Merge plot methods for nlme.mmkin and saem.mmkin

This avoids code duplication
author: Johannes Ranke <jranke@uni-bremen.de> 2020-11-09 16:33:19 +0100
committer: Johannes Ranke <jranke@uni-bremen.de> 2020-11-09 16:33:19 +0100
commit: a1631098acfc3352e19c331e568bd6f5766b3c3d (patch)
tree: 6475ead3d4a0f6e754426d713514b594cefadb73 /docs
parent: 6464d3999338d34c081f360694dbc0bc0abf68cb (diff)
12 files changed, 557 insertions, 23 deletions
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index e14af5e0..4b2b76f7 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
   web_only/NAFTA_examples: NAFTA_examples.html
   web_only/benchmarks: benchmarks.html
   web_only/compiled_models: compiled_models.html
-last_built: 2020-11-09T13:23Z
+last_built: 2020-11-09T15:29Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png
index cd2014eb..8ada7133 100644
--- a/docs/dev/reference/Rplot002.png
+++ b/docs/dev/reference/Rplot002.png
diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png
index 7514f1a4..cd2014eb 100644
--- a/docs/dev/reference/Rplot003.png
+++ b/docs/dev/reference/Rplot003.png
diff --git a/docs/dev/reference/dot-plot_mixed.html b/docs/dev/reference/dot-plot_mixed.html
new file mode 100644
index 00000000..e359c5ea
--- /dev/null
+++ b/docs/dev/reference/dot-plot_mixed.html
@@ -0,0 +1,203 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Not intended to be called directly by the user — .plot_mixed • mkin</title>
+
+
+<!-- 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="Not intended to be called directly by the user — .plot_mixed" />
+<meta property="og:description" content="Not intended to be called directly by the user" />
+
+
+<meta name="robots" content="noindex">
+
+<!-- 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 data-spy="scroll" data-target="#toc">
+    <div class="container template-reference-topic">
+      <header>
+      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">mkin</a>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="../reference/index.html">Functions and data</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/mkin.html">Introduction to mkin</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+    </li>
+    <li>
+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+    </li>
+  </ul>
+</li>
+<li>
+  <a href="../news/index.html">News</a>
+</li>
+      </ul>
+      <ul class="nav navbar-nav navbar-right">
+        <li>
+  <a href="https://github.com/jranke/mkin/">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
+      
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header>
+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Not intended to be called directly by the user</h1>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot_mixed.R'><code>R/plot_mixed.R</code></a></small>
+    <div class="hidden name"><code>dot-plot_mixed.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Not intended to be called directly by the user</p>
+    </div>
+
+    <pre class="usage"><span class='fu'>.plot_mixed</span><span class='op'>(</span>
+  <span class='va'>x</span>,
+  i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>,
+  <span class='va'>degparms_optim</span>,
+  <span class='va'>degparms_pop</span>,
+  <span class='va'>residuals</span>,
+  obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
+  standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
+  xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>,
+  resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>,
+  ymax <span class='op'>=</span> <span class='st'>"auto"</span>,
+  maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
+  ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>,
+  nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>,
+  rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>,
+  rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>,
+  pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>,
+  col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>,
+  lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>,
+  frame <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  <span class='va'>...</span>
+<span class='op'>)</span></pre>
+
+
+
+  </div>
+  <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>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
diff --git a/docs/dev/reference/get_deg_func.html b/docs/dev/reference/get_deg_func.html
index ea0676cc..a266bf5f 100644
--- a/docs/dev/reference/get_deg_func.html
+++ b/docs/dev/reference/get_deg_func.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -120,7 +120,7 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -139,7 +139,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Retrieve a degradation function from the mmkin namespace</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a></small>
     <div class="hidden name"><code>get_deg_func.Rd</code></div>
     </div>
 
@@ -147,7 +147,7 @@
     <p>Retrieve a degradation function from the mmkin namespace</p>
     </div>
 
-    <pre class="usage"><span class='fu'>get_deg_func</span>()</pre>
+    <pre class="usage"><span class='fu'>get_deg_func</span><span class='op'>(</span><span class='op'>)</span></pre>
 
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -170,7 +170,7 @@ nlme.mmkin</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index f5621402..5ed2044b 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -325,9 +325,9 @@ of an mmkin object</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="plot.nlme.mmkin.html">plot(<i>&lt;nlme.mmkin&gt;</i>)</a></code> </p>
+          <p><code><a href="plot_mixed.html">plot(<i>&lt;saem.mmkin&gt;</i>)</a></code> <code><a href="plot_mixed.html">plot(<i>&lt;nlme.mmkin&gt;</i>)</a></code> </p>
         </td>
-        <td><p>Plot a fitted nonlinear mixed model obtained via an mmkin row object</p></td>
+        <td><p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p></td>
       </tr><tr>
         
         <td>
@@ -349,12 +349,6 @@ of an mmkin object</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="plot.saem.mmkin.html">plot(<i>&lt;saem.mmkin&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Plot an saem fitted nonlinear mixed model obtained via an mmkin row object</p></td>
-      </tr><tr>
-        
-        <td>
           <p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">mean_degparms()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p>
         </td>
         <td><p>Helper functions to create nlme models from mmkin row objects</p></td>
diff --git a/docs/dev/reference/plot_mixed-1.png b/docs/dev/reference/plot_mixed-1.png
new file mode 100644
index 00000000..5cb33214
--- /dev/null
+++ b/docs/dev/reference/plot_mixed-1.png
diff --git a/docs/dev/reference/plot_mixed-2.png b/docs/dev/reference/plot_mixed-2.png
new file mode 100644
index 00000000..c0d67204
--- /dev/null
+++ b/docs/dev/reference/plot_mixed-2.png
diff --git a/docs/dev/reference/plot_mixed-3.png b/docs/dev/reference/plot_mixed-3.png
new file mode 100644
index 00000000..67058e6c
--- /dev/null
+++ b/docs/dev/reference/plot_mixed-3.png
diff --git a/docs/dev/reference/plot_mixed.html b/docs/dev/reference/plot_mixed.html
new file mode 100644
index 00000000..b5b3ba49
--- /dev/null
+++ b/docs/dev/reference/plot_mixed.html
@@ -0,0 +1,336 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot_mixed • mkin</title>
+
+
+<!-- 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="Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot_mixed" />
+<meta property="og:description" content="Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object" />
+
+
+<meta name="robots" content="noindex">
+
+<!-- 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 data-spy="scroll" data-target="#toc">
+    <div class="container template-reference-topic">
+      <header>
+      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
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+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">mkin</a>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="../reference/index.html">Functions and data</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/mkin.html">Introduction to mkin</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+    </li>
+    <li>
+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+    </li>
+  </ul>
+</li>
+<li>
+  <a href="../news/index.html">News</a>
+</li>
+      </ul>
+      <ul class="nav navbar-nav navbar-right">
+        <li>
+  <a href="https://github.com/jranke/mkin/">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
+      
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header>
+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</h1>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot_mixed.R'><code>R/plot_mixed.R</code></a></small>
+    <div class="hidden name"><code>plot_mixed.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p>
+    </div>
+
+    <pre class="usage"><span class='co'># S3 method for saem.mmkin</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
+  <span class='va'>x</span>,
+  i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>,
+  obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
+  standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
+  xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>,
+  resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>,
+  ymax <span class='op'>=</span> <span class='st'>"auto"</span>,
+  maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
+  ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>,
+  nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>,
+  rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>,
+  rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>,
+  pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>,
+  col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>,
+  lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>,
+  frame <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  <span class='va'>...</span>
+<span class='op'>)</span>
+
+<span class='co'># S3 method for nlme.mmkin</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
+  <span class='va'>x</span>,
+  i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>,
+  obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
+  standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
+  xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>,
+  resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>,
+  ymax <span class='op'>=</span> <span class='st'>"auto"</span>,
+  maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
+  ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>,
+  nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>,
+  rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>,
+  rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>,
+  pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>,
+  col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>,
+  lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>,
+  frame <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  <span class='va'>...</span>
+<span class='op'>)</span></pre>
+
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>x</th>
+      <td><p>An object of class <a href='saem.html'>saem.mmkin</a> or <a href='nlme.mmkin.html'>nlme.mmkin</a></p></td>
+    </tr>
+    <tr>
+      <th>i</th>
+      <td><p>A numeric index to select datasets for which to plot the individual predictions,
+in case plots get too large</p></td>
+    </tr>
+    <tr>
+      <th>obs_vars</th>
+      <td><p>A character vector of names of the observed variables for
+which the data and the model should be plotted. Defauls to all observed
+variables in the model.</p></td>
+    </tr>
+    <tr>
+      <th>standardized</th>
+      <td><p>Should the residuals be standardized? Only takes effect if
+<code>resplot = "time"</code>.</p></td>
+    </tr>
+    <tr>
+      <th>xlab</th>
+      <td><p>Label for the x axis.</p></td>
+    </tr>
+    <tr>
+      <th>xlim</th>
+      <td><p>Plot range in x direction.</p></td>
+    </tr>
+    <tr>
+      <th>resplot</th>
+      <td><p>Should the residuals plotted against time or against
+predicted values?</p></td>
+    </tr>
+    <tr>
+      <th>ymax</th>
+      <td><p>Vector of maximum y axis values</p></td>
+    </tr>
+    <tr>
+      <th>maxabs</th>
+      <td><p>Maximum absolute value of the residuals. This is used for the
+scaling of the y axis and defaults to "auto".</p></td>
+    </tr>
+    <tr>
+      <th>ncol.legend</th>
+      <td><p>Number of columns to use in the legend</p></td>
+    </tr>
+    <tr>
+      <th>nrow.legend</th>
+      <td><p>Number of rows to use in the legend</p></td>
+    </tr>
+    <tr>
+      <th>rel.height.legend</th>
+      <td><p>The relative height of the legend shown on top</p></td>
+    </tr>
+    <tr>
+      <th>rel.height.bottom</th>
+      <td><p>The relative height of the bottom plot row</p></td>
+    </tr>
+    <tr>
+      <th>pch_ds</th>
+      <td><p>Symbols to be used for plotting the data.</p></td>
+    </tr>
+    <tr>
+      <th>col_ds</th>
+      <td><p>Colors used for plotting the observed data and the
+corresponding model prediction lines for the different datasets.</p></td>
+    </tr>
+    <tr>
+      <th>lty_ds</th>
+      <td><p>Line types to be used for the model predictions.</p></td>
+    </tr>
+    <tr>
+      <th>frame</th>
+      <td><p>Should a frame be drawn around the plots?</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>The functions are called for their side effect.</p>
+    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+    <p>Johannes Ranke</p>
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
+ <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"ds "</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span>
+<span class='va'>dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
+  A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='co'># \dontrun{</span>
+<span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='img'><img src='plot_mixed-1.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span>
+<span class='co'># For this fit we need to increase pnlsMaxiter, and we increase the</span>
+<span class='co'># tolerance in order to speed up the fit for this example evaluation</span>
+<span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-3</span><span class='op'>)</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span>
+</div><div class='img'><img src='plot_mixed-2.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='va'>f_saem</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Running main SAEM algorithm
+#&gt; [1] "Mon Nov  9 16:07:05 2020"
+#&gt; ....
+#&gt;     Minimisation finished
+#&gt; [1] "Mon Nov  9 16:07:14 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span>
+</div><div class='img'><img src='plot_mixed-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
+</div></pre>
+  </div>
+  <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>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
diff --git a/docs/dev/reference/reexports.html b/docs/dev/reference/reexports.html
index fe27de4b..f12a2690 100644
--- a/docs/dev/reference/reexports.html
+++ b/docs/dev/reference/reexports.html
@@ -45,6 +45,8 @@ below to see their documentation.
 
   lmtestlrtest
 
+  nlmenlme
+
 " />
 
 
@@ -77,7 +79,7 @@ below to see their documentation.
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -125,7 +127,7 @@ below to see their documentation.
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -144,16 +146,18 @@ below to see their documentation.
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Objects exported from other packages</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/lrtest.mkinfit.R'><code>R/lrtest.mkinfit.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/lrtest.mkinfit.R'><code>R/lrtest.mkinfit.R</code></a>, <a href='https://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a></small>
     <div class="hidden name"><code>reexports.Rd</code></div>
     </div>
 
     <div class="ref-description">
     <p>These objects are imported from other packages. Follow the links
 below to see their documentation.</p>
-<dl'>
+<dl>
   <dt>lmtest</dt><dd><p><code><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></code></p></dd>
 
+  <dt>nlme</dt><dd><p><code><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></code></p></dd>
+
 </dl>
     </div>
 
@@ -175,7 +179,7 @@ below to see their documentation.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml
index d6f55550..5cfca07a 100644
--- a/docs/dev/sitemap.xml
+++ b/docs/dev/sitemap.xml
@@ -157,10 +157,7 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/plot.nafta.html</loc>
   </url>
   <url>
-    <loc>https://pkgdown.jrwb.de/mkin/reference/plot.nlme.mmkin.html</loc>
-  </url>
-  <url>
-    <loc>https://pkgdown.jrwb.de/mkin/reference/plot.saem.mmkin.html</loc>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/plot_mixed.html</loc>
   </url>
   <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/print.mkinds.html</loc>
author	Johannes Ranke <jranke@uni-bremen.de>	2020-11-09 16:33:19 +0100
committer	Johannes Ranke <jranke@uni-bremen.de>	2020-11-09 16:33:19 +0100
commit	a1631098acfc3352e19c331e568bd6f5766b3c3d (patch)
tree	6475ead3d4a0f6e754426d713514b594cefadb73 /docs
parent	6464d3999338d34c081f360694dbc0bc0abf68cb (diff)