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diff --git a/docs/dev/reference/anova.saem.mmkin.html b/docs/dev/reference/anova.saem.mmkin.html new file mode 100644 index 00000000..abe77c65 --- /dev/null +++ b/docs/dev/reference/anova.saem.mmkin.html @@ -0,0 +1,161 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Anova method for saem.mmkin objects — anova.saem.mmkin • 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="Anova method for saem.mmkin objects — anova.saem.mmkin"><meta property="og:description" content="Generate an anova object. The method to calculate the BIC is that from +the saemix package. As in other prominent anova methods, models are sorted"><meta name="robots" content="noindex"><!-- 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</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" data-bs-toggle="dropdown" 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/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</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="https://github.com/jranke/mkin/" class="external-link"> + <span class="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>Anova method for saem.mmkin objects</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/anova.saem.mmkin.R" class="external-link"><code>R/anova.saem.mmkin.R</code></a></small> + <div class="hidden name"><code>anova.saem.mmkin.Rd</code></div> + </div> + + <div class="ref-description"> + <p>Generate an anova object. The method to calculate the BIC is that from +the saemix package. As in other prominent anova methods, models are sorted</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> <span class="va">...</span>,</span> +<span> method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"is"</span>, <span class="st">"lin"</span>, <span class="st">"gq"</span><span class="op">)</span>,</span> +<span> test <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> model.names <span class="op">=</span> <span class="cn">NULL</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An <a href="saem.html">saem.mmkin</a> object</p></dd> + + +<dt>...</dt> +<dd><p>further such objects</p></dd> + + +<dt>method</dt> +<dd><p>Method for likelihood calculation: "is" (importance sampling), +"lin" (linear approximation), or "gq" (Gaussian quadrature). Passed +to <a href="https://rdrr.io/pkg/saemix/man/logLik.html" class="external-link">saemix::logLik.SaemixObject</a></p></dd> + + +<dt>test</dt> +<dd><p>Should a likelihood ratio test be performed? If TRUE, +the alternative models are tested against the first model. Should +only be done for nested models.</p></dd> + + +<dt>model.names</dt> +<dd><p>Optional character vector of model names</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>an "anova" data frame; the traditional (S3) result of anova()</p> + </div> + + </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></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index cbd44762..3d9d40b7 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -217,6 +217,14 @@ degradation models and one or more error models</p></td> </td> <td><p>Summary method for class "saem.mmkin"</p></td> </tr><tr><td> + <p><code><a href="anova.saem.mmkin.html">anova(<i><saem.mmkin></i>)</a></code> </p> + </td> + <td><p>Anova method for saem.mmkin objects</p></td> + </tr><tr><td> + <p><code><a href="logLik.saem.mmkin.html">logLik(<i><saem.mmkin></i>)</a></code> </p> + </td> + <td><p>logLik method for saem.mmkin objects</p></td> + </tr><tr><td> <p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p> </td> <td><p>Helper functions to create nlme models from mmkin row objects</p></td> @@ -237,7 +245,7 @@ degradation models and one or more error models</p></td> </td> <td><p>Confidence intervals for parameters in saem.mmkin objects</p></td> </tr><tr><td> - <p><code><a href="multistart.html">multistart()</a></code> <code><a href="multistart.html">print(<i><multistart></i>)</a></code> </p> + <p><code><a href="multistart.html">multistart()</a></code> <code><a href="multistart.html">print(<i><multistart></i>)</a></code> <code><a href="multistart.html">best()</a></code> <code><a href="multistart.html">which.best()</a></code> </p> </td> <td><p>Perform a hierarchical model fit with multiple starting values</p></td> </tr><tr><td> @@ -341,6 +349,10 @@ degradation models and one or more error models</p></td> </td> <td><p>Normalisation factors for aerobic soil degradation according to FOCUS guidance</p></td> </tr><tr><td> + <p><code><a href="set_nd_nq.html">set_nd_nq()</a></code> <code><a href="set_nd_nq.html">set_nd_nq_focus()</a></code> </p> + </td> + <td><p>Set non-detects and unquantified values in residue series without replicates</p></td> + </tr><tr><td> <p><code><a href="max_twa_parent.html">max_twa_parent()</a></code> <code><a href="max_twa_parent.html">max_twa_sfo()</a></code> <code><a href="max_twa_parent.html">max_twa_fomc()</a></code> <code><a href="max_twa_parent.html">max_twa_dfop()</a></code> <code><a href="max_twa_parent.html">max_twa_hs()</a></code> </p> </td> <td><p>Function to calculate maximum time weighted average concentrations from diff --git a/docs/dev/reference/llhist.html b/docs/dev/reference/llhist.html index 2eb77a82..e110416e 100644 --- a/docs/dev/reference/llhist.html +++ b/docs/dev/reference/llhist.html @@ -1,7 +1,6 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Plot the distribution of log likelihoods from multistart objects — llhist • 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="Plot the distribution of log likelihoods from multistart objects — llhist"><meta property="og:description" content="Produces a histogram of log-likelihoods, and an overlayed kernel density -estimate. In addition, the likelihood of the original fit is shown as -a red vertical line."><meta name="robots" content="noindex"><!-- 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]> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Plot the distribution of log likelihoods from multistart objects — llhist • 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="Plot the distribution of log likelihoods from multistart objects — llhist"><meta property="og:description" content="Produces a histogram of log-likelihoods. In addition, the likelihood of the +original fit is shown as a red vertical line."><meta name="robots" content="noindex"><!-- 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"> @@ -46,12 +45,15 @@ a red vertical line."><meta name="robots" content="noindex"><!-- mathjax --><scr <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> @@ -85,9 +87,8 @@ a red vertical line."><meta name="robots" content="noindex"><!-- mathjax --><scr </div> <div class="ref-description"> - <p>Produces a histogram of log-likelihoods, and an overlayed kernel density -estimate. In addition, the likelihood of the original fit is shown as -a red vertical line.</p> + <p>Produces a histogram of log-likelihoods. In addition, the likelihood of the +original fit is shown as a red vertical line.</p> </div> <div id="ref-usage"> diff --git a/docs/dev/reference/logLik.saem.mmkin.html b/docs/dev/reference/logLik.saem.mmkin.html new file mode 100644 index 00000000..9694232c --- /dev/null +++ b/docs/dev/reference/logLik.saem.mmkin.html @@ -0,0 +1,135 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>logLik method for saem.mmkin objects — logLik.saem.mmkin • 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" 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</button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</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" data-bs-toggle="dropdown" 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/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</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="https://github.com/jranke/mkin/" class="external-link"> + <span class="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>logLik method for saem.mmkin objects</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/saem.R" class="external-link"><code>R/saem.R</code></a></small> + <div class="hidden name"><code>logLik.saem.mmkin.Rd</code></div> + </div> + + <div class="ref-description"> + <p>logLik method for saem.mmkin objects</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"lin"</span>, <span class="st">"is"</span>, <span class="st">"gq"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>The fitted <a href="saem.html">saem.mmkin</a> object</p></dd> + + +<dt>...</dt> +<dd><p>Passed to <a href="https://rdrr.io/pkg/saemix/man/logLik.html" class="external-link">saemix::logLik.SaemixObject</a></p></dd> + + +<dt>method</dt> +<dd><p>Passed to <a href="https://rdrr.io/pkg/saemix/man/logLik.html" class="external-link">saemix::logLik.SaemixObject</a></p></dd> + +</dl></div> + + </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></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/dev/reference/multistart-1.png b/docs/dev/reference/multistart-1.png Binary files differnew file mode 100644 index 00000000..ee9c1b5a --- /dev/null +++ b/docs/dev/reference/multistart-1.png diff --git a/docs/dev/reference/multistart-2.png b/docs/dev/reference/multistart-2.png Binary files differnew file mode 100644 index 00000000..e54938ab --- /dev/null +++ b/docs/dev/reference/multistart-2.png diff --git a/docs/dev/reference/multistart.html b/docs/dev/reference/multistart.html index 714cb2fc..83af8dbb 100644 --- a/docs/dev/reference/multistart.html +++ b/docs/dev/reference/multistart.html @@ -112,7 +112,17 @@ mixed-effects models by Duchesne et al (2021).</p> <span><span class="fu">multistart</span><span class="op">(</span><span class="va">object</span>, n <span class="op">=</span> <span class="fl">50</span>, cores <span class="op">=</span> <span class="fl">1</span>, cluster <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for multistart</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for default</span></span> +<span><span class="fu">best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">which.best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for default</span></span> +<span><span class="fu">which.best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -149,6 +159,12 @@ for parallel execution.</p></dd> <p>A list of <a href="saem.html">saem.mmkin</a> objects, with class attributes 'multistart.saem.mmkin' and 'multistart'.</p> + + +<p>The object with the highest likelihood</p> + + +<p>The index of the object with the highest likelihood</p> </div> <div id="details"> <h2>Details</h2> @@ -187,11 +203,14 @@ doi: 10.1186/s12859-021-04373-4.</p> <span class="r-in"><span><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">7</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">f_saem_full</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">f_saem_full_multi</span> <span class="op"><-</span> <span class="fu">multistart</span><span class="op">(</span><span class="va">f_saem_full</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span></span> -<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>all scheduled cores encountered errors in user code</span> <span class="r-in"><span><span class="fu"><a href="parhist.html">parhist</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span>, lpos <span class="op">=</span> <span class="st">"bottomright"</span><span class="op">)</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in UseMethod("parms", object):</span> no applicable method for 'parms' applied to an object of class "try-error"</span> +<span class="r-plt img"><img src="multistart-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_full</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] "sd(log_k2)"</span> <span class="r-in"><span></span></span> -<span class="r-in"><span><span class="va">f_saem_reduced</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_full</span>, covariance.model <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/diag.html" class="external-link">diag</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">0</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_saem_reduced</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_full</span>, no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> character(0)</span> <span class="r-in"><span><span class="co"># On Windows, we need to create a cluster first. When working with</span></span></span> <span class="r-in"><span><span class="co"># such a cluster, we need to export the mmkin object to the cluster</span></span></span> <span class="r-in"><span><span class="co"># nodes, as it is referred to when updating the saem object on the nodes.</span></span></span> @@ -200,10 +219,8 @@ doi: 10.1186/s12859-021-04373-4.</p> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">clusterExport</a></span><span class="op">(</span><span class="va">cl</span>, <span class="st">"f_mmkin"</span><span class="op">)</span></span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in get(name, envir = envir):</span> object 'f_mmkin' not found</span> <span class="r-in"><span><span class="va">f_saem_reduced_multi</span> <span class="op"><-</span> <span class="fu">multistart</span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cluster <span class="op">=</span> <span class="va">cl</span><span class="op">)</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in checkForRemoteErrors(val):</span> 12 nodes produced errors; first error: object 'f_mmkin' not found</span> <span class="r-in"><span><span class="fu"><a href="parhist.html">parhist</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"bottomright"</span><span class="op">)</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in parhist(f_saem_reduced_multi, lpos = "bottomright"):</span> object 'f_saem_reduced_multi' not found</span> -<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>calling par(new=TRUE) with no plot</span> +<span class="r-plt img"><img src="multistart-2.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> diff --git a/docs/dev/reference/parhist.html b/docs/dev/reference/parhist.html index bc230c21..27fc116f 100644 --- a/docs/dev/reference/parhist.html +++ b/docs/dev/reference/parhist.html @@ -1,6 +1,7 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Plot parameter distributions from multistart objects — parhist • 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="Plot parameter distributions from multistart objects — parhist"><meta property="og:description" content="Produces a boxplot with all parameters from the multiple runs, divided by -using their medians as in the paper by Duchesne et al. 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(2021)."><meta name="robots" content="noindex"><!-- 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"> @@ -87,12 +88,20 @@ using their medians as in the paper by Duchesne et al. (2021)."><meta name="robo </div> <div class="ref-description"> - <p>Produces a boxplot with all parameters from the multiple runs, divided by -using their medians as in the paper by Duchesne et al. (2021).</p> + <p>Produces a boxplot with all parameters from the multiple runs, scaled +either by the parameters of the run with the highest likelihood, +or by their medians as proposed in the paper by Duchesne et al. (2021).</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">parhist</span><span class="op">(</span><span class="va">object</span>, lpos <span class="op">=</span> <span class="st">"bottomleft"</span>, main <span class="op">=</span> <span class="st">""</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">parhist</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> llmin <span class="op">=</span> <span class="op">-</span><span class="cn">Inf</span>,</span> +<span> scale <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"best"</span>, <span class="st">"median"</span><span class="op">)</span>,</span> +<span> lpos <span class="op">=</span> <span class="st">"bottomleft"</span>,</span> +<span> main <span class="op">=</span> <span class="st">""</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -101,6 +110,15 @@ using their medians as in the paper by Duchesne et al. (2021).</p> <dd><p>The <a href="multistart.html">multistart</a> object</p></dd> +<dt>llmin</dt> +<dd><p>The minimum likelihood of objects to be shown</p></dd> + + +<dt>scale</dt> +<dd><p>By default, scale parameters using the best available fit. +If 'median', parameters are scaled using the median parameters from all fits.</p></dd> + + <dt>lpos</dt> <dd><p>Positioning of the legend.</p></dd> diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index ce3d428c..c8a7504f 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -46,12 +46,15 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> @@ -101,6 +104,10 @@ Expectation Maximisation algorithm (SAEM).</p> <span> test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span> <span> solution_type <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> covariance.model <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> covariates <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span> <span> nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">300</span>, <span class="fl">100</span><span class="op">)</span>,</span> <span> control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>displayProgress <span class="op">=</span> <span class="cn">FALSE</span>, print <span class="op">=</span> <span class="cn">FALSE</span>, nbiter.saemix <span class="op">=</span> <span class="va">nbiter.saemix</span>,</span> <span> save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> @@ -118,13 +125,17 @@ Expectation Maximisation algorithm (SAEM).</p> <span> solution_type <span class="op">=</span> <span class="st">"auto"</span>,</span> <span> transformations <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mkin"</span>, <span class="st">"saemix"</span><span class="op">)</span>,</span> <span> degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> covariance.model <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> covariates <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="cn">NULL</span>,</span> <span> test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>,</span> <span> conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span> <span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span> <span> <span class="va">...</span></span> <span><span class="op">)</span></span> <span></span> -<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span> +<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, covariates <span class="op">=</span> <span class="cn">NULL</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for saem.mmkin</span></span> <span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">object</span>, ci <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> @@ -171,6 +182,29 @@ for parameter that are tested if requested by 'test_log_parms'.</p></dd> automatic choice is not desired</p></dd> +<dt>covariance.model</dt> +<dd><p>Will be passed to <code><a href="https://rdrr.io/pkg/saemix/man/SaemixModel-class.html" class="external-link">saemix::SaemixModel()</a></code>. Per +default, uncorrelated random effects are specified for all degradation +parameters.</p></dd> + + +<dt>covariates</dt> +<dd><p>A data frame with covariate data for use in +'covariate_models', with dataset names as row names.</p></dd> + + +<dt>covariate_models</dt> +<dd><p>A list containing linear model formulas with one explanatory +variable, i.e. of the type 'parameter ~ covariate'. Covariates must be available +in the 'covariates' data frame.</p></dd> + + +<dt>no_random_effect</dt> +<dd><p>Character vector of degradation parameters for +which there should be no variability over the groups. Only used +if the covariance model is not explicitly specified.</p></dd> + + <dt>nbiter.saemix</dt> <dd><p>Convenience option to increase the number of iterations</p></dd> @@ -249,40 +283,43 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><span><span class="va">f_saem_sfo</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">f_saem_fomc</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">f_saem_dfop</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> [1] "sd(g_qlogis)"</span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop</span>, covariance.model <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/diag.html" class="external-link">diag</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by SAEM</span> -<span class="r-out co"><span class="r-pr">#></span> Structural model:</span> -<span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> -<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span> -<span class="r-out co"><span class="r-pr">#></span> * parent</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_sfo</span>, <span class="va">f_saem_fomc</span>, <span class="va">f_saem_dfop</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Data:</span> -<span class="r-out co"><span class="r-pr">#></span> 90 observations of 1 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_sfo 5 624.26 622.31 -307.13</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_fomc 7 467.87 465.13 -226.93</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop 9 493.98 490.47 -237.99</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_sfo</span>, <span class="va">f_saem_dfop</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> -<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 490.6 487.5 -237.3</span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik Chisq Df Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_sfo 5 624.26 622.31 -307.13 </span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop 9 493.98 490.47 -237.99 138.28 4 < 2.2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] "sd(g_qlogis)"</span> +<span class="r-in"><span><span class="va">f_saem_dfop_red</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop</span>, no_random_effect <span class="op">=</span> <span class="st">"g_qlogis"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_dfop</span>, <span class="va">f_saem_dfop_red</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> estimate lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 93.902 91.3695 96.4339</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.936 -3.9950 -1.8762</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.091 -4.9290 -1.2523</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.366 -0.6484 -0.0836</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 2.385 2.0033 2.7664</span> -<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.476 0.3890 4.5623</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.195 0.4381 1.9517</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.092 0.7906 3.3932</span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_saem_dfop</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> [1] 493.9811</span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik Chisq Df Pr(>Chisq)</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_red 8 490.64 487.52 -237.32 </span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop 9 493.98 490.47 -237.99 0 1 1</span> <span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_sfo</span>, <span class="va">f_saem_fomc</span>, <span class="va">f_saem_dfop</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_sfo 5 624.26 622.31 -307.13</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_fomc 7 467.87 465.13 -226.93</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop 9 493.98 490.47 -237.99</span> <span class="r-in"><span><span class="co"># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span></span></span> <span class="r-in"><span><span class="co"># functions from saemix</span></span></span> <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: npde</span> -<span class="r-msg co"><span class="r-pr">#></span> Package saemix, version 3.1</span> +<span class="r-msg co"><span class="r-pr">#></span> Package saemix, version 3.2</span> <span class="r-msg co"><span class="r-pr">#></span> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-msg co"><span class="r-pr">#></span> Attaching package: ‘saemix’</span> @@ -308,11 +345,12 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">f_mmkin_parent_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_mmkin_parent</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">f_saem_fomc_tc</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent_tc</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_fomc_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> Likelihoods calculated by importance sampling</span> -<span class="r-out co"><span class="r-pr">#></span> AIC BIC</span> -<span class="r-out co"><span class="r-pr">#></span> 1 467.8664 465.1324</span> -<span class="r-out co"><span class="r-pr">#></span> 2 469.8018 466.6773</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_fomc</span>, <span class="va">f_saem_fomc_tc</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik Chisq Df Pr(>Chisq)</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_fomc 7 467.87 465.13 -226.93 </span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_fomc_tc 8 469.80 466.68 -226.90 0.0645 1 0.7995</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> @@ -370,11 +408,11 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.1 </span> +<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Sep 16 10:30:47 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Sep 16 10:30:47 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Oct 26 09:20:37 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Oct 26 09:20:37 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -389,7 +427,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.651 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.902 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Constant variance </span> @@ -410,13 +448,20 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> 842 836.9 -408</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 93.7701 91.1458 96.3945</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_A1 -5.8116 -7.5998 -4.0234</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.9608 -1.3654 -0.5562</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.5841 -3.6876 -1.4805</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.5228 -5.3254 -1.7203</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.1027 -0.8719 0.6665</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 93.7701 91.1458 96.3945</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_A1 -5.8116 -7.5998 -4.0234</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.9608 -1.3654 -0.5562</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.5841 -3.6876 -1.4805</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.5228 -5.3254 -1.7203</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.1027 -0.8719 0.6665</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 1.8856 1.6676 2.1037</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.7682 0.7668 4.7695</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_A1 1.7447 0.4047 3.0848</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4525 0.1620 0.7431</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.2423 0.4560 2.0285</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.0390 0.7601 3.3180</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3069 1.1947</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> parnt_0 lg_k_A1 f_prnt_ log_k1 log_k2 </span> diff --git a/docs/dev/reference/set_nd_nq.html b/docs/dev/reference/set_nd_nq.html new file mode 100644 index 00000000..26a28339 --- /dev/null +++ b/docs/dev/reference/set_nd_nq.html @@ -0,0 +1,258 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Set non-detects and unquantified values in residue series without replicates — set_nd_nq • mkin</title><!-- jquery --><script 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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="Set non-detects and unquantified values in residue series without replicates — set_nd_nq"><meta property="og:description" content="This function automates replacing unquantified values in residue time and +depth series. For time series, the function performs part of the residue +processing proposed in the FOCUS kinetics guidance for parent compounds +and metabolites. For two-dimensional residue series over time and depth, +it automates the proposal of Boesten et al (2015)."><meta name="robots" content="noindex"><!-- 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</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" data-bs-toggle="dropdown" 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/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</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="https://github.com/jranke/mkin/" class="external-link"> + <span class="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>Set non-detects and unquantified values in residue series without replicates</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/set_nd_nq.R" class="external-link"><code>R/set_nd_nq.R</code></a></small> + <div class="hidden name"><code>set_nd_nq.Rd</code></div> + </div> + + <div class="ref-description"> + <p>This function automates replacing unquantified values in residue time and +depth series. For time series, the function performs part of the residue +processing proposed in the FOCUS kinetics guidance for parent compounds +and metabolites. For two-dimensional residue series over time and depth, +it automates the proposal of Boesten et al (2015).</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">res_raw</span>, <span class="va">lod</span>, loq <span class="op">=</span> <span class="cn">NA</span>, time_zero_presence <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">set_nd_nq_focus</span><span class="op">(</span></span> +<span> <span class="va">res_raw</span>,</span> +<span> <span class="va">lod</span>,</span> +<span> loq <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> set_first_sample_nd <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> first_sample_nd_value <span class="op">=</span> <span class="fl">0</span>,</span> +<span> ignore_below_loq_after_first_nd <span class="op">=</span> <span class="cn">TRUE</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>res_raw</dt> +<dd><p>Character vector of a residue time series, or matrix of +residue values with rows representing depth profiles for a specific sampling +time, and columns representing time series of residues at the same depth. +Values below the limit of detection (lod) have to be coded as "nd", values +between the limit of detection and the limit of quantification, if any, have +to be coded as "nq". Samples not analysed have to be coded as "na". All +values that are not "na", "nd" or "nq" have to be coercible to numeric</p></dd> + + +<dt>lod</dt> +<dd><p>Limit of detection (numeric)</p></dd> + + +<dt>loq</dt> +<dd><p>Limit of quantification(numeric). Must be specified if the FOCUS rule to +stop after the first non-detection is to be applied</p></dd> + + +<dt>time_zero_presence</dt> +<dd><p>Do we assume that residues occur at time zero? +This only affects samples from the first sampling time that have been +reported as "nd" (not detected).</p></dd> + + +<dt>set_first_sample_nd</dt> +<dd><p>Should the first sample be set to "first_sample_nd_value" +in case it is a non-detection?</p></dd> + + +<dt>first_sample_nd_value</dt> +<dd><p>Value to be used for the first sample if it is a non-detection</p></dd> + + +<dt>ignore_below_loq_after_first_nd</dt> +<dd><p>Should we ignore values below the LOQ after the first +non-detection that occurs after the quantified values?</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A numeric vector, if a vector was supplied, or a numeric matrix otherwise</p> + </div> + <div id="functions"> + <h2>Functions</h2> + +<ul><li><p><code>set_nd_nq_focus()</code>: Set non-detects in residue time series according to FOCUS rules</p></li> +</ul></div> + <div id="references"> + <h2>References</h2> + <p>Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H. +J. and Pol, J. W. (2015). Leaching of plant protection products and their +transformation products; Proposals for improving the assessment of leaching +to groundwater in the Netherlands — Version 2. Alterra report 2630, Alterra +Wageningen UR (University & Research centre)</p> +<p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation +Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, +18 December 2014, p. 251</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># FOCUS (2014) p. 75/76 and 131/132</span></span></span> +<span class="r-in"><span><span class="va">parent_1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">.12</span>, <span class="fl">.09</span>, <span class="fl">.05</span>, <span class="fl">.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">parent_1</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA</span> +<span class="r-in"><span><span class="va">parent_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">.12</span>, <span class="fl">.09</span>, <span class="fl">.05</span>, <span class="fl">.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="fl">.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">parent_2</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.03 0.01 NA NA</span> +<span class="r-in"><span><span class="fu">set_nd_nq_focus</span><span class="op">(</span><span class="va">parent_2</span>, <span class="fl">0.02</span>, loq <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA</span> +<span class="r-in"><span><span class="va">parent_3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">.12</span>, <span class="fl">.09</span>, <span class="fl">.05</span>, <span class="fl">.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="fl">.06</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">parent_3</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA</span> +<span class="r-in"><span><span class="fu">set_nd_nq_focus</span><span class="op">(</span><span class="va">parent_3</span>, <span class="fl">0.02</span>, loq <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA</span> +<span class="r-in"><span><span class="va">metabolite</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="fl">0.03</span>, <span class="fl">0.06</span>, <span class="fl">0.10</span>, <span class="fl">0.11</span>, <span class="fl">0.10</span>, <span class="fl">0.09</span>, <span class="fl">0.05</span>, <span class="fl">0.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">metabolite</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] NA NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01 NA</span> +<span class="r-in"><span><span class="fu">set_nd_nq_focus</span><span class="op">(</span><span class="va">metabolite</span>, <span class="fl">0.02</span>, <span class="fl">0.05</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.00 NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01 NA</span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># Boesten et al. (2015), p. 57/58</span></span></span> +<span class="r-in"><span><span class="va">table_8</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nq"</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">2</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fl">10</span>, <span class="fl">10</span>, <span class="fl">10</span>, <span class="st">"nq"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>,</span></span> +<span class="r-in"><span> <span class="st">"nq"</span>, <span class="fl">10</span>, <span class="st">"nq"</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">3</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="st">"nd"</span>, <span class="st">"nq"</span>, <span class="st">"nq"</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">3</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">6</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">6</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> ncol <span class="op">=</span> <span class="fl">6</span>, byrow <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">table_8</span>, <span class="fl">0.5</span>, <span class="fl">1.5</span>, time_zero_presence <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [,1] [,2] [,3] [,4] [,5] [,6]</span> +<span class="r-out co"><span class="r-pr">#></span> [1,] 10.00 10.00 0.25 0.25 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [2,] 10.00 10.00 1.00 1.00 0.25 NA</span> +<span class="r-out co"><span class="r-pr">#></span> [3,] 10.00 10.00 10.00 1.00 0.25 NA</span> +<span class="r-out co"><span class="r-pr">#></span> [4,] 1.00 10.00 1.00 0.25 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [5,] 0.25 1.00 1.00 0.25 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [6,] NA 0.25 0.25 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [7,] NA NA NA NA NA NA</span> +<span class="r-in"><span><span class="va">table_10</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fl">10</span>, <span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">3</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="st">"nd"</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">18</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> ncol <span class="op">=</span> <span class="fl">6</span>, byrow <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">table_10</span>, <span class="fl">0.5</span>, time_zero_presence <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [,1] [,2] [,3] [,4] [,5] [,6]</span> +<span class="r-out co"><span class="r-pr">#></span> [1,] 10.00 10.00 0.25 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [2,] 10.00 10.00 0.25 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [3,] 10.00 10.00 10.00 0.25 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [4,] 0.25 10.00 0.25 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [5,] NA 0.25 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [6,] NA NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [7,] NA NA NA NA NA NA</span> +</code></pre></div> + </div> + </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></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + |
