Static documentation rebuilt by pkgdown

1 files changed, 80 insertions, 45 deletions

diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
index b2f24d45..3e87b90d 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.html
@@ -10,23 +10,27 @@
 
 
 <!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<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/5.7.1/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" />
+<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<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/0.9.4/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>
+<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">
@@ -37,8 +41,9 @@
 
 <meta property="og:title" content="Logistic kinetics — logistic.solution" />
 <meta property="og:description" content="Function describing exponential decline from a defined starting value, with
+an increasing rate constant, supposedly caused by microbial growth
+Function describing exponential decline from a defined starting value, with
 an increasing rate constant, supposedly caused by microbial growth" />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -56,7 +61,7 @@ an increasing rate constant, supposedly caused by microbial growth" />
 
   </head>
 
-  <body>
+  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -70,7 +75,7 @@ an increasing rate constant, supposedly caused by microbial growth" />
       </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>
 
@@ -114,7 +119,12 @@ an increasing rate constant, supposedly caused by microbial growth" />
 </li>
       </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 -->
@@ -129,16 +139,20 @@ an increasing rate constant, supposedly caused by microbial growth" />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Logistic kinetics</h1>
-    
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/logistic.solution.R'><code>R/logistic.solution.R</code></a>, <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small>
     <div class="hidden name"><code>logistic.solution.Rd</code></div>
     </div>
 
     <div class="ref-description">
     <p>Function describing exponential decline from a defined starting value, with
 an increasing rate constant, supposedly caused by microbial growth</p>
+<p>Function describing exponential decline from a defined starting value, with
+an increasing rate constant, supposedly caused by microbial growth</p>
     </div>
 
-    <pre class="usage"><span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</span>)</pre>
+    <pre class="usage"><span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</span>)
+
+<span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</span>)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -148,7 +162,7 @@ an increasing rate constant, supposedly caused by microbial growth</p>
       <td><p>Time.</p></td>
     </tr>
     <tr>
-      <th>parent.0</th>
+      <th>parent_0</th>
       <td><p>Starting value for the response variable at time zero.</p></td>
     </tr>
     <tr>
@@ -163,6 +177,10 @@ an increasing rate constant, supposedly caused by microbial growth</p>
       <th>r</th>
       <td><p>Growth rate of the increase in the rate constant.</p></td>
     </tr>
+    <tr>
+      <th>parent.0</th>
+      <td><p>Starting value for the response variable at time zero.</p></td>
+    </tr>
     </table>
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -172,6 +190,8 @@ an increasing rate constant, supposedly caused by microbial growth</p>
 
     <p>The solution of the logistic model reduces to the
   <code><a href='SFO.solution.html'>SFO.solution</a></code> if <code>k0</code> is equal to <code>kmax</code>.</p>
+<p>The solution of the logistic model reduces to the
+  <code><a href='SFO.solution.html'>SFO.solution</a></code> if <code>k0</code> is equal to <code>kmax</code>.</p>
     <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
 
     <p>FOCUS (2014) &#8220;Generic guidance for Estimating Persistence
@@ -179,16 +199,25 @@ an increasing rate constant, supposedly caused by microbial growth</p>
   EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
   Version 1.1, 18 December 2014
   <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+    <div class='dont-index'><p>Other parent solutions: 
+<code><a href='DFOP.solution.html'>DFOP.solution</a>()</code>,
+<code><a href='FOMC.solution.html'>FOMC.solution</a>()</code>,
+<code><a href='HS.solution.html'>HS.solution</a>()</code>,
+<code><a href='IORE.solution.html'>IORE.solution</a>()</code>,
+<code><a href='SFO.solution.html'>SFO.solution</a>()</code>,
+<code><a href='SFORB.solution.html'>SFORB.solution</a>()</code></p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
   <span class='co'># Reproduce the plot on page 57 of FOCUS (2014)</span>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.2</span>),
+  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.2</span>),
        <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>ylim</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'>100</span>),
-       <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'>"Residue"</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.4</span>),
-       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.8</span>),
-       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>3</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.001</span>, <span class='fl'>0.2</span>),
-       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>4</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.08</span>, <span class='fl'>0.2</span>),
+       <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'>"Residue"</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.4</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.8</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>3</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.001</span>, <span class='fl'>0.2</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>4</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.08</span>, <span class='fl'>0.2</span>),
        <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></span>(<span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fl'>0.05</span>,
          <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='st'>"k0 = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.001</span>, <span class='fl'>0.08</span>),
                          <span class='st'>", r = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.2</span>, <span class='fl'>0.4</span>, <span class='fl'>0.8</span>, <span class='fl'>0.2</span>, <span class='fl'>0.2</span>)),
@@ -205,32 +234,38 @@ an increasing rate constant, supposedly caused by microbial growth</p>
     <span class='kw'>sdfunc</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='sigma_twocomp.html'>sigma_twocomp</a></span>(<span class='no'>x</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span>),
     <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>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'>5</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>)<span class='kw'>[[</span><span class='fl'>1</span>]]
 
-  <span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt;              Estimate   se_notrans   t value       Pr(&gt;t)        Lower
-#&gt; parent_0 1.057896e+02 1.9023449649 55.610120 3.768361e-16 1.016451e+02
-#&gt; kmax     6.398190e-02 0.0143201029  4.467978 3.841828e-04 3.929235e-02
-#&gt; k0       1.612775e-04 0.0005866813  0.274898 3.940351e-01 5.846685e-08
-#&gt; r        2.263946e-01 0.1718110773  1.317695 1.061044e-01 4.335843e-02
-#&gt; sigma    5.332935e+00 0.9145907310  5.830952 4.036926e-05 3.340213e+00
-#&gt;                Upper
-#&gt; parent_0 109.9341588
-#&gt; kmax       0.1041853
-#&gt; k0         0.4448750
-#&gt; r          1.1821121
-#&gt; sigma      7.3256566</div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt;            DT50     DT90  DT50_k0 DT50_kmax
-#&gt; parent 36.86533 62.41511 4297.854  10.83349</div><div class='input'>
+  <span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in (function (t, parent_0, kmax, k0, r) {    parent = parent_0 * (kmax/(kmax - k0 + k0 * exp(r * t)))^(kmax/r)})(t = c(0, 1, 1.21212121212121, 2.42424242424242, 3, 3.63636363636364, 4.84848484848485, 6.06060606060606, 7, 7.27272727272727, 8.48484848484848, 9.6969696969697, 10.9090909090909, 12.1212121212121, 13.3333333333333, 14, 14.5454545454545, 15.7575757575758, 16.969696969697, 18.1818181818182, 19.3939393939394, 20.6060606060606, 21.8181818181818, 23.030303030303, 24.2424242424242, 25.4545454545455, 26.6666666666667, 27.8787878787879, 28, 29.0909090909091, 30.3030303030303, 31.5151515151515, 32.7272727272727, 33.9393939393939, 35.1515151515152, 36.3636363636364, 37.5757575757576, 38.7878787878788, 40, 41.2121212121212, 42.4242424242424, 43.6363636363636, 44.8484848484849, 46.0606060606061, 47.2727272727273, 48.4848484848485, 49.6969696969697, 50.9090909090909, 52.1212121212121, 53.3333333333333, 54.5454545454545, 55.7575757575758, 56.969696969697, 58.1818181818182, 59.3939393939394, 60, 60.6060606060606, 61.8181818181818, 63.030303030303, 64.2424242424242, 65.4545454545455, 66.6666666666667, 67.8787878787879, 69.0909090909091, 70.3030303030303, 71.5151515151515, 72.7272727272727, 73.9393939393939, 75.1515151515152, 76.3636363636364, 77.5757575757576, 78.7878787878788, 80, 81.2121212121212, 82.4242424242424, 83.6363636363636, 84.8484848484848, 86.0606060606061, 87.2727272727273, 88.4848484848485, 89.6969696969697, 90, 90.9090909090909, 92.1212121212121, 93.3333333333333, 94.5454545454545, 95.7575757575758, 96.969696969697, 98.1818181818182, 99.3939393939394, 100.606060606061, 101.818181818182, 103.030303030303, 104.242424242424, 105.454545454545, 106.666666666667, 107.878787878788, 109.090909090909, 110.30303030303, 111.515151515152, 112.727272727273, 113.939393939394, 115.151515151515, 116.363636363636, 117.575757575758, 118.787878787879, 120), parent.0 = c(parent = 101.95687), kmax = 0.1,     k0 = 1e-04, r = 0.2): unbenutztes Argument (parent.0 = 101.95687)</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.001 0 0.001</span></div><div class='input'>  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='output co'>#&gt; <span class='error'>Error in identical(fit$err_mod, "const"): Objekt 'm' nicht gefunden</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='error'>Error in summary(m): Objekt 'm' nicht gefunden</span></div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt; <span class='error'>Error in endpoints(m): Objekt 'm' nicht gefunden</span></div><div class='input'>
+
+  <span class='co'># Reproduce the plot on page 57 of FOCUS (2014)</span>
+  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.2</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>ylim</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'>100</span>),
+       <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'>"Residue"</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.4</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.8</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>3</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.001</span>, <span class='fl'>0.2</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>4</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.08</span>, <span class='fl'>0.2</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></span>(<span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fl'>0.05</span>,
+         <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='st'>"k0 = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.001</span>, <span class='fl'>0.08</span>),
+                         <span class='st'>", r = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.2</span>, <span class='fl'>0.4</span>, <span class='fl'>0.8</span>, <span class='fl'>0.2</span>, <span class='fl'>0.2</span>)),
+         <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'>
+  <span class='co'># Fit with synthetic data</span>
+  <span class='no'>logistic</span> <span class='kw'>&lt;-</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'>"logistic"</span>))
+
+  <span class='no'>sampling_times</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'>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='no'>parms_logistic</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>kmax</span> <span class='kw'>=</span> <span class='fl'>0.08</span>, <span class='kw'>k0</span> <span class='kw'>=</span> <span class='fl'>0.0001</span>, <span class='kw'>r</span> <span class='kw'>=</span> <span class='fl'>0.2</span>)
+  <span class='no'>d_logistic</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>logistic</span>,
+    <span class='no'>parms_logistic</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>),
+    <span class='no'>sampling_times</span>)
+  <span class='no'>d_2_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_logistic</span>,
+    <span class='kw'>sdfunc</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='sigma_twocomp.html'>sigma_twocomp</a></span>(<span class='no'>x</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span>),
+    <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>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'>5</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>)<span class='kw'>[[</span><span class='fl'>1</span>]]
+
+  <span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in (function (t, parent_0, kmax, k0, r) {    parent = parent_0 * (kmax/(kmax - k0 + k0 * exp(r * t)))^(kmax/r)})(t = c(0, 1, 1.21212121212121, 2.42424242424242, 3, 3.63636363636364, 4.84848484848485, 6.06060606060606, 7, 7.27272727272727, 8.48484848484848, 9.6969696969697, 10.9090909090909, 12.1212121212121, 13.3333333333333, 14, 14.5454545454545, 15.7575757575758, 16.969696969697, 18.1818181818182, 19.3939393939394, 20.6060606060606, 21.8181818181818, 23.030303030303, 24.2424242424242, 25.4545454545455, 26.6666666666667, 27.8787878787879, 28, 29.0909090909091, 30.3030303030303, 31.5151515151515, 32.7272727272727, 33.9393939393939, 35.1515151515152, 36.3636363636364, 37.5757575757576, 38.7878787878788, 40, 41.2121212121212, 42.4242424242424, 43.6363636363636, 44.8484848484849, 46.0606060606061, 47.2727272727273, 48.4848484848485, 49.6969696969697, 50.9090909090909, 52.1212121212121, 53.3333333333333, 54.5454545454545, 55.7575757575758, 56.969696969697, 58.1818181818182, 59.3939393939394, 60, 60.6060606060606, 61.8181818181818, 63.030303030303, 64.2424242424242, 65.4545454545455, 66.6666666666667, 67.8787878787879, 69.0909090909091, 70.3030303030303, 71.5151515151515, 72.7272727272727, 73.9393939393939, 75.1515151515152, 76.3636363636364, 77.5757575757576, 78.7878787878788, 80, 81.2121212121212, 82.4242424242424, 83.6363636363636, 84.8484848484848, 86.0606060606061, 87.2727272727273, 88.4848484848485, 89.6969696969697, 90, 90.9090909090909, 92.1212121212121, 93.3333333333333, 94.5454545454545, 95.7575757575758, 96.969696969697, 98.1818181818182, 99.3939393939394, 100.606060606061, 101.818181818182, 103.030303030303, 104.242424242424, 105.454545454545, 106.666666666667, 107.878787878788, 109.090909090909, 110.30303030303, 111.515151515152, 112.727272727273, 113.939393939394, 115.151515151515, 116.363636363636, 117.575757575758, 118.787878787879, 120), parent.0 = c(parent = 101.95687), kmax = 0.1,     k0 = 1e-04, r = 0.2): unbenutztes Argument (parent.0 = 101.95687)</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'>  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='output co'>#&gt; <span class='error'>Error in identical(fit$err_mod, "const"): Objekt 'm' nicht gefunden</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='error'>Error in summary(m): Objekt 'm' nicht gefunden</span></div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt; <span class='error'>Error in endpoints(m): Objekt 'm' nicht gefunden</span></div><div class='input'>
 </div></pre>
   </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>
-      <li><a href="#note">Note</a></li>
-      <li><a href="#references">References</a></li>
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
   </div>
 </div>
 
@@ -241,7 +276,7 @@ an increasing rate constant, supposedly caused by microbial growth</p>
 </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>