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-rw-r--r--docs/reference/transform_odeparms.html39
1 files changed, 19 insertions, 20 deletions
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index ab5ce062..ccd56ca4 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -61,7 +61,12 @@
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin">
+ <span class="fa fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
@@ -83,7 +88,7 @@
constants and other paramters that can only take on positive values, a
simple log transformation is used. For compositional parameters, such as
the formations fractions that should always sum up to 1 and can not be
- negative, the <code><a href='ilr.html'>ilr</a></code> transformation is used.</p>
+ negative, the <code>ilr</code> transformation is used.</p>
<p>The transformation of sets of formation fractions is fragile, as it supposes
the same ordering of the components in forward and backward transformation.
@@ -109,7 +114,7 @@
<dd>
The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the names of
the model variables that are needed for grouping the formation fractions
- before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter names and
+ before <code>ilr</code> transformation, the parameter names and
the information if the pathway to sink is included in the model.
</dd>
<dt>transform_rates</dt>
@@ -128,7 +133,7 @@
assumption of normal distribution of the estimator. The default (TRUE) is
to do transformations. The g parameter of the DFOP and HS models are also
transformed, as they can also be seen as compositional data. The
- transformation used for these transformations is the <code><a href='ilr.html'>ilr</a></code>
+ transformation used for these transformations is the <code>ilr</code>
transformation.
</dd>
</dl>
@@ -139,18 +144,15 @@
as the original parameters.</p>
- <h2 class="hasAnchor" id="examples">
- <a class="anchor" href="#examples"></a>
- Examples
- </h2>
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version: 0.9.44.9000
-#&gt; R version: 3.3.1
-#&gt; Date of fit: Wed Oct 26 23:50:51 2016
-#&gt; Date of summary: Wed Oct 26 23:50:51 2016
+#&gt; R version: 3.3.2
+#&gt; Date of fit: Thu Nov 3 17:46:36 2016
+#&gt; Date of summary: Thu Nov 3 17:46:36 2016
#&gt;
#&gt; Equations:
#&gt; d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -158,7 +160,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.629 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.657 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -221,8 +223,7 @@
#&gt; Estimated disappearance times:
#&gt; DT50 DT90
#&gt; parent 7.023 23.33
-#&gt; m1 131.761 437.70
-#&gt; </div><div class='input'>
+#&gt; m1 131.761 437.70</div><div class='input'>
<span class='co'>## Not run: ------------------------------------</span>
<span class='co'># fit.2 &lt;- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)</span>
<span class='co'># summary(fit.2, data=FALSE) </span>
@@ -233,10 +234,8 @@
<span class='no'>transformed</span> <span class='kw'>&lt;-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span>
<span class='fu'>names</span>(<span class='no'>transformed</span>) <span class='kw'>&lt;-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start_transformed</span>)
<span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
-#&gt; 100.750000 -2.302585 -2.301586 -2.300587
-#&gt; </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt; parent_0 k_parent_sink k_parent_m1 k_m1_sink
-#&gt; 100.7500 0.1000 0.1001 0.1002
-#&gt; </div><div class='input'>
+#&gt; 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt; parent_0 k_parent_sink k_parent_m1 k_m1_sink
+#&gt; 100.7500 0.1000 0.1001 0.1002 </div><div class='input'>
<span class='co'>## Not run: ------------------------------------</span>
<span class='co'># # The case of formation fractions</span>
<span class='co'># SFO_SFO.ff &lt;- mkinmod(</span>
@@ -280,7 +279,7 @@
<footer>
<div class="copyright">
- <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+ <p>Developed by Johannes Ranke.</p>
</div>
<div class="pkgdown">

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