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If two fitted mkinfit objects are given as arguments, it is checked if they have been fitted to the same data. It is the responsibility of the user to make sure that the models are nested, i.e. one of them has less degrees of freedom and can be expressed by fixing the parameters of the other."><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">1.2.2</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">Benchmark timings for mkin</a> </li> <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</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>Likelihood ratio test for mkinfit models</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/lrtest.mkinfit.R" class="external-link"><code>R/lrtest.mkinfit.R</code></a></small> <div class="hidden name"><code>lrtest.mkinfit.Rd</code></div> </div> <div class="ref-description"> <p>Compare two mkinfit models based on their likelihood. If two fitted mkinfit objects are given as arguments, it is checked if they have been fitted to the same data. It is the responsibility of the user to make sure that the models are nested, i.e. one of them has less degrees of freedom and can be expressed by fixing the parameters of the other.</p> </div> <div id="ref-usage"> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> <span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">object</span>, object_2 <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 mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></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"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>An <code><a href="mkinfit.html">mkinfit</a></code> object, or an <code><a href="mmkin.html">mmkin</a></code> column object containing two fits to the same data.</p></dd> <dt>object_2</dt> <dd><p>Optionally, another mkinfit object fitted to the same data.</p></dd> <dt>...</dt> <dd><p>Argument to <code><a href="mkinfit.html">mkinfit</a></code>, passed to <code><a href="update.mkinfit.html">update.mkinfit</a></code> for creating the alternative fitted object.</p></dd> </dl></div> <div id="details"> <h2>Details</h2> <p>Alternatively, an argument to mkinfit can be given which is then passed to <code><a href="update.mkinfit.html">update.mkinfit</a></code> to obtain the alternative model.</p> <p>The comparison is then made by the <code><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest.default</a></code> method from the lmtest package. The model with the higher number of fitted parameters (alternative hypothesis) is listed first, then the model with the lower number of fitted parameters (null hypothesis).</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"># \dontrun{</span></span></span> <span class="r-in"><span><span class="va">test_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">sfo_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">test_data</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">dfop_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">dfop_fit</span>, <span class="va">sfo_fit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model const</span> <span class="r-out co"><span class="r-pr">#></span> Model 2: SFO with error model const</span> <span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> <span class="r-out co"><span class="r-pr">#></span> 1 5 -42.453 </span> <span class="r-out co"><span class="r-pr">#></span> 2 3 -63.954 -2 43.002 4.594e-10 ***</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="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">sfo_fit</span>, <span class="va">dfop_fit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model const</span> <span class="r-out co"><span class="r-pr">#></span> Model 2: SFO with error model const</span> <span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> <span class="r-out co"><span class="r-pr">#></span> 1 5 -42.453 </span> <span class="r-out co"><span class="r-pr">#></span> 2 3 -63.954 -2 43.002 4.594e-10 ***</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></span> <span class="r-in"><span><span class="co"># The following two examples are commented out as they fail during</span></span></span> <span class="r-in"><span><span class="co"># generation of the static help pages by pkgdown</span></span></span> <span class="r-in"><span><span class="co">#lrtest(dfop_fit, error_model = "tc")</span></span></span> <span class="r-in"><span><span class="co">#lrtest(dfop_fit, fixed_parms = c(k2 = 0))</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># However, this equivalent syntax also works for static help pages</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">dfop_fit</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">dfop_fit</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model tc</span> <span class="r-out co"><span class="r-pr">#></span> Model 2: DFOP with error model const</span> <span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> <span class="r-out co"><span class="r-pr">#></span> 1 6 -34.587 </span> <span class="r-out co"><span class="r-pr">#></span> 2 5 -42.453 -1 15.731 7.302e-05 ***</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="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">dfop_fit</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">dfop_fit</span>, fixed_parms <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>k2 <span class="op">=</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> Likelihood ratio test</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model const</span> <span class="r-out co"><span class="r-pr">#></span> Model 2: DFOP with error model const and fixed parameter(s) k2</span> <span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> <span class="r-out co"><span class="r-pr">#></span> 1 5 -42.453 </span> <span class="r-out co"><span class="r-pr">#></span> 2 4 -57.340 -1 29.776 4.851e-08 ***</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="co"># }</span></span></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>