diff options
| -rw-r--r-- | _pkgdown.yml | 1 | ||||
| -rw-r--r-- | docs/articles/web_only/compiled_models.html | 12 | ||||
| -rw-r--r-- | docs/news/index.html | 1 | ||||
| -rw-r--r-- | docs/reference/index.html | 6 | ||||
| -rw-r--r-- | docs/reference/mkinsub.html | 11 | ||||
| -rw-r--r-- | docs/reference/nlme.html | 199 | ||||
| -rw-r--r-- | docs/sitemap.xml | 3 |
7 files changed, 222 insertions, 11 deletions
diff --git a/_pkgdown.yml b/_pkgdown.yml index 6bb05b3e..0cecdc30 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -33,6 +33,7 @@ reference: - "`[.mmkin`" - plot.mmkin - AIC.mmkin + - nlme_function - title: Datasets and known results contents: - FOCUS_2006_A diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 6daabd5e..0e58496e 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -90,7 +90,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-04-02</h4> + <h4 class="date">2020-04-04</h4> <div class="hidden name"><code>compiled_models.Rmd</code></div> @@ -139,9 +139,9 @@ <a class="sourceLine" id="cb6-15" title="15"> <span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="st">"R package rbenchmark is not available"</span>)</a> <a class="sourceLine" id="cb6-16" title="16">}</a></code></pre></div> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 3.239 1.000 3.237 0 -## 1 deSolve, not compiled 3 29.758 9.187 29.739 0 -## 2 Eigenvalue based 3 4.558 1.407 4.554 0 +## 3 deSolve, compiled 3 3.107 1.000 3.105 0 +## 1 deSolve, not compiled 3 28.765 9.258 28.749 0 +## 2 Eigenvalue based 3 4.446 1.431 4.445 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -170,8 +170,8 @@ <a class="sourceLine" id="cb8-16" title="16">}</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 4.984 1.000 4.981 0.000 -## 1 deSolve, not compiled 3 55.358 11.107 55.326 0.003 +## 2 deSolve, compiled 3 4.844 1.000 4.842 0 +## 1 deSolve, not compiled 3 53.833 11.113 53.807 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> diff --git a/docs/news/index.html b/docs/news/index.html index fc9a0765..cb5e6df3 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -134,6 +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>‘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> <li><p>‘plot.mmkin’: Add the argument ‘standardized’ to avoid warnings that occurred when it was passed as part of the additional arguments captured by the dots (…)</p></li> diff --git a/docs/reference/index.html b/docs/reference/index.html index 6ccc9255..a3547e29 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -270,6 +270,12 @@ of an mmkin object</p></td> <p><code><a href="AIC.mmkin.html">AIC(<i><mmkin></i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i><mmkin></i>)</a></code> </p> </td> <td><p>Calculate the AIC for a column of an mmkin object</p></td> + </tr><tr> + + <td> + <p><code><a href="nlme.html">mean_degparms()</a></code> <code><a href="nlme.html">nlme_data()</a></code> <code><a href="nlme.html">nlme_function()</a></code> </p> + </td> + <td><p>Estimation of parameter distributions from mmkin row objects</p></td> </tr> </tbody><tbody> <tr> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index e38c153c..b3be7c2c 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -70,7 +70,7 @@ mkinmod." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -181,10 +181,11 @@ results on other operating systems or system configurations.</p></td> <span class='no'>SFO_SFO.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> -<span class='co'># Now supplying full names</span> -<span class='no'>SFO_SFO.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( - <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Test compound"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='co'># \dontrun{</span> + <span class='co'># Now supplying full names</span> + <span class='no'>SFO_SFO.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( + <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Test compound"</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> # } </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html new file mode 100644 index 00000000..b939d1c3 --- /dev/null +++ b/docs/reference/nlme.html @@ -0,0 +1,199 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Estimation of parameter distributions from mmkin row objects — mean_degparms • mkin</title> + + +<!-- jquery --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> + +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> + +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + + + + +<meta property="og:title" content="Estimation of parameter distributions from mmkin row objects — mean_degparms" /> +<meta property="og:description" content="This function sets up and attempts to fit a mixed effects model to +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." /> +<meta name="twitter:card" content="summary" /> + + + + +<!-- mathjax --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + + + + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Estimation of parameter distributions from mmkin row objects</h1> + + <div class="hidden name"><code>nlme.Rd</code></div> + </div> + + <div class="ref-description"> + <p>This function sets up and attempts to fit a mixed effects model to +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> + </div> + + <pre class="usage"><span class='fu'>mean_degparms</span>(<span class='no'>object</span>) + +<span class='fu'>nlme_data</span>(<span class='no'>object</span>) + +<span class='fu'>nlme_function</span>(<span class='no'>object</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>object</th> + <td><p>An mmkin row object containing several fits of the same model to different datasets</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>A named vector containing mean values of the fitted degradation model parameters</p> +<p>A groupedData data object</p> +<p>A function that can be used with nlme</p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"></pre> + </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="#arguments">Arguments</a></li> + <li><a href="#value">Value</a></li> + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index a8d6dfa4..8ba032de 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -130,6 +130,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/nafta.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/nlme.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/nobs.mkinfit.html</loc> </url> <url> |