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-rw-r--r--docs/reference/parms.html123
1 files changed, 100 insertions, 23 deletions
diff --git a/docs/reference/parms.html b/docs/reference/parms.html
index f62b3898..30dc7770 100644
--- a/docs/reference/parms.html
+++ b/docs/reference/parms.html
@@ -74,7 +74,7 @@ considering the error structure that was assumed for the fit." />
</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">0.9.50.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span>
</span>
</div>
@@ -111,6 +111,9 @@ considering the error structure that was assumed for the fit." />
<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>
@@ -119,7 +122,7 @@ considering the error structure that was assumed for the fit." />
</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>
@@ -138,7 +141,7 @@ considering the error structure that was assumed for the fit." />
<div class="col-md-9 contents">
<div class="page-header">
<h1>Extract model parameters from mkinfit models</h1>
- <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parms.mkinfit.R'><code>R/parms.mkinfit.R</code></a></small>
+ <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/parms.mkinfit.R'><code>R/parms.mkinfit.R</code></a></small>
<div class="hidden name"><code>parms.Rd</code></div>
</div>
@@ -148,17 +151,21 @@ model parameters, in order to avoid working with a fitted model without
considering the error structure that was assumed for the fit.</p>
</div>
- <pre class="usage"><span class='fu'>parms</span>(<span class='no'>object</span>, <span class='no'>...</span>)
+ <pre class="usage"><span class='fu'>parms</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='co'># S3 method for mkinfit</span>
-<span class='fu'>parms</span>(<span class='no'>object</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
+<span class='fu'>parms</span><span class='op'>(</span><span class='va'>object</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
+
+<span class='co'># S3 method for mmkin</span>
+<span class='fu'>parms</span><span class='op'>(</span><span class='va'>object</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</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>object</th>
- <td><p>A fitted model object</p></td>
+ <td><p>A fitted model object. Methods are implemented for
+<code><a href='mkinfit.html'>mkinfit()</a></code> objects and for <code><a href='mmkin.html'>mmkin()</a></code> objects.</p></td>
</tr>
<tr>
<th>...</th>
@@ -173,24 +180,94 @@ as used internally during the optimisation?</p></td>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>A numeric vector of fitted model parameters</p>
+ <p>For mkinfit objects, a numeric vector of fitted model parameters.
+For mmkin row objects, a matrix with the parameters with a
+row for each dataset. If the mmkin object has more than one row, a list of
+such matrices is returned.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#&gt; <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#&gt; Sum of squared residuals at call 1: 2388.077
-#&gt; Sum of squared residuals at call 3: 2388.077
-#&gt; Sum of squared residuals at call 4: 247.1962
-#&gt; Sum of squared residuals at call 7: 200.6791
-#&gt; Sum of squared residuals at call 10: 197.7231
-#&gt; Sum of squared residuals at call 11: 197.0872
-#&gt; Sum of squared residuals at call 14: 196.535
-#&gt; Sum of squared residuals at call 15: 196.535
-#&gt; Sum of squared residuals at call 16: 196.535
-#&gt; Sum of squared residuals at call 17: 196.5334
-#&gt; Sum of squared residuals at call 20: 196.5334
-#&gt; Sum of squared residuals at call 25: 196.5334
-#&gt; Negative log-likelihood at call 31: 26.64668</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='input'><span class='fu'>parms</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 k_parent_sink sigma
-#&gt; 82.4921598 0.3060633 4.6730124 </div><div class='input'><span class='fu'>parms</span>(<span class='no'>fit</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink sigma
-#&gt; 82.492160 -1.183963 4.673012 </div></pre>
+ <pre class="examples"><div class='input'><span class='co'># mkinfit objects</span>
+<span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='fu'>parms</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; parent_0 k_parent sigma
+#&gt; 82.4921598 0.3060633 4.6730124 </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fit</span>, transformed <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; parent_0 log_k_parent sigma
+#&gt; 82.492160 -1.183963 4.673012 </div><div class='input'>
+<span class='co'># mmkin objects</span>
+<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='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</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='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='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'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span>
+<span class='co'># \dontrun{</span>
+<span class='va'>fits</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/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'>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>
+</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 = 0.00408</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0492</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.00985</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.00815</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='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
+#&gt; parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450
+#&gt; k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421
+#&gt; sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673</div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; $SFO
+#&gt; Dataset 7
+#&gt; parent_0 82.666781678
+#&gt; k_parent 0.009647805
+#&gt; sigma 7.040168584
+#&gt;
+#&gt; $FOMC
+#&gt; Dataset 7
+#&gt; parent_0 92.6837649
+#&gt; alpha 0.4967832
+#&gt; beta 14.1451255
+#&gt; sigma 1.9167519
+#&gt;
+#&gt; $DFOP
+#&gt; Dataset 7
+#&gt; parent_0 91.058971503
+#&gt; k1 0.044946770
+#&gt; k2 0.002868336
+#&gt; g 0.526942415
+#&gt; sigma 2.221302196
+#&gt; </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; $SFO
+#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
+#&gt; parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450
+#&gt; k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421
+#&gt; sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673
+#&gt;
+#&gt; $FOMC
+#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
+#&gt; parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481458
+#&gt; alpha 1.338667 0.4967832 1.639099 1.074460 0.2805272
+#&gt; beta 13.033315 14.1451255 5.007077 4.397126 6.9052224
+#&gt; sigma 1.847671 1.9167519 1.066063 3.146056 1.6222778
+#&gt;
+#&gt; $DFOP
+#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
+#&gt; parent_0 96.55213663 91.058971503 90.34509469 98.14858850 94.311323409
+#&gt; k1 0.21954589 0.044946770 0.41232289 0.31697588 0.080663853
+#&gt; k2 0.02957934 0.002868336 0.07581767 0.03260384 0.003425417
+#&gt; g 0.44845068 0.526942415 0.66091965 0.65322767 0.342652880
+#&gt; sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831
+#&gt; </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span>, transformed <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; $SFO
+#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
+#&gt; parent_0 88.522754 82.666782 86.854731 91.777931 82.148094
+#&gt; log_k_parent -2.848234 -4.641025 -1.559232 -2.093737 -4.933090
+#&gt; sigma 5.152745 7.040169 3.676964 6.466923 6.504577
+#&gt;
+#&gt; $FOMC
+#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
+#&gt; parent_0 95.5585751 92.6837649 90.7197870 98.38393897 94.848146
+#&gt; log_alpha 0.2916741 -0.6996015 0.4941466 0.07181816 -1.271085
+#&gt; log_beta 2.5675088 2.6493701 1.6108523 1.48095106 1.932278
+#&gt; sigma 1.8476712 1.9167519 1.0660627 3.14605557 1.622278
+#&gt;
+#&gt; $DFOP
+#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
+#&gt; parent_0 96.5521366 91.05897150 90.3450947 98.1485885 94.311323
+#&gt; log_k1 -1.5161940 -3.10227638 -0.8859485 -1.1489296 -2.517465
+#&gt; log_k2 -3.5206791 -5.85402317 -2.5794240 -3.4233253 -5.676532
+#&gt; g_ilr -0.1463234 0.07627854 0.4719196 0.4477805 -0.460676
+#&gt; sigma 1.3569047 2.22130220 1.3416908 2.8715985 1.942068
+#&gt; </div><div class='input'><span class='co'># }</span>
+</div></pre>
</div>
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<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -206,7 +283,7 @@ as used internally during the optimisation?</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>
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