Z0 2.23601 0.146904 15.221 9.1477e-15 1.95354 2.5593
@@ -180,52 +187,51 @@
<h1 class="hasAnchor">
<a href="#metabolites-z2-and-z3" class="anchor"></a>Metabolites Z2 and Z3</h1>
<p>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.</p>
-<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1">Z<span class="fl">.5</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb23-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb23-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb23"><html><body><pre class="r"><span class="no">Z.5</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>),
+ <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>),
+ <span class="kw">Z2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/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>)</pre></body></html></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="1">m.Z<span class="fl">.5</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb25"><html><body><pre class="r"><span class="no">m.Z.5</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.5</span>, <span class="no">FOCUS_2006_Z_mkin</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
<pre><code>## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
## value of zero were removed from the data</code></pre>
-<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.5</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb27"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.5</span>)</pre></body></html></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png" width="700"></p>
<p>Finally, metabolite Z3 is added to the model. We use the optimised differential equation parameter values from the previous fit in order to accelerate the optimization.</p>
-<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" title="1">Z.FOCUS &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb28-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb28-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a>
-<a class="sourceLine" id="cb28-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a>
-<a class="sourceLine" id="cb28-5" title="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb28"><html><body><pre class="r"><span class="no">Z.FOCUS</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>),
+ <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>),
+ <span class="kw">Z2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),
+ <span class="kw">Z3</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/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>)</pre></body></html></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" title="1">m.Z.FOCUS &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.FOCUS, FOCUS_<span class="dv">2006</span>_Z_mkin,</a>
-<a class="sourceLine" id="cb30-2" title="2"> <span class="dt">parms.ini =</span> m.Z<span class="fl">.5</span><span class="op">$</span>bparms.ode,</a>
-<a class="sourceLine" id="cb30-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
-<pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.
-## 5$bparms.ode, : Observations with value of zero were removed from the data</code></pre>
-<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb32-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.FOCUS)</a></code></pre></div>
+<div class="sourceCode" id="cb30"><html><body><pre class="r"><span class="no">m.Z.FOCUS</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.FOCUS</span>, <span class="no">FOCUS_2006_Z_mkin</span>,
+ <span class="kw">parms.ini</span> <span class="kw">=</span> <span class="no">m.Z.5</span>$<span class="no">bparms.ode</span>,
+ <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
+<pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, :
+## Observations with value of zero were removed from the data</code></pre>
+<pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation did not converge:
+## false convergence (8)</code></pre>
+<div class="sourceCode" id="cb33"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.FOCUS</span>)</pre></body></html></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p>
-<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
+<div class="sourceCode" id="cb34"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.Z.FOCUS</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)$<span class="no">bpar</span></pre></body></html></div>
<pre><code>## Estimate se_notrans t value Pr(&gt;t) Lower Upper
-## Z0_0 96.838607 1.994273 48.5584 4.0283e-42 92.826626 100.850589
-## k_Z0 2.215405 0.118459 18.7018 1.0415e-23 1.989465 2.467003
-## k_Z1 0.478300 0.028257 16.9267 6.2408e-22 0.424701 0.538662
-## k_Z2 0.451618 0.042138 10.7177 1.6308e-14 0.374328 0.544867
-## k_Z3 0.058693 0.015246 3.8498 1.7806e-04 0.034805 0.098978
-## f_Z2_to_Z3 0.471508 0.058352 8.0804 9.6648e-11 0.357735 0.588320
+## Z0_0 96.838721 1.994275 48.5584 4.0283e-42 92.826878 100.850563
+## k_Z0 2.215400 0.118459 18.7019 1.0414e-23 1.989462 2.466998
+## k_Z1 0.478301 0.028257 16.9267 6.2411e-22 0.424705 0.538662
+## k_Z2 0.451623 0.042138 10.7176 1.6313e-14 0.374336 0.544867
+## k_Z3 0.058694 0.015246 3.8499 1.7804e-04 0.034809 0.098967
+## f_Z2_to_Z3 0.471510 0.058352 8.0804 9.6640e-11 0.357775 0.588283
## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</code></pre>
-<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb35-1" title="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.FOCUS)</a></code></pre></div>
+<div class="sourceCode" id="cb36"><html><body><pre class="r"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span>(<span class="no">m.Z.FOCUS</span>)</pre></body></html></div>
<pre><code>## $ff
## Z2_Z3 Z2_sink
## 0.47151 0.52849
##
-## $SFORB
-## logical(0)
-##
## $distimes
## DT50 DT90
## Z0 0.31288 1.0394
## Z1 1.44919 4.8141
-## Z2 1.53481 5.0985
-## Z3 11.80965 39.2308</code></pre>
+## Z2 1.53479 5.0985
+## Z3 11.80955 39.2305</code></pre>
<p>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.</p>
</div>
<div id="using-the-sforb-model" class="section level1">
@@ -233,87 +239,85 @@
<a href="#using-the-sforb-model" class="anchor"></a>Using the SFORB model</h1>
<p>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.</p>
<p>Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the <span class="math inline">\(\chi^2\)</span> 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.</p>
-<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" title="1">Z.mkin<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb37-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb37-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a>
-<a class="sourceLine" id="cb37-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb38"><html><body><pre class="r"><span class="no">Z.mkin.1</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>),
+ <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>),
+ <span class="kw">Z2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),
+ <span class="kw">Z3</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</pre></body></html></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb39"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb39-1" title="1">m.Z.mkin<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.1</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
-<pre><code>## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations
-## with value of zero were removed from the data</code></pre>
-<div class="sourceCode" id="cb41"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb41-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.1</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb40"><html><body><pre class="r"><span class="no">m.Z.mkin.1</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.mkin.1</span>, <span class="no">FOCUS_2006_Z_mkin</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
+<pre><code>## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
+## value of zero were removed from the data</code></pre>
+<div class="sourceCode" id="cb42"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.mkin.1</span>)</pre></body></html></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p>
-<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div>
+<div class="sourceCode" id="cb43"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.Z.mkin.1</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)$<span class="no">cov.unscaled</span></pre></body></html></div>
<pre><code>## NULL</code></pre>
<p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p>
-<div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" title="1">Z.mkin<span class="fl">.3</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb44-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb44-3" title="3"> <span class="dt">Z2 =</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="cb45"><html><body><pre class="r"><span class="no">Z.mkin.3</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>),
+ <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>),
+ <span class="kw">Z2</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="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" title="1">m.Z.mkin<span class="fl">.3</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
-<pre><code>## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations
-## with value of zero were removed from the data</code></pre>
-<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.3</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb47"><html><body><pre class="r"><span class="no">m.Z.mkin.3</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.mkin.3</span>, <span class="no">FOCUS_2006_Z_mkin</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
+<pre><code>## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
+## value of zero were removed from the data</code></pre>
+<div class="sourceCode" id="cb49"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.mkin.3</span>)</pre></body></html></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="700"></p>
<p>This results in a much better representation of the behaviour of the parent compound Z0.</p>
<p>Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.</p>
-<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" title="1">Z.mkin<span class="fl">.4</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb49-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb49-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a>
-<a class="sourceLine" id="cb49-4" title="4"> <span class="dt">Z3 =</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="cb50"><html><body><pre class="r"><span class="no">Z.mkin.4</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>),
+ <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>),
+ <span class="kw">Z2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),
+ <span class="kw">Z3</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="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" title="1">m.Z.mkin<span class="fl">.4</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.4</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a>
-<a class="sourceLine" id="cb51-2" title="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.3</span><span class="op">$</span>bparms.ode,</a>
-<a class="sourceLine" id="cb51-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb52"><html><body><pre class="r"><span class="no">m.Z.mkin.4</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.mkin.4</span>, <span class="no">FOCUS_2006_Z_mkin</span>,
+ <span class="kw">parms.ini</span> <span class="kw">=</span> <span class="no">m.Z.mkin.3</span>$<span class="no">bparms.ode</span>,
+ <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
<pre><code>## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin.
## 3$bparms.ode, : Observations with value of zero were removed from the data</code></pre>
-<div class="sourceCode" id="cb53"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb53-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.4</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb54"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.mkin.4</span>)</pre></body></html></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png" width="700"></p>
<p>The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.</p>
-<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1">Z.mkin<span class="fl">.5</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb54-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb54-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a>
-<a class="sourceLine" id="cb54-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb55"><html><body><pre class="r"><span class="no">Z.mkin.5</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">Z0</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>),
+ <span class="kw">Z1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="kw">sink</span> <span class="kw">=</span> <span class="fl">FALSE</span>),
+ <span class="kw">Z2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),
+ <span class="kw">Z3</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</pre></body></html></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb56"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb56-1" title="1">m.Z.mkin<span class="fl">.5</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a>
-<a class="sourceLine" id="cb56-2" title="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.4</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>],</a>
-<a class="sourceLine" id="cb56-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb57"><html><body><pre class="r"><span class="no">m.Z.mkin.5</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.mkin.5</span>, <span class="no">FOCUS_2006_Z_mkin</span>,
+ <span class="kw">parms.ini</span> <span class="kw">=</span> <span class="no">m.Z.mkin.4</span>$<span class="no">bparms.ode</span>[<span class="fl">1</span>:<span class="fl">4</span>],
+ <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
<pre><code>## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin.
-## 4$bparms.ode[1:4], : Observations with value of zero were removed from the
-## data</code></pre>
-<div class="sourceCode" id="cb58"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb58-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>)</a></code></pre></div>
+## 4$bparms.ode[1:4], : Observations with value of zero were removed from the data</code></pre>
+<div class="sourceCode" id="cb59"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.mkin.5</span>)</pre></body></html></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png" width="700"></p>
<p>The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized is excessively small, it seems reasonable to fix it to zero.</p>
-<div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" title="1">m.Z.mkin<span class="fl">.5</span>a &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a>
-<a class="sourceLine" id="cb59-2" title="2"> <span class="dt">parms.ini =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(m.Z.mkin<span class="fl">.5</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">7</span>],</a>
-<a class="sourceLine" id="cb59-3" title="3"> <span class="dt">k_Z3_bound_free =</span> <span class="dv">0</span>),</a>
-<a class="sourceLine" id="cb59-4" title="4"> <span class="dt">fixed_parms =</span> <span class="st">"k_Z3_bound_free"</span>,</a>
-<a class="sourceLine" id="cb59-5" title="5"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb60"><html><body><pre class="r"><span class="no">m.Z.mkin.5a</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">Z.mkin.5</span>, <span class="no">FOCUS_2006_Z_mkin</span>,
+ <span class="kw">parms.ini</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">m.Z.mkin.5</span>$<span class="no">bparms.ode</span>[<span class="fl">1</span>:<span class="fl">7</span>],
+ <span class="kw">k_Z3_bound_free</span> <span class="kw">=</span> <span class="fl">0</span>),
+ <span class="kw">fixed_parms</span> <span class="kw">=</span> <span class="st">"k_Z3_bound_free"</span>,
+ <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
<pre><code>## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = c(m.Z.mkin.
-## 5$bparms.ode[1:7], : Observations with value of zero were removed from the
-## data</code></pre>
-<div class="sourceCode" id="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div>
+## 5$bparms.ode[1:7], : Observations with value of zero were removed from the data</code></pre>
+<div class="sourceCode" id="cb62"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.mkin.5a</span>)</pre></body></html></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png" width="700"></p>
<p>As expected, the residual plots for Z0 and Z3 are more random than in the case of the all SFO model for which they were shown above. In conclusion, the model is proposed as the best-fit model for the dataset from Appendix 7 of the FOCUS report.</p>
<p>A graphical representation of the confidence intervals can finally be obtained.</p>
-<div class="sourceCode" id="cb62"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb62-1" title="1"><span class="kw"><a href="../../reference/mkinparplot.html">mkinparplot</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div>
+<div class="sourceCode" id="cb63"><html><body><pre class="r"><span class="fu"><a href="../../reference/mkinparplot.html">mkinparplot</a></span>(<span class="no">m.Z.mkin.5a</span>)</pre></body></html></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png" width="700"></p>
<p>The endpoints obtained with this model are</p>
-<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb63-1" title="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div>
+<div class="sourceCode" id="cb64"><html><body><pre class="r"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span>(<span class="no">m.Z.mkin.5a</span>)</pre></body></html></div>
<pre><code>## $ff
-## Z0_free_Z1 Z1_Z2 Z2_sink Z2_Z3_free Z3_free_sink
-## 1.00000 1.00000 0.46344 0.53656 1.00000
+## Z0_free Z2_Z3 Z2_sink Z3_free
+## 1.00000 0.53656 0.46344 1.00000
##
## $SFORB
## Z0_b1 Z0_b2 Z3_b1 Z3_b2
-## 2.4471381 0.0075124 0.0800075 0.0000000
+## 2.4471358 0.0075126 0.0800073 0.0000000
##
## $distimes
## DT50 DT90 DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2
-## Z0 0.3043 1.1848 0.28325 92.267 NA NA
+## Z0 0.3043 1.1848 0.28325 92.265 NA NA
## Z1 1.5148 5.0320 NA NA NA NA
## Z2 1.6414 5.4526 NA NA NA NA
-## Z3 NA NA NA NA 8.6635 Inf</code></pre>
+## Z3 NA NA NA NA 8.6636 Inf</code></pre>
<p>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.</p>
</div>
<div id="references" class="section level1">
@@ -328,20 +332,11 @@
</div>
</div>
- <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <div id="tocnav">
- <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
- <ul class="nav nav-pills nav-stacked">
-<li><a href="#the-data">The data</a></li>
- <li><a href="#parent-and-one-metabolite">Parent and one metabolite</a></li>
- <li><a href="#metabolites-z2-and-z3">Metabolites Z2 and Z3</a></li>
- <li><a href="#using-the-sforb-model">Using the SFORB model</a></li>
- <li><a href="#references">References</a></li>
- </ul>
+ <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
+ </nav>
</div>
- </div>
</div>
@@ -352,7 +347,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>

Contact - Imprint