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authorJohannes Ranke <jranke@uni-bremen.de>2022-02-08 17:17:29 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-02-08 17:17:29 +0100
commit0fa8a770812775d697717ad723f7f61fb04b7fef (patch)
tree17473ddf787541745d47dab063bc643ec59a9557 /docs/dev/reference/mmkin.html
parentd081384ddcb75a9f92fad33e4e3f6d6796f98e67 (diff)
parentc0638c84568d475b3b059e2c6e593e6f03b846bc (diff)
Merge branch 'nlmixr'
Diffstat (limited to 'docs/dev/reference/mmkin.html')
-rw-r--r--docs/dev/reference/mmkin.html36
1 files changed, 21 insertions, 15 deletions
diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html
index 651eb9a6..c385bbf6 100644
--- a/docs/dev/reference/mmkin.html
+++ b/docs/dev/reference/mmkin.html
@@ -75,7 +75,7 @@ datasets specified in its first two arguments." />
</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">1.0.5</span>
</span>
</div>
@@ -124,7 +124,7 @@ datasets specified in its first two arguments." />
<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>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -155,10 +155,13 @@ datasets specified in its first two arguments.</p>
<pre class="usage"><span class='fu'>mmkin</span><span class='op'>(</span>
models <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'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>,
<span class='va'>datasets</span>,
- cores <span class='op'>=</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span>,
+ cores <span class='op'>=</span> <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>[</span><span class='st'>"sysname"</span><span class='op'>]</span> <span class='op'>==</span> <span class='st'>"Windows"</span><span class='op'>)</span> <span class='fl'>1</span> <span class='kw'>else</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span>,
cluster <span class='op'>=</span> <span class='cn'>NULL</span>,
<span class='va'>...</span>
-<span class='op'>)</span></pre>
+<span class='op'>)</span>
+
+<span class='co'># S3 method for mmkin</span>
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</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">
@@ -180,7 +183,8 @@ data for <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
is only used when the <code>cluster</code> argument is <code>NULL</code>. On Windows
machines, cores &gt; 1 is not supported, you need to use the <code>cluster</code>
argument to use multiple logical processors. Per default, all cores
-detected by <code><a href='https://rdrr.io/r/parallel/detectCores.html'>parallel::detectCores()</a></code> are used.</p></td>
+detected by <code><a href='https://rdrr.io/r/parallel/detectCores.html'>parallel::detectCores()</a></code> are used, except on Windows where
+the default is 1.</p></td>
</tr>
<tr>
<th>cluster</th>
@@ -189,7 +193,11 @@ for parallel execution.</p></td>
</tr>
<tr>
<th>...</th>
- <td><p>Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
+ <td><p>Not used.</p></td>
+ </tr>
+ <tr>
+ <th>x</th>
+ <td><p>An mmkin object.</p></td>
</tr>
</table>
@@ -227,19 +235,19 @@ plotting.</p></div>
<span class='va'>time_default</span>
</div><div class='output co'>#&gt; user system elapsed
-#&gt; 4.968 0.427 1.342 </div><div class='input'><span class='va'>time_1</span>
+#&gt; 4.771 0.576 1.803 </div><div class='input'><span class='va'>time_1</span>
</div><div class='output co'>#&gt; user system elapsed
-#&gt; 5.365 0.000 5.368 </div><div class='input'>
+#&gt; 5.779 0.000 5.781 </div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
-#&gt; 0.7340478 0.2659522 0.7505687 0.2494313
+#&gt; 0.7340481 0.2659519 0.7505683 0.2494317
#&gt;
#&gt; $distimes
#&gt; DT50 DT90
#&gt; parent 0.877769 2.915885
-#&gt; M1 2.325746 7.725960
-#&gt; M2 33.720083 112.015691
+#&gt; M1 2.325744 7.725956
+#&gt; M2 33.720100 112.015749
#&gt; </div><div class='input'>
<span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='op'>]</span><span class='op'>)</span>
@@ -266,12 +274,10 @@ plotting.</p></div>
#&gt; dataset
#&gt; model A B C D
#&gt; SFO OK OK OK OK
-#&gt; FOMC C OK OK OK
+#&gt; FOMC OK OK OK OK
#&gt; DFOP OK OK OK OK
#&gt;
-#&gt; OK: No warnings
-#&gt; C: Optimisation did not converge:
-#&gt; false convergence (8)</div><div class='input'><span class='co'># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span>
+#&gt; OK: No warnings</div><div class='input'><span class='co'># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span>
<span class='co'># dataset is really SFO, and the FOMC fit is overparameterised</span>
<span class='fu'>stopCluster</span><span class='op'>(</span><span class='va'>cl</span><span class='op'>)</span>
<span class='co'># }</span>

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