From dd80ab5d64bc6b56587b0542dc95e965a3a25590 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 24 Oct 2020 00:32:00 +0200
Subject: Plot method for nlme.mmkin objects

Update docs
---
 docs/dev/reference/plot.nlme.mmkin.html | 141 +++++++++++++++++++++-----------
 1 file changed, 95 insertions(+), 46 deletions(-)

(limited to 'docs/dev/reference/plot.nlme.mmkin.html')

diff --git a/docs/dev/reference/plot.nlme.mmkin.html b/docs/dev/reference/plot.nlme.mmkin.html
index 7e6124a1..f17a23e3 100644
--- a/docs/dev/reference/plot.nlme.mmkin.html
+++ b/docs/dev/reference/plot.nlme.mmkin.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>Plot a fitted nonlinear mixed model obtained via an mmkin row object</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/plot.nlme.mmkin.R'><code>R/plot.nlme.mmkin.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.nlme.mmkin.R'><code>R/plot.nlme.mmkin.R</code></a></small>
     <div class="hidden name"><code>plot.nlme.mmkin.Rd</code></div>
     </div>
 
@@ -148,21 +148,29 @@
     </div>
 
     <pre class="usage"><span class='co'># S3 method for nlme.mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(
-  <span class='no'>x</span>,
-  <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span>(<span class='no'>x</span>$<span class='no'>mmkin_orig</span>),
-  <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
-  <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>,
-  <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"time"</span>, <span class='st'>"errmod"</span>),
-  <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>errmin_var</span> <span class='kw'>=</span> <span class='st'>"All data"</span>,
-  <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>,
-  <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>,
-  <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>,
-  <span class='kw'>ymax</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
-  <span class='no'>...</span>
-)</pre>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
+  <span class='va'>x</span>,
+  i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin_orig</span><span class='op'>)</span>,
+  main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin_orig</span><span class='op'>)</span>,
+  obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
+  standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
+  ylab <span class='op'>=</span> <span class='st'>"Observed"</span>,
+  xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>,
+  legends <span class='op'>=</span> <span class='fl'>1</span>,
+  lpos <span class='op'>=</span> <span class='st'>"topright"</span>,
+  inset <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='fl'>0.05</span>, <span class='fl'>0.05</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>,
+  cex <span class='op'>=</span> <span class='fl'>0.7</span>,
+  rel.height.middle <span class='op'>=</span> <span class='fl'>0.9</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">
@@ -180,36 +188,56 @@ in case plots get too large</p></td>
       <th>main</th>
       <td><p>The main title placed on the outer margin of the plot.</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>ylab</th>
+      <td><p>Label for the y axis.</p></td>
+    </tr>
+    <tr>
+      <th>xlim</th>
+      <td><p>Plot range in x direction.</p></td>
+    </tr>
     <tr>
       <th>legends</th>
       <td><p>An index for the fits for which legends should be shown.</p></td>
     </tr>
     <tr>
-      <th>resplot</th>
-      <td><p>Should the residuals plotted against time, using
-<code><a href='mkinresplot.html'>mkinresplot</a></code>, or as squared residuals against predicted
-values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td>
+      <th>lpos</th>
+      <td><p>Position(s) of the legend(s). Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> as
+the first argument.  If not length one, this should be of the same length
+as the obs_var argument.</p></td>
     </tr>
     <tr>
-      <th>standardized</th>
-      <td><p>Should the residuals be standardized? This option
-is passed to <code><a href='mkinresplot.html'>mkinresplot</a></code>, it only takes effect if
-<code>resplot = "time"</code>.</p></td>
+      <th>inset</th>
+      <td><p>Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> if applicable.</p></td>
     </tr>
     <tr>
-      <th>show_errmin</th>
-      <td><p>Should the chi2 error level be shown on top of the plots
-to the left?</p></td>
+      <th>resplot</th>
+      <td><p>Should the residuals plotted against time or against
+predicted values?</p></td>
     </tr>
     <tr>
-      <th>errmin_var</th>
-      <td><p>The variable for which the FOCUS chi2 error value should
-be shown.</p></td>
+      <th>ymax</th>
+      <td><p>Vector of maximum y axis values</p></td>
     </tr>
     <tr>
-      <th>errmin_digits</th>
-      <td><p>The number of significant digits for rounding the FOCUS
-chi2 error percentage.</p></td>
+      <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>cex</th>
@@ -221,8 +249,21 @@ chi2 error percentage.</p></td>
 than two rows of plots are shown.</p></td>
     </tr>
     <tr>
-      <th>ymax</th>
-      <td><p>Maximum y axis value for <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p></td>
+      <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>
@@ -234,16 +275,24 @@ than two rows of plots are shown.</p></td>
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>The function is called for its 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='no'>ds</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>],
- <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)], <span class='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>))
-<span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='st'>"SFO"</span>, <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.0195</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.011</span></div><div class='input'><span class='co'>#plot(f) # too many panels for pkgdown</span>
-<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f</span>[, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='plot.nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>)
-<span class='no'>f_nlme</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>)
-
-<span class='co'>#plot(f_nlme) # too many panels for pkgdown</span>
-<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='plot.nlme.mmkin-2.png' alt='' width='700' height='433' /></div></pre>
+    <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='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>, cores <span class='op'>=</span> <span class='fl'>1</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.nlme.mmkin-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-4</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.nlme.mmkin-2.png' alt='' width='700' height='433' /></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -259,7 +308,7 @@ than two rows of plots are shown.</p></td>
 </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>
 
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