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-rw-r--r--docs/reference/get_deg_func.html176
-rw-r--r--docs/reference/index.html6
-rw-r--r--docs/reference/nlme.mmkin.html12
3 files changed, 188 insertions, 6 deletions
diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html
new file mode 100644
index 00000000..c5b8e38c
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@@ -0,0 +1,176 @@
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+ <div class="page-header">
+ <h1>Retrieve a degradation function from the mmkin namespace</h1>
+
+ <div class="hidden name"><code>get_deg_func.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Retrieve a degradation function from the mmkin namespace</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>get_deg_func</span>()</pre>
+
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A function that was likely previously assigned from within
+ nlme.mmkin</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#value">Value</a></li>
+ </ul>
+
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+
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+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
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diff --git a/docs/reference/index.html b/docs/reference/index.html
index f4de5bd8..04e3b8b9 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -296,6 +296,12 @@ of an mmkin object</p></td>
<p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">mean_degparms()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p>
</td>
<td><p>Helper functions to create nlme models from mmkin row objects</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="get_deg_func.html">get_deg_func()</a></code> </p>
+ </td>
+ <td><p>Retrieve a degradation function from the mmkin namespace</p></td>
</tr>
</tbody><tbody>
<tr>
diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html
index 9af9cbf7..33cc9164 100644
--- a/docs/reference/nlme.mmkin.html
+++ b/docs/reference/nlme.mmkin.html
@@ -258,7 +258,7 @@ parameters taken from the mmkin object are used</p></td>
#&gt; parent 11.96183 39.73634
#&gt; </div><div class='input'><span class='no'>f_nlme</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>)
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>f_nlme</span>)</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
-#&gt; Model: value ~ deg_func(name, time, parent_0, log_k_parent_sink)
+#&gt; Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent_sink)
#&gt; Data: "Not shown"
#&gt; Log-likelihood: -307.5269
#&gt; Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
@@ -276,9 +276,10 @@ parameters taken from the mmkin object are used</p></td>
#&gt; Number of Groups: 5 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme</span>)</div><div class='output co'>#&gt; $distimes
#&gt; DT50 DT90
#&gt; parent 17.51545 58.18505
-#&gt; </div><div class='input'><span class='no'>f_nlme_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>, <span class='kw'>start</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent_0</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>log_k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))
-<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>f_nlme_2</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='no'>parent_0</span> ~ <span class='fl'>1</span>)</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
-#&gt; Model: value ~ deg_func(name, time, parent_0, log_k_parent_sink)
+#&gt; </div><div class='input'><span class='co'># \dontrun{</span>
+ <span class='no'>f_nlme_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>, <span class='kw'>start</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent_0</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>log_k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))
+ <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>f_nlme_2</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='no'>parent_0</span> ~ <span class='fl'>1</span>)</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
+#&gt; Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent_sink)
#&gt; Data: "Not shown"
#&gt; Log-likelihood: -404.3729
#&gt; Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
@@ -291,8 +292,7 @@ parameters taken from the mmkin object are used</p></td>
#&gt; StdDev: 0.002416792 21.63027
#&gt;
#&gt; Number of Observations: 90
-#&gt; Number of Groups: 5 </div><div class='input'><span class='co'># \dontrun{</span>
- <span class='co'># Test on some real data</span>
+#&gt; Number of Groups: 5 </div><div class='input'> <span class='co'># Test on some real data</span>
<span class='no'>ds_2</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='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='no'>m_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'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"A1"</span>),

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