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authorJohannes Ranke <jranke@uni-bremen.de>2020-05-14 17:10:59 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-05-14 17:10:59 +0200
commitb6e278759127dab5bb78bc3016926a66e8a9758f (patch)
tree0dc20ce2fa58805b736d77035dbff40667272fff
parent218a9c55bd80fb708b15fa7196422f759bfe4b27 (diff)
Test markdown link, article update due to .rmd extension
-rw-r--r--R/nlme.R2
-rw-r--r--cran-comments.md5
-rw-r--r--docs/articles/FOCUS_D.html15
-rw-r--r--docs/articles/FOCUS_L.html43
-rw-r--r--docs/articles/mkin.html9
-rw-r--r--docs/articles/twa.html9
-rw-r--r--docs/articles/web_only/FOCUS_Z.html9
-rw-r--r--docs/articles/web_only/NAFTA_examples.html9
-rw-r--r--docs/articles/web_only/benchmarks.html24
-rw-r--r--docs/articles/web_only/compiled_models.html23
-rw-r--r--docs/pkgdown.yml2
-rw-r--r--docs/reference/nlme-1.pngbin71651 -> 70555 bytes
-rw-r--r--docs/reference/nlme.html25
-rw-r--r--man/nlme.Rd2
-rw-r--r--vignettes/web_only/mkin_benchmarks.rdabin854 -> 856 bytes
15 files changed, 98 insertions, 79 deletions
diff --git a/R/nlme.R b/R/nlme.R
index fa69db3c..3ee7b9fd 100644
--- a/R/nlme.R
+++ b/R/nlme.R
@@ -3,7 +3,7 @@
#' These functions facilitate setting up a nonlinear mixed effects model for
#' an mmkin row object. An mmkin row object is essentially a list of mkinfit
#' objects that have been obtained by fitting the same model to a list of
-#' datasets.
+#' datasets. They are used internally by the [nlme.mmkin()] method.
#'
#' @param object An mmkin row object containing several fits of the same model to different datasets
#' @import nlme
diff --git a/cran-comments.md b/cran-comments.md
index e630e0a8..e69de29b 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,5 +0,0 @@
-Update of yesterdays release, addressing a platform specific test outcome on Solaris that
-was revealed by the CRAN checks.
-
-This update also fixes a number of spelling errors that were found with the help of
-devtools::spell_check().
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 10b8f685..243ebee1 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -68,6 +68,9 @@
<li>
<a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
+ <li>
+ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
</ul>
</li>
<li>
@@ -97,10 +100,10 @@
<h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-12</h4>
+ <h4 class="date">2020-05-14</h4>
- <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.Rmd"><code>vignettes/FOCUS_D.Rmd</code></a></small>
- <div class="hidden name"><code>FOCUS_D.Rmd</code></div>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.rmd"><code>vignettes/FOCUS_D.rmd</code></a></small>
+ <div class="hidden name"><code>FOCUS_D.rmd</code></div>
</div>
@@ -177,8 +180,8 @@
<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">fit</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:36 2020
-## Date of summary: Tue May 12 15:31:36 2020
+## Date of fit: Thu May 14 17:07:12 2020
+## Date of summary: Thu May 14 17:07:12 2020
##
## Equations:
## d_parent/dt = - k_parent * parent
@@ -186,7 +189,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 421 model solutions performed in 0.165 s
+## Fitted using 421 model solutions performed in 0.167 s
##
## Error model: Constant variance
##
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 742718cb..df5c77c4 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -68,6 +68,9 @@
<li>
<a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
+ <li>
+ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
</ul>
</li>
<li>
@@ -97,10 +100,10 @@
<h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-12</h4>
+ <h4 class="date">2020-05-14</h4>
- <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_L.Rmd"><code>vignettes/FOCUS_L.Rmd</code></a></small>
- <div class="hidden name"><code>FOCUS_L.Rmd</code></div>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_L.rmd"><code>vignettes/FOCUS_L.rmd</code></a></small>
+ <div class="hidden name"><code>FOCUS_L.rmd</code></div>
</div>
@@ -123,15 +126,15 @@
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L1.SFO</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:38 2020
-## Date of summary: Tue May 12 15:31:38 2020
+## Date of fit: Thu May 14 17:07:14 2020
+## Date of summary: Thu May 14 17:07:14 2020
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 133 model solutions performed in 0.03 s
+## Fitted using 133 model solutions performed in 0.032 s
##
## Error model: Constant variance
##
@@ -224,8 +227,8 @@
## doubtful</code></pre>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:38 2020
-## Date of summary: Tue May 12 15:31:38 2020
+## Date of fit: Thu May 14 17:07:14 2020
+## Date of summary: Thu May 14 17:07:14 2020
##
##
## Warning: Optimisation did not converge:
@@ -332,8 +335,8 @@
<div class="sourceCode" id="cb17"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L2.FOMC</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:39 2020
-## Date of summary: Tue May 12 15:31:39 2020
+## Date of fit: Thu May 14 17:07:15 2020
+## Date of summary: Thu May 14 17:07:15 2020
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -411,8 +414,8 @@
<div class="sourceCode" id="cb20"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L2.DFOP</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:39 2020
-## Date of summary: Tue May 12 15:31:39 2020
+## Date of fit: Thu May 14 17:07:15 2020
+## Date of summary: Thu May 14 17:07:15 2020
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -421,7 +424,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 572 model solutions performed in 0.13 s
+## Fitted using 572 model solutions performed in 0.131 s
##
## Error model: Constant variance
##
@@ -514,8 +517,8 @@
<div class="sourceCode" id="cb24"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">mm.L3</span><span class="kw">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span>]])</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:39 2020
-## Date of summary: Tue May 12 15:31:40 2020
+## Date of fit: Thu May 14 17:07:16 2020
+## Date of summary: Thu May 14 17:07:16 2020
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -623,8 +626,8 @@
<div class="sourceCode" id="cb29"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">mm.L4</span><span class="kw">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span>]], <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:40 2020
-## Date of summary: Tue May 12 15:31:40 2020
+## Date of fit: Thu May 14 17:07:16 2020
+## Date of summary: Thu May 14 17:07:16 2020
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
@@ -687,15 +690,15 @@
<div class="sourceCode" id="cb31"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">mm.L4</span><span class="kw">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span>]], <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:40 2020
-## Date of summary: Tue May 12 15:31:40 2020
+## Date of fit: Thu May 14 17:07:16 2020
+## Date of summary: Thu May 14 17:07:16 2020
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 224 model solutions performed in 0.044 s
+## Fitted using 224 model solutions performed in 0.043 s
##
## Error model: Constant variance
##
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 0d4ced0f..37b7b1a1 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -68,6 +68,9 @@
<li>
<a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
+ <li>
+ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
</ul>
</li>
<li>
@@ -97,10 +100,10 @@
<h1 data-toc-skip>Introduction to mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-12</h4>
+ <h4 class="date">2020-05-14</h4>
- <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/mkin.Rmd"><code>vignettes/mkin.Rmd</code></a></small>
- <div class="hidden name"><code>mkin.Rmd</code></div>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/mkin.rmd"><code>vignettes/mkin.rmd</code></a></small>
+ <div class="hidden name"><code>mkin.rmd</code></div>
</div>
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index b58306f1..c231e17d 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -68,6 +68,9 @@
<li>
<a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
+ <li>
+ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
</ul>
</li>
<li>
@@ -97,10 +100,10 @@
<h1 data-toc-skip>Calculation of time weighted average concentrations with mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-12</h4>
+ <h4 class="date">2020-05-14</h4>
- <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/twa.Rmd"><code>vignettes/twa.Rmd</code></a></small>
- <div class="hidden name"><code>twa.Rmd</code></div>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/twa.rmd"><code>vignettes/twa.rmd</code></a></small>
+ <div class="hidden name"><code>twa.rmd</code></div>
</div>
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 0c34d77d..3427afb6 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -68,6 +68,9 @@
<li>
<a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
+ <li>
+ <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
</ul>
</li>
<li>
@@ -97,10 +100,10 @@
<h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-12</h4>
+ <h4 class="date">2020-05-14</h4>
- <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/FOCUS_Z.Rmd"><code>vignettes/web_only/FOCUS_Z.Rmd</code></a></small>
- <div class="hidden name"><code>FOCUS_Z.Rmd</code></div>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/FOCUS_Z.rmd"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small>
+ <div class="hidden name"><code>FOCUS_Z.rmd</code></div>
</div>
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index 411341b8..46cb7aa5 100644
--- a/docs/articles/web_only/NAFTA_examples.html
+++ b/docs/articles/web_only/NAFTA_examples.html
@@ -68,6 +68,9 @@
<li>
<a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
+ <li>
+ <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
</ul>
</li>
<li>
@@ -97,10 +100,10 @@
<h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-12</h4>
+ <h4 class="date">2020-05-14</h4>
- <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.Rmd"><code>vignettes/web_only/NAFTA_examples.Rmd</code></a></small>
- <div class="hidden name"><code>NAFTA_examples.Rmd</code></div>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.rmd"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small>
+ <div class="hidden name"><code>NAFTA_examples.rmd</code></div>
</div>
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 202ec25f..97e22303 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -100,7 +100,7 @@
<h1 data-toc-skip>Benchmark timings for mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-13</h4>
+ <h4 class="date">2020-05-14</h4>
<small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/benchmarks.rmd"><code>vignettes/web_only/benchmarks.rmd</code></a></small>
<div class="hidden name"><code>benchmarks.rmd</code></div>
@@ -210,8 +210,8 @@
</tr>
<tr class="even">
<td align="left">0.9.50.2</td>
-<td align="right">1.704</td>
-<td align="right">3.909</td>
+<td align="right">1.714</td>
+<td align="right">3.971</td>
</tr>
</tbody>
</table>
@@ -260,9 +260,9 @@
</tr>
<tr class="even">
<td align="left">0.9.50.2</td>
-<td align="right">1.370</td>
-<td align="right">6.147</td>
-<td align="right">2.747</td>
+<td align="right">1.402</td>
+<td align="right">6.174</td>
+<td align="right">2.764</td>
</tr>
</tbody>
</table>
@@ -329,12 +329,12 @@
</tr>
<tr class="even">
<td align="left">0.9.50.2</td>
-<td align="right">0.761</td>
-<td align="right">1.213</td>
-<td align="right">1.287</td>
-<td align="right">2.886</td>
-<td align="right">2.054</td>
-<td align="right">2.984</td>
+<td align="right">0.777</td>
+<td align="right">1.236</td>
+<td align="right">1.332</td>
+<td align="right">2.872</td>
+<td align="right">2.069</td>
+<td align="right">2.987</td>
</tr>
</tbody>
</table>
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 85134720..837b288b 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -68,6 +68,9 @@
<li>
<a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
+ <li>
+ <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
</ul>
</li>
<li>
@@ -97,10 +100,10 @@
<h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-12</h4>
+ <h4 class="date">2020-05-14</h4>
- <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/compiled_models.Rmd"><code>vignettes/web_only/compiled_models.Rmd</code></a></small>
- <div class="hidden name"><code>compiled_models.Rmd</code></div>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/compiled_models.rmd"><code>vignettes/web_only/compiled_models.rmd</code></a></small>
+ <div class="hidden name"><code>compiled_models.rmd</code></div>
</div>
@@ -149,10 +152,10 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="st">"R package rbenchmark is not available"</span>)
}</pre></body></html></div>
<pre><code>## test replications relative elapsed
-## 4 analytical 1 1.000 0.190
-## 3 deSolve, compiled 1 1.774 0.337
-## 2 Eigenvalue based 1 2.105 0.400
-## 1 deSolve, not compiled 1 42.763 8.125</code></pre>
+## 4 analytical 1 1.000 0.191
+## 3 deSolve, compiled 1 1.801 0.344
+## 2 Eigenvalue based 1 2.105 0.402
+## 1 deSolve, not compiled 1 42.864 8.187</code></pre>
<p>We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.</p>
</div>
<div id="model-without-analytical-solution" class="section level2">
@@ -178,9 +181,9 @@
}</pre></body></html></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<pre><code>## test replications relative elapsed
-## 2 deSolve, compiled 1 1.000 0.476
-## 1 deSolve, not compiled 1 30.103 14.329</code></pre>
-<p>Here we get a performance benefit of a factor of 30 using the version of the differential equation model compiled from C code!</p>
+## 2 deSolve, compiled 1 1.000 0.466
+## 1 deSolve, not compiled 1 30.942 14.419</code></pre>
+<p>Here we get a performance benefit of a factor of 31 using the version of the differential equation model compiled from C code!</p>
<p>This vignette was built with mkin 0.9.50.2 on</p>
<pre><code>## R version 4.0.0 (2020-04-24)
## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 922e556c..eb3f0f6e 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
NAFTA_examples: web_only/NAFTA_examples.html
benchmarks: web_only/benchmarks.html
compiled_models: web_only/compiled_models.html
-last_built: 2020-05-13T14:16Z
+last_built: 2020-05-14T15:07Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png
index 8db1f999..68ccb43f 100644
--- a/docs/reference/nlme-1.png
+++ b/docs/reference/nlme-1.png
Binary files differ
diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html
index 8ef7e7c9..b2d415dc 100644
--- a/docs/reference/nlme.html
+++ b/docs/reference/nlme.html
@@ -43,7 +43,7 @@
<meta property="og:description" content="These functions facilitate setting up a nonlinear mixed effects model for
an mmkin row object. An mmkin row object is essentially a list of mkinfit
objects that have been obtained by fitting the same model to a list of
-datasets." />
+datasets. They are used internally by the nlme.mmkin() method." />
@@ -112,6 +112,9 @@ datasets." />
<li>
<a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
+ <li>
+ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
</ul>
</li>
<li>
@@ -147,7 +150,7 @@ datasets." />
<p>These functions facilitate setting up a nonlinear mixed effects model for
an mmkin row object. An mmkin row object is essentially a list of mkinfit
objects that have been obtained by fitting the same model to a list of
-datasets.</p>
+datasets. They are used internally by the <code><a href='nlme.mmkin.html'>nlme.mmkin()</a></code> method.</p>
</div>
<pre class="usage"><span class='fu'>nlme_function</span>(<span class='no'>object</span>)
@@ -222,28 +225,28 @@ nlme for the case of a single grouping variable ds?</p>
#&gt; Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink)
#&gt; Data: grouped_data
#&gt; AIC BIC logLik
-#&gt; 252.7798 262.1358 -121.3899
+#&gt; 298.2781 307.7372 -144.1391
#&gt;
#&gt; Random effects:
#&gt; Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
#&gt; Level: ds
#&gt; Structure: Diagonal
-#&gt; parent_0 log_k_parent_sink Residual
-#&gt; StdDev: 0.0006768135 0.6800777 2.489397
+#&gt; parent_0 log_k_parent_sink Residual
+#&gt; StdDev: 0.9374733 0.7098105 3.83543
#&gt;
#&gt; Fixed effects: parent_0 + log_k_parent_sink ~ 1
-#&gt; Value Std.Error DF t-value p-value
-#&gt; parent_0 101.74884 0.6456014 44 157.60321 0
-#&gt; log_k_parent_sink -3.05575 0.4015811 44 -7.60929 0
+#&gt; Value Std.Error DF t-value p-value
+#&gt; parent_0 101.76838 1.1445444 45 88.91606 0
+#&gt; log_k_parent_sink -3.05444 0.4195622 45 -7.28008 0
#&gt; Correlation:
#&gt; prnt_0
-#&gt; log_k_parent_sink 0.026
+#&gt; log_k_parent_sink 0.034
#&gt;
#&gt; Standardized Within-Group Residuals:
#&gt; Min Q1 Med Q3 Max
-#&gt; -2.1317488 -0.6878121 0.0828385 0.8592270 2.9529864
+#&gt; -2.6169360 -0.2185329 0.0574070 0.5720937 3.0459868
#&gt;
-#&gt; Number of Observations: 48
+#&gt; Number of Observations: 49
#&gt; Number of Groups: 3 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/augPred.html'>augPred</a></span>(<span class='no'>m_nlme</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0</span>:<span class='fl'>1</span>), <span class='kw'>layout</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>1</span>))</div><div class='img'><img src='nlme-1.png' alt='' width='700' height='433' /></div><div class='input'># augPred does not seem to work on fits with more than one state
# variable
diff --git a/man/nlme.Rd b/man/nlme.Rd
index bf527320..5e981a14 100644
--- a/man/nlme.Rd
+++ b/man/nlme.Rd
@@ -31,7 +31,7 @@ A \code{\link{groupedData}} object
These functions facilitate setting up a nonlinear mixed effects model for
an mmkin row object. An mmkin row object is essentially a list of mkinfit
objects that have been obtained by fitting the same model to a list of
-datasets.
+datasets. They are used internally by the \code{\link[=nlme.mmkin]{nlme.mmkin()}} method.
}
\examples{
sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda
index c88ca4d6..a95680c0 100644
--- a/vignettes/web_only/mkin_benchmarks.rda
+++ b/vignettes/web_only/mkin_benchmarks.rda
Binary files differ

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