diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-14 17:10:59 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-14 17:10:59 +0200 |
| commit | b6e278759127dab5bb78bc3016926a66e8a9758f (patch) | |
| tree | 0dc20ce2fa58805b736d77035dbff40667272fff | |
| parent | 218a9c55bd80fb708b15fa7196422f759bfe4b27 (diff) | |
Test markdown link, article update due to .rmd extension
| -rw-r--r-- | R/nlme.R | 2 | ||||
| -rw-r--r-- | cran-comments.md | 5 | ||||
| -rw-r--r-- | docs/articles/FOCUS_D.html | 15 | ||||
| -rw-r--r-- | docs/articles/FOCUS_L.html | 43 | ||||
| -rw-r--r-- | docs/articles/mkin.html | 9 | ||||
| -rw-r--r-- | docs/articles/twa.html | 9 | ||||
| -rw-r--r-- | docs/articles/web_only/FOCUS_Z.html | 9 | ||||
| -rw-r--r-- | docs/articles/web_only/NAFTA_examples.html | 9 | ||||
| -rw-r--r-- | docs/articles/web_only/benchmarks.html | 24 | ||||
| -rw-r--r-- | docs/articles/web_only/compiled_models.html | 23 | ||||
| -rw-r--r-- | docs/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/reference/nlme-1.png | bin | 71651 -> 70555 bytes | |||
| -rw-r--r-- | docs/reference/nlme.html | 25 | ||||
| -rw-r--r-- | man/nlme.Rd | 2 | ||||
| -rw-r--r-- | vignettes/web_only/mkin_benchmarks.rda | bin | 854 -> 856 bytes |
15 files changed, 98 insertions, 79 deletions
@@ -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 Binary files differindex 8db1f999..68ccb43f 100644 --- a/docs/reference/nlme-1.png +++ b/docs/reference/nlme-1.png 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> #> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) #> Data: grouped_data #> AIC BIC logLik -#> 252.7798 262.1358 -121.3899 +#> 298.2781 307.7372 -144.1391 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1) #> Level: ds #> Structure: Diagonal -#> parent_0 log_k_parent_sink Residual -#> StdDev: 0.0006768135 0.6800777 2.489397 +#> parent_0 log_k_parent_sink Residual +#> StdDev: 0.9374733 0.7098105 3.83543 #> #> Fixed effects: parent_0 + log_k_parent_sink ~ 1 -#> Value Std.Error DF t-value p-value -#> parent_0 101.74884 0.6456014 44 157.60321 0 -#> log_k_parent_sink -3.05575 0.4015811 44 -7.60929 0 +#> Value Std.Error DF t-value p-value +#> parent_0 101.76838 1.1445444 45 88.91606 0 +#> log_k_parent_sink -3.05444 0.4195622 45 -7.28008 0 #> Correlation: #> prnt_0 -#> log_k_parent_sink 0.026 +#> log_k_parent_sink 0.034 #> #> Standardized Within-Group Residuals: #> Min Q1 Med Q3 Max -#> -2.1317488 -0.6878121 0.0828385 0.8592270 2.9529864 +#> -2.6169360 -0.2185329 0.0574070 0.5720937 3.0459868 #> -#> Number of Observations: 48 +#> Number of Observations: 49 #> 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 Binary files differindex c88ca4d6..a95680c0 100644 --- a/vignettes/web_only/mkin_benchmarks.rda +++ b/vignettes/web_only/mkin_benchmarks.rda |
