From d518c4cfa22994db5ba81a6b01c6cb4c4186872e Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 15 Apr 2020 20:42:29 +0200
Subject: Adapt endpoint() to also work for nlme.mmkin objects

---
 docs/news/index.html           |  2 +-
 docs/reference/endpoints.html  | 29 ++++++++++++++++++++++-------
 docs/reference/nlme.mmkin.html | 29 ++++++++++++++++++++++++++---
 3 files changed, 49 insertions(+), 11 deletions(-)

(limited to 'docs')

diff --git a/docs/news/index.html b/docs/news/index.html
index 5fd97344..cb18664e 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -134,7 +134,7 @@
 <a href="#mkin-0-9-49-10-unreleased" class="anchor"></a>mkin 0.9.49.10 (unreleased)<small> Unreleased </small>
 </h1>
 <ul>
-<li><p>‘nlme.mmkin’: An nlme method for mmkin row objects and an associated class with plot method</p></li>
+<li><p>‘nlme.mmkin’: An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods</p></li>
 <li><p>‘mean_degparms, nlme_data, nlme_function’: Three new functions to facilitate building nlme models from mmkin row objects</p></li>
 <li><p>‘endpoints’: Don’t return the SFORB list component if it’s empty. This reduces distraction and complies with the documentation</p></li>
 <li><p>Article in compiled models: Add some platform specific code and suppress warnings about zero values being removed from the FOCUS D dataset</p></li>
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index 68af5fcf..ef38c521 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -154,13 +154,17 @@ advantage that the SFORB model can also be used for metabolites.</p>
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>fit</th>
-      <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
+      <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code> or
+<code><a href='nlme.mmkin.html'>nlme.mmkin</a></code></p></td>
     </tr>
     </table>
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>A list with the components mentioned above.</p>
+    <p>A list with a matrix of dissipation times named distimes,
+  and, if applicable, a vector of formation fractions named ff
+  and, if the SFORB model was in use, a vector of eigenvalues
+  of these SFORB models, equivalent to DFOP rate constants</p>
     <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
 
     <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
@@ -168,13 +172,24 @@ advantage that the SFORB model can also be used for metabolites.</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'>"FOMC"</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'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
-#&gt; logical(0)
-#&gt; 
-#&gt; $distimes
+  <span class='fu'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $distimes
 #&gt;            DT50    DT90 DT50back
 #&gt; parent 1.785233 15.1479 4.559973
-#&gt; </div><div class='input'>
+#&gt; </div><div class='input'>  <span class='co'># \dontrun{</span>
+    <span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFORB"</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'>endpoints</span>(<span class='no'>fit_2</span>)</div><div class='output co'>#&gt; $ff
+#&gt; parent_free_sink 
+#&gt;                1 
+#&gt; 
+#&gt; $SFORB
+#&gt; parent_b1 parent_b2 
+#&gt; 0.4595574 0.0178488 
+#&gt; 
+#&gt; $distimes
+#&gt;            DT50     DT90 DT50_parent_b1 DT50_parent_b2
+#&gt; parent 1.886925 21.25106       1.508293       38.83438
+#&gt; </div><div class='input'>  # }
+
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html
index 01287dda..9af9cbf7 100644
--- a/docs/reference/nlme.mmkin.html
+++ b/docs/reference/nlme.mmkin.html
@@ -253,7 +253,10 @@ parameters taken from the mmkin object are used</p></td>
  <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<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='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>))
 <span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='st'>"SFO"</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>)
 <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>)
-<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='endpoints.html'>endpoints</a></span>(<span class='no'>f</span><span class='kw'>[[</span><span class='fl'>1</span>]])</div><div class='output co'>#&gt; $distimes
+#&gt;            DT50     DT90
+#&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;   Data: "Not shown" 
@@ -270,7 +273,10 @@ parameters taken from the mmkin object are used</p></td>
 #&gt; StdDev:  1.30857          1.288591 6.304906
 #&gt; 
 #&gt; Number of Observations: 90
-#&gt; Number of Groups: 5 </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>))
+#&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;   Data: "Not shown" 
@@ -410,7 +416,24 @@ parameters taken from the mmkin object are used</p></td>
 #&gt; f_nlme_fomc_sfo     2 11  818.5149  853.0087 -398.2575 1 vs 2  21.33913  &lt;.0001
 #&gt; f_nlme_sfo_sfo      3  9 1085.1821 1113.4042 -533.5910 2 vs 3 270.66712  &lt;.0001</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>) <span class='co'># if we ignore FOMC</span></div><div class='output co'>#&gt;                 Model df       AIC       BIC   logLik   Test L.Ratio p-value
 #&gt; f_nlme_dfop_sfo     1 13  843.8541  884.6194 -408.927                       
-#&gt; f_nlme_sfo_sfo      2  9 1085.1821 1113.4042 -533.591 1 vs 2 249.328  &lt;.0001</div><div class='input'># }
+#&gt; f_nlme_sfo_sfo      2  9 1085.1821 1113.4042 -533.591 1 vs 2 249.328  &lt;.0001</div><div class='input'>
+  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#&gt; $ff
+#&gt; parent_sink   parent_A1     A1_sink 
+#&gt;   0.5912435   0.4087565   1.0000000 
+#&gt; 
+#&gt; $distimes
+#&gt;            DT50      DT90
+#&gt; parent 19.13517  63.56565
+#&gt; A1     66.02149 219.31865
+#&gt; </div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme_dfop_sfo</span>)</div><div class='output co'>#&gt; $ff
+#&gt;   parent_A1 parent_sink     A1_sink 
+#&gt;   0.2768571   0.7231429   1.0000000 
+#&gt; 
+#&gt; $distimes
+#&gt;             DT50     DT90  DT50_k1 DT50_k2
+#&gt; parent  11.07092 104.6325 4.462389 46.2085
+#&gt; A1     162.30937 539.1801       NA      NA
+#&gt; </div><div class='input'># }
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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