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-rw-r--r--docs/dev/reference/parms.html67
1 files changed, 37 insertions, 30 deletions
diff --git a/docs/dev/reference/parms.html b/docs/dev/reference/parms.html
index bd35d3c1..ba0e89bb 100644
--- a/docs/dev/reference/parms.html
+++ b/docs/dev/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-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>
@@ -122,7 +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>
@@ -141,7 +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>
@@ -151,13 +151,13 @@ 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>)
+<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='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></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -187,19 +187,24 @@ 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='co'># mkinfit objects</span>
-<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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>parms</span>(<span class='no'>fit</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='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 sigma
+<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='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>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)]))
-<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>ds</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>6</span>:<span class='fl'>10</span>)
+<span class='va'>ds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
+ <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</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='no'>fits</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</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 = 0.00408</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='no'>fits</span>[<span class='st'>"SFO"</span>, ])</div><div class='output co'>#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
+<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>
+<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='no'>fits</span>[, <span class='fl'>2</span>])</div><div class='output co'>#&gt; $SFO
+#&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
@@ -214,12 +219,13 @@ such matrices is returned.</p>
#&gt;
#&gt; $DFOP
#&gt; Dataset 7
-#&gt; parent_0 91.058971503
+#&gt; parent_0 91.058971597
#&gt; k1 0.044946770
#&gt; k2 0.002868336
-#&gt; g 0.526942415
+#&gt; g 0.526942414
#&gt; sigma 2.221302196
-#&gt; </div><div class='input'><span class='fu'>parms</span>(<span class='no'>fits</span>)</div><div class='output co'>#&gt; $SFO
+#&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
@@ -234,12 +240,13 @@ such matrices is returned.</p>
#&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; parent_0 96.55213663 91.058971597 90.34509493 98.14858820 94.311323733
+#&gt; k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857
+#&gt; k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417
+#&gt; g 0.44845068 0.526942414 0.66091967 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='no'>fits</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; $SFO
+#&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
@@ -253,13 +260,13 @@ such matrices is returned.</p>
#&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'># }
+#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
+#&gt; parent_0 96.5521366 91.0589716 90.3450949 98.1485882 94.3113237
+#&gt; log_k1 -1.5161940 -3.1022764 -0.8859486 -1.1489296 -2.5174647
+#&gt; log_k2 -3.5206791 -5.8540232 -2.5794240 -3.4233253 -5.6765322
+#&gt; g_qlogis -0.2069326 0.1078741 0.6673953 0.6332573 -0.6514943
+#&gt; sigma 1.3569047 2.2213022 1.3416908 2.8715985 1.9420678
+#&gt; </div><div class='input'><span class='co'># }</span>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -276,7 +283,7 @@ such matrices is returned.</p>
</div>
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- <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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