Merge branch 'nlmixr'

1 files changed, 22 insertions, 9 deletions

diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html
index 55c411e7..69345b2f 100644
--- a/docs/dev/reference/plot.mixed.mmkin.html
+++ b/docs/dev/reference/plot.mixed.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">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span>
       </span>
     </div>
 
@@ -157,11 +157,13 @@
   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>,
   pred_over <span class='op'>=</span> <span class='cn'>NULL</span>,
+  test_log_parms <span class='op'>=</span> <span class='cn'>FALSE</span>,
+  conf.level <span class='op'>=</span> <span class='fl'>0.6</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.legend <span class='op'>=</span> <span class='fl'>0.02</span> <span class='op'>+</span> <span class='fl'>0.07</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>,
@@ -212,6 +214,16 @@ predicted values?</p></td>
 from <a href='mkinpredict.html'>mkinpredict</a> with a compatible <a href='mkinmod.html'>mkinmod</a>.</p></td>
     </tr>
     <tr>
+      <th>test_log_parms</th>
+      <td><p>Passed to <a href='mean_degparms.html'>mean_degparms</a> in the case of an
+<a href='mixed.html'>mixed.mmkin</a> object</p></td>
+    </tr>
+    <tr>
+      <th>conf.level</th>
+      <td><p>Passed to <a href='mean_degparms.html'>mean_degparms</a> in the case of an
+<a href='mixed.html'>mixed.mmkin</a> object</p></td>
+    </tr>
+    <tr>
       <th>ymax</th>
       <td><p>Vector of maximum y axis values</p></td>
     </tr>
@@ -278,23 +290,24 @@ corresponding model prediction lines for the different datasets.</p></td>
 </div><div class='img'><img src='plot.mixed.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'>
 <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='co'># It still takes 20 seconds to run</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.mmkin-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>, transformations <span class='op'>=</span> <span class='st'>"saemix"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Dec 21 05:58:23 2020"
-#&gt; ....
-#&gt;     Minimisation finished
-#&gt; [1] "Mon Dec 21 05:58:30 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.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
+</div><div class='output co'>#&gt; <span class='error'>Error in saem(f, transformations = "saemix"): unused argument (transformations = "saemix")</span></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='output co'>#&gt; <span class='error'>Error in plot(f_saem): object 'f_saem' not found</span></div><div class='input'>
+<span class='va'>f_obs</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>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span>
+<span class='va'>f_nlmix</span> <span class='op'>&lt;-</span> <span class='fu'>nlmix</span><span class='op'>(</span><span class='va'>f_obs</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='error'>Error in nlmix(f_obs): could not find function "nlmix"</span></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_nlmix</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='error'>Error in plot(f_nlmix): object 'f_nlmix' not found</span></div><div class='input'>
 <span class='co'># We can overlay the two variants if we generate predictions</span>
 <span class='va'>pred_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>dfop_sfo</span>,
   <span class='va'>f_nlme</span><span class='op'>$</span><span class='va'>bparms.optim</span><span class='op'>[</span><span class='op'>-</span><span class='fl'>1</span><span class='op'>]</span>,
   <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='va'>f_nlme</span><span class='op'>$</span><span class='va'>bparms.optim</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span>, A1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>,
   <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>180</span>, by <span class='op'>=</span> <span class='fl'>0.2</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_saem</span>, pred_over <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>nlme <span class='op'>=</span> <span class='va'>pred_nlme</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='img'><img src='plot.mixed.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
+</div><div class='output co'>#&gt; <span class='error'>Error in plot(f_saem, pred_over = list(nlme = pred_nlme)): object 'f_saem' not found</span></div><div class='input'><span class='co'># }</span>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">