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-rw-r--r--docs/news/index.html2
-rw-r--r--docs/reference/endpoints.html29
-rw-r--r--docs/reference/nlme.mmkin.html29
3 files changed, 49 insertions, 11 deletions
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>
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