diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-25 13:01:23 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-25 13:01:23 +0200 |
| commit | 9f9336d59e68690472888bfdeb12944176d7d272 (patch) | |
| tree | 0d50debb2a06daa506e8c45925637ccb862a8787 /docs | |
| parent | f345762ddcdac65b0d565c7a622d32c1f849e7c7 (diff) | |
First working version of saemix helper functions
saemix_data depends on a development version of saemix, see
pull request saemixdevelopment/saemixextension#2
Diffstat (limited to 'docs')
| -rw-r--r-- | docs/news/index.html | 3 | ||||
| -rw-r--r-- | docs/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/reference/get_deg_func.html | 5 | ||||
| -rw-r--r-- | docs/reference/index.html | 6 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 22 | ||||
| -rw-r--r-- | docs/reference/nlme.mmkin.html | 5 | ||||
| -rw-r--r-- | docs/reference/saemix-1.png | bin | 0 -> 37443 bytes | |||
| -rw-r--r-- | docs/reference/saemix-2.png | bin | 0 -> 38557 bytes | |||
| -rw-r--r-- | docs/reference/saemix-3.png | bin | 0 -> 40023 bytes | |||
| -rw-r--r-- | docs/reference/saemix-4.png | bin | 0 -> 37936 bytes | |||
| -rw-r--r-- | docs/reference/saemix-5.png | bin | 0 -> 12062 bytes | |||
| -rw-r--r-- | docs/reference/saemix.html | 489 | ||||
| -rw-r--r-- | docs/reference/transform_odeparms.html | 16 | ||||
| -rw-r--r-- | docs/sitemap.xml | 3 |
14 files changed, 526 insertions, 25 deletions
diff --git a/docs/news/index.html b/docs/news/index.html index b8b7dacd..149fc98e 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -146,7 +146,8 @@ <a href="#mkin-0-9-50-3-unreleased" class="anchor"></a>mkin 0.9.50.3 (unreleased)<small> Unreleased </small> </h1> <ul> -<li>‘parms’: Add a method for mmkin objects</li> +<li><p>‘parms’: Add a method for mmkin objects</p></li> +<li><p>‘saemix_model’, ‘saemix_data’: Helper functions to fit nonlinear mixed-effects models for mmkin row objects using the saemix package</p></li> </ul> </div> <div id="mkin-0-9-50-2-2020-05-12" class="section level1"> diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 4756397e..0bb01ef4 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: 2020-05-15T05:30Z +last_built: 2020-05-25T10:48Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index 812b25d7..6eedafd2 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -72,7 +72,7 @@ </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">0.9.50.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span> </span> </div> @@ -109,6 +109,9 @@ <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> diff --git a/docs/reference/index.html b/docs/reference/index.html index b418b6ab..10d3b53a 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -331,6 +331,12 @@ of an mmkin object</p></td> </tr><tr> <td> + <p><code><a href="saemix.html">saemix_model()</a></code> <code><a href="saemix.html">saemix_data()</a></code> </p> + </td> + <td><p>Create saemix models from mmkin row objects</p></td> + </tr><tr> + + <td> <p><code><a href="get_deg_func.html">get_deg_func()</a></code> </p> </td> <td><p>Retrieve a degradation function from the mmkin namespace</p></td> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 0c1540d2..ced0cb54 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -424,8 +424,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</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'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50.3 #> R version used for fitting: 4.0.0 -#> Date of fit: Fri May 15 07:30:32 2020 -#> Date of summary: Fri May 15 07:30:32 2020 +#> Date of fit: Mon May 25 12:29:22 2020 +#> Date of summary: Mon May 25 12:29:22 2020 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -509,7 +509,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> user system elapsed -#> 0.413 0.005 0.419 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma +#> 0.407 0.013 0.423 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma #> 99.598483222 0.098697734 0.005260651 0.514475962 3.125503875 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_m1 parent_sink #> 0.514476 0.485524 @@ -599,7 +599,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> Sum of squared residuals at call 166: 371.2134 #> Sum of squared residuals at call 168: 371.2134 #> Negative log-likelihood at call 178: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> user system elapsed -#> 0.354 0.000 0.354 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma +#> 0.351 0.000 0.352 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma #> 99.598480759 0.098697739 0.005260651 0.514475958 3.125503874 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff #> parent_m1 parent_sink #> 0.514476 0.485524 @@ -633,8 +633,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class='no'>SFO_SFO.ff</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'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50.3 #> R version used for fitting: 4.0.0 -#> Date of fit: Fri May 15 07:30:37 2020 -#> Date of summary: Fri May 15 07:30:37 2020 +#> Date of fit: Mon May 25 12:29:28 2020 +#> Date of summary: Mon May 25 12:29:28 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -755,8 +755,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> 120 m1 25.15 28.78984 -3.640e+00 #> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50.3 #> R version used for fitting: 4.0.0 -#> Date of fit: Fri May 15 07:30:38 2020 -#> Date of summary: Fri May 15 07:30:38 2020 +#> Date of fit: Mon May 25 12:29:28 2020 +#> Date of summary: Mon May 25 12:29:28 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -892,8 +892,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> 120 m1 25.15 28.80429 -3.654e+00 #> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50.3 #> R version used for fitting: 4.0.0 -#> Date of fit: Fri May 15 07:30:39 2020 -#> Date of summary: Fri May 15 07:30:39 2020 +#> Date of fit: Mon May 25 12:29:29 2020 +#> Date of summary: Mon May 25 12:29:29 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -901,7 +901,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> #> Model predictions using solution type analytical #> -#> Fitted using 1875 model solutions performed in 0.658 s +#> Fitted using 1875 model solutions performed in 0.644 s #> #> Error model: Two-component variance function #> diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 928ee378..2ada9501 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." /> </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">0.9.50.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span> </span> </div> @@ -111,6 +111,9 @@ have been obtained by fitting the same model to a list of 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> diff --git a/docs/reference/saemix-1.png b/docs/reference/saemix-1.png Binary files differnew file mode 100644 index 00000000..529588ce --- /dev/null +++ b/docs/reference/saemix-1.png diff --git a/docs/reference/saemix-2.png b/docs/reference/saemix-2.png Binary files differnew file mode 100644 index 00000000..b85f878f --- /dev/null +++ b/docs/reference/saemix-2.png diff --git a/docs/reference/saemix-3.png b/docs/reference/saemix-3.png Binary files differnew file mode 100644 index 00000000..7ccfd0ff --- /dev/null +++ b/docs/reference/saemix-3.png diff --git a/docs/reference/saemix-4.png b/docs/reference/saemix-4.png Binary files differnew file mode 100644 index 00000000..55698bba --- /dev/null +++ b/docs/reference/saemix-4.png diff --git a/docs/reference/saemix-5.png b/docs/reference/saemix-5.png Binary files differnew file mode 100644 index 00000000..27db3938 --- /dev/null +++ b/docs/reference/saemix-5.png diff --git a/docs/reference/saemix.html b/docs/reference/saemix.html new file mode 100644 index 00000000..1737a21c --- /dev/null +++ b/docs/reference/saemix.html @@ -0,0 +1,489 @@ +<!-- 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>Create saemix models from mmkin row objects — saemix_model • mkin</title> + + +<!-- jquery --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> + +<!-- bootstrap-toc --> +<link rel="stylesheet" href="../bootstrap-toc.css"> +<script src="../bootstrap-toc.js"></script> + +<!-- Font Awesome icons --> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> + +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> + +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/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="Create saemix models from mmkin row objects — saemix_model" /> +<meta property="og:description" content="This function sets up a nonlinear mixed effects model for an mmkin row +object for use with the saemix package. 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." /> + + + + +<!-- 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 data-spy="scroll" data-target="#toc"> + <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">0.9.50.3</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> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Create saemix models from mmkin row objects</h1> + <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/saemix.R'><code>R/saemix.R</code></a></small> + <div class="hidden name"><code>saemix.Rd</code></div> + </div> + + <div class="ref-description"> + <p>This function sets up a nonlinear mixed effects model for an mmkin row +object for use with the saemix package. 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'>saemix_model</span>(<span class='no'>object</span>) + +<span class='fu'>saemix_data</span>(<span class='no'>object</span>, <span class='no'>...</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> + <tr> + <th>...</th> + <td><p>Further parameters passed to <a href='https://rdrr.io/pkg/saemix/man/saemixData.html'>saemix::saemixData</a></p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixModel-class.html'>saemix::SaemixModel</a> object.</p> +<p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixData-class.html'>saemix::SaemixData</a> object.</p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>ds</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>], + <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='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>ds</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>6</span>:<span class='fl'>10</span>) +<span class='no'>sfo_sfo</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'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"A1"</span>), + <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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='no'>f_mmkin</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>sfo_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'>5</span>) +<span class='co'># \dontrun{</span> +<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>saemix</span>)) { + <span class='no'>m_saemix</span> <span class='kw'><-</span> <span class='fu'>saemix_model</span>(<span class='no'>f_mmkin</span>) + <span class='no'>d_saemix</span> <span class='kw'><-</span> <span class='fu'>saemix_data</span>(<span class='no'>f_mmkin</span>) + <span class='no'>saemix_options</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>, <span class='kw'>save</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>save.graphs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) + <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span>(<span class='no'>m_saemix</span>, <span class='no'>d_saemix</span>, <span class='no'>saemix_options</span>) +}</div><div class='output co'>#> <span class='message'>Loading required package: saemix</span></div><div class='output co'>#> <span class='message'>Package saemix, version 3.1.9000</span> +#> <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='output co'>#> +#> +#> The following SaemixModel object was successfully created: +#> +#> Nonlinear mixed-effects model +#> Model function: Mixed model generated from mmkin object Model type: structural +#> function (psi, id, xidep) +#> { +#> uid <- unique(id) +#> res_list <- parallel::mclapply(uid, function(i) { +#> transparms_optim <- psi[i, ] +#> names(transparms_optim) <- names(degparms_optim) +#> odeini_optim <- transparms_optim[odeini_optim_parm_names] +#> names(odeini_optim) <- gsub("_0$", "", odeini_optim_parm_names) +#> odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)] +#> ode_transparms_optim_names <- setdiff(names(transparms_optim), +#> odeini_optim_parm_names) +#> odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], +#> mkin_model, transform_rates = object[[1]]$transform_rates, +#> transform_fractions = object[[1]]$transform_fractions) +#> odeparms <- c(odeparms_optim, odeparms_fixed) +#> xidep_i <- subset(xidep, id == i) +#> if (analytical) { +#> out_values <- mkin_model$deg_func(xidep_i, odeini, +#> odeparms) +#> } +#> else { +#> i_time <- xidep_i$time +#> i_name <- xidep_i$name +#> out_wide <- mkinpredict(mkin_model, odeparms = odeparms, +#> odeini = odeini, solution_type = object[[1]]$solution_type, +#> outtimes = sort(unique(i_time))) +#> out_index <- cbind(as.character(i_time), as.character(i_name)) +#> out_values <- out_wide[out_index] +#> } +#> return(out_values) +#> }, mc.cores = 15) +#> res <- unlist(res_list) +#> return(res) +#> } +#> <bytecode: 0x555559875398> +#> <environment: 0x55555973a248> +#> Nb of parameters: 4 +#> parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1 +#> distribution: +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_k_parent normal Estimated +#> [3,] log_k_A1 normal Estimated +#> [4,] f_parent_ilr_1 normal Estimated +#> Variance-covariance matrix: +#> parent_0 log_k_parent log_k_A1 f_parent_ilr_1 +#> parent_0 1 0 0 0 +#> log_k_parent 0 1 0 0 +#> log_k_A1 0 0 1 0 +#> f_parent_ilr_1 0 0 0 1 +#> Error model: constant , initial values: a.1=1 +#> No covariate in the model. +#> Initial values +#> parent_0 log_k_parent log_k_A1 f_parent_ilr_1 +#> Pop.CondInit 86.53449 -3.207005 -3.060308 -1.920449 +#> +#> +#> The following SaemixData object was successfully created: +#> +#> Object of class SaemixData +#> longitudinal data for use with the SAEM algorithm +#> Dataset ds_saemix +#> Structured data: value ~ time + name | ds +#> X variable for graphs: time () +#> Running main SAEM algorithm +#> [1] "Mon May 25 12:48:51 2020" +#> .</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#> .</div><div class='img'><img src='saemix-2.png' alt='' width='700' height='433' /></div><div class='output co'>#> .</div><div class='img'><img src='saemix-3.png' alt='' width='700' height='433' /></div><div class='output co'>#> .</div><div class='img'><img src='saemix-4.png' alt='' width='700' height='433' /></div><div class='output co'>#> +#> Minimisation finished +#> [1] "Mon May 25 12:56:39 2020"</div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm +#> ----------------------------------- +#> ---- Data ---- +#> ----------------------------------- +#> Object of class SaemixData +#> longitudinal data for use with the SAEM algorithm +#> Dataset ds_saemix +#> Structured data: value ~ time + name | ds +#> X variable for graphs: time () +#> Dataset characteristics: +#> number of subjects: 5 +#> number of observations: 170 +#> average/min/max nb obs: 34.00 / 30 / 38 +#> First 10 lines of data: +#> ds time name value mdv cens occ ytype +#> 1 Dataset 6 0 parent 97.2 0 0 1 1 +#> 2 Dataset 6 0 parent 96.4 0 0 1 1 +#> 3 Dataset 6 3 parent 71.1 0 0 1 1 +#> 4 Dataset 6 3 parent 69.2 0 0 1 1 +#> 5 Dataset 6 6 parent 58.1 0 0 1 1 +#> 6 Dataset 6 6 parent 56.6 0 0 1 1 +#> 7 Dataset 6 10 parent 44.4 0 0 1 1 +#> 8 Dataset 6 10 parent 43.4 0 0 1 1 +#> 9 Dataset 6 20 parent 33.3 0 0 1 1 +#> 10 Dataset 6 20 parent 29.2 0 0 1 1 +#> ----------------------------------- +#> ---- Model ---- +#> ----------------------------------- +#> Nonlinear mixed-effects model +#> Model function: Mixed model generated from mmkin object Model type: structural +#> function (psi, id, xidep) +#> { +#> uid <- unique(id) +#> res_list <- parallel::mclapply(uid, function(i) { +#> transparms_optim <- psi[i, ] +#> names(transparms_optim) <- names(degparms_optim) +#> odeini_optim <- transparms_optim[odeini_optim_parm_names] +#> names(odeini_optim) <- gsub("_0$", "", odeini_optim_parm_names) +#> odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)] +#> ode_transparms_optim_names <- setdiff(names(transparms_optim), +#> odeini_optim_parm_names) +#> odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], +#> mkin_model, transform_rates = object[[1]]$transform_rates, +#> transform_fractions = object[[1]]$transform_fractions) +#> odeparms <- c(odeparms_optim, odeparms_fixed) +#> xidep_i <- subset(xidep, id == i) +#> if (analytical) { +#> out_values <- mkin_model$deg_func(xidep_i, odeini, +#> odeparms) +#> } +#> else { +#> i_time <- xidep_i$time +#> i_name <- xidep_i$name +#> out_wide <- mkinpredict(mkin_model, odeparms = odeparms, +#> odeini = odeini, solution_type = object[[1]]$solution_type, +#> outtimes = sort(unique(i_time))) +#> out_index <- cbind(as.character(i_time), as.character(i_name)) +#> out_values <- out_wide[out_index] +#> } +#> return(out_values) +#> }, mc.cores = 15) +#> res <- unlist(res_list) +#> return(res) +#> } +#> <bytecode: 0x555559875398> +#> <environment: 0x55555973a248> +#> Nb of parameters: 4 +#> parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1 +#> distribution: +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_k_parent normal Estimated +#> [3,] log_k_A1 normal Estimated +#> [4,] f_parent_ilr_1 normal Estimated +#> Variance-covariance matrix: +#> parent_0 log_k_parent log_k_A1 f_parent_ilr_1 +#> parent_0 1 0 0 0 +#> log_k_parent 0 1 0 0 +#> log_k_A1 0 0 1 0 +#> f_parent_ilr_1 0 0 0 1 +#> Error model: constant , initial values: a.1=1 +#> No covariate in the model. +#> Initial values +#> parent_0 log_k_parent log_k_A1 f_parent_ilr_1 +#> Pop.CondInit 86.53449 -3.207005 -3.060308 -1.920449 +#> ----------------------------------- +#> ---- Key algorithm options ---- +#> ----------------------------------- +#> Estimation of individual parameters (MAP) +#> Estimation of standard errors and linearised log-likelihood +#> Estimation of log-likelihood by importance sampling +#> Number of iterations: K1=300, K2=100 +#> Number of chains: 10 +#> Seed: 123456 +#> Number of MCMC iterations for IS: 5000 +#> Simulations: +#> nb of simulated datasets used for npde: 1000 +#> nb of simulated datasets used for VPC: 100 +#> Input/output +#> save the results to a file: FALSE +#> save the graphs to files: FALSE +#> ---------------------------------------------------- +#> ---- Results ---- +#> ---------------------------------------------------- +#> ----------------- Fixed effects ------------------ +#> ---------------------------------------------------- +#> Parameter Estimate SE CV(%) +#> [1,] parent_0 86.21 1.51 1.7 +#> [2,] log_k_parent -3.21 0.59 18.5 +#> [3,] log_k_A1 -4.64 0.29 6.3 +#> [4,] f_parent_ilr_1 -0.32 0.30 93.2 +#> [5,] a.1 4.69 0.27 5.8 +#> ---------------------------------------------------- +#> ----------- Variance of random effects ----------- +#> ---------------------------------------------------- +#> Parameter Estimate SE CV(%) +#> parent_0 omega2.parent_0 6.07 7.08 117 +#> log_k_parent omega2.log_k_parent 1.75 1.11 63 +#> log_k_A1 omega2.log_k_A1 0.26 0.26 101 +#> f_parent_ilr_1 omega2.f_parent_ilr_1 0.38 0.27 71 +#> ---------------------------------------------------- +#> ------ Correlation matrix of random effects ------ +#> ---------------------------------------------------- +#> omega2.parent_0 omega2.log_k_parent omega2.log_k_A1 +#> omega2.parent_0 1 0 0 +#> omega2.log_k_parent 0 1 0 +#> omega2.log_k_A1 0 0 1 +#> omega2.f_parent_ilr_1 0 0 0 +#> omega2.f_parent_ilr_1 +#> omega2.parent_0 0 +#> omega2.log_k_parent 0 +#> omega2.log_k_A1 0 +#> omega2.f_parent_ilr_1 1 +#> ---------------------------------------------------- +#> --------------- Statistical criteria ------------- +#> ---------------------------------------------------- +#> Likelihood computed by linearisation +#> -2LL= 1064.397 +#> AIC = 1082.397 +#> BIC = 1078.882 +#> +#> Likelihood computed by importance sampling +#> -2LL= 1063.161 +#> AIC = 1081.161 +#> BIC = 1077.646 +#> ----------------------------------------------------</div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm +#> ----------------------------------------- +#> ---- Data and Model ---- +#> ----------------------------------------- +#> Data +#> Dataset ds_saemix +#> Longitudinal data: value ~ time + name | ds +#> +#> Model: +#> Mixed model generated from mmkin object +#> 4 parameters: parent_0 log_k_parent log_k_A1 f_parent_ilr_1 +#> error model: constant +#> No covariate +#> +#> Key options +#> Estimation of individual parameters (MAP) +#> Estimation of standard errors and linearised log-likelihood +#> Estimation of log-likelihood by importance sampling +#> Number of iterations: K1=300, K2=100 +#> Number of chains: 10 +#> Seed: 123456 +#> Number of MCMC iterations for IS: 5000 +#> Input/output +#> results not saved +#> no graphs +#> ---------------------------------------------------- +#> ---- Results ---- +#> Fixed effects +#> Parameter Estimate SE CV(%) +#> parent_0 86.214 1.506 1.75 +#> log_k_parent -3.210 0.593 18.47 +#> log_k_A1 -4.643 0.294 6.34 +#> f_parent_ilr_1 -0.322 0.300 93.24 +#> a.1 4.689 0.270 5.76 +#> +#> Variance of random effects +#> Parameter Estimate SE CV(%) +#> omega2.parent_0 6.068 7.078 116.7 +#> omega2.log_k_parent 1.752 1.111 63.4 +#> omega2.log_k_A1 0.256 0.257 100.5 +#> omega2.f_parent_ilr_1 0.385 0.273 70.8 +#> +#> Statistical criteria +#> Likelihood computed by linearisation +#> -2LL= 1064.397 +#> AIC= 1082.397 +#> BIC= 1078.882 +#> Likelihood computed by importance sampling +#> -2LL= 1063.161 +#> AIC= 1081.161 +#> BIC= 1077.646 </div><div class='input'># } +</div><div class='img'><img src='saemix-5.png' alt='' width='700' height='433' /></div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> + </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> 1.5.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 61ed96d7..7a9198de 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -77,7 +77,7 @@ the ilr transformation is used." /> </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">0.9.50.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span> </span> </div> @@ -114,6 +114,9 @@ the ilr transformation is used." /> <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> @@ -211,19 +214,12 @@ fitting procedure.</p></td> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A vector of transformed or backtransformed parameters with the same -names as the original parameters.</p> + <p>A vector of transformed or backtransformed parameters</p> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <p>The transformation of sets of formation fractions is fragile, as it supposes the same ordering of the components in forward and backward transformation. This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit</a></code>.</p> - <h2 class="hasAnchor" id="functions"><a class="anchor" href="#functions"></a>Functions</h2> - - -<ul> -<li><p><code>backtransform_odeparms</code>: Backtransform the set of transformed parameters</p></li> -</ul> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> @@ -245,7 +241,7 @@ This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit< #> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'> <span class='co'># \dontrun{</span> <span class='co'># Compare to the version without transforming rate parameters</span> -<span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='error'>Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", cost.current, "\n", sep = "")}: Fehlender Wert, wo TRUE/FALSE nötig ist</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0.003 0 0.003</span></div><div class='input'><span class='no'>fit.2.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</span>)</div><div class='output co'>#> <span class='error'>Error in summary(fit.2): Objekt 'fit.2' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in print(fit.2.s$par, 3): Objekt 'fit.2.s' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in print(fit.2.s$bpar, 3): Objekt 'fit.2.s' nicht gefunden</span></div><div class='input'><span class='co'># }</span> +<span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='error'>Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", cost.current, "\n", sep = "")}: missing value where TRUE/FALSE needed</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0.002 0.001 0.002</span></div><div class='input'><span class='no'>fit.2.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</span>)</div><div class='output co'>#> <span class='error'>Error in summary(fit.2): object 'fit.2' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in print(fit.2.s$par, 3): object 'fit.2.s' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in print(fit.2.s$bpar, 3): object 'fit.2.s' not found</span></div><div class='input'><span class='co'># }</span> <span class='no'>initials</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>initials</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>fit</span>$<span class='no'>start</span>) diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 81368436..e284abf6 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -172,6 +172,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/residuals.mkinfit.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/saemix.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/schaefer07_complex_case.html</loc> </url> <url> |
