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Diffstat (limited to 'docs/articles/web_only/multistart.html')
| -rw-r--r-- | docs/articles/web_only/multistart.html | 28 |
1 files changed, 15 insertions, 13 deletions
diff --git a/docs/articles/web_only/multistart.html b/docs/articles/web_only/multistart.html index 04093e82..b9224bb0 100644 --- a/docs/articles/web_only/multistart.html +++ b/docs/articles/web_only/multistart.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -134,7 +134,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 20 April 2023 -(rebuilt 2023-04-20)</h4> +(rebuilt 2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/multistart.rmd" class="external-link"><code>vignettes/web_only/multistart.rmd</code></a></small> <div class="hidden name"><code>multistart.rmd</code></div> @@ -175,7 +175,7 @@ assessment using multiple runs with different starting values.</p> parameter, so we reduce the parameter distribution model by removing the intersoil variability for k2.</p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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> +<code class="sourceCode R"><span><span class="va">f_saem_reduced</span> <span class="op"><-</span> <span class="fu">stats</span><span class="fu">::</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="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span> <span><span class="va">f_saem_reduced_multi</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">f_saem_reduced</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="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span>, ylim <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">0.5</span>, <span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> @@ -190,18 +190,20 @@ runs:</p> <p>We can use the <code>anova</code> method to compare the models.</p> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> <code class="sourceCode R"><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_full</span>, <span class="fu"><a href="../../reference/multistart.html">best</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span><span class="op">)</span>,</span> -<span> <span class="va">f_saem_reduced</span>, <span class="fu"><a href="../../reference/multistart.html">best</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<span> <span class="va">f_saem_reduced</span>, <span class="fu"><a href="../../reference/multistart.html">best</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span><span class="op">)</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Data: 155 observations of 1 variable(s) grouped in 6 datasets</span></span> <span><span class="co">## </span></span> -<span><span class="co">## npar AIC BIC Lik</span></span> -<span><span class="co">## f_saem_reduced 9 663.73 661.86 -322.86</span></span> -<span><span class="co">## best(f_saem_reduced_multi) 9 663.69 661.82 -322.85</span></span> -<span><span class="co">## f_saem_full 10 669.77 667.69 -324.89</span></span> -<span><span class="co">## best(f_saem_full_multi) 10 665.56 663.48 -322.78</span></span></code></pre> -<p>The reduced model gives the lowest information criteria and similar -likelihoods as the best variant of the full model. The multistart method -leads to a much lower improvement of the likelihood for the reduced -model, indicating that it converges faster.</p> +<span><span class="co">## npar AIC BIC Lik Chisq Df Pr(>Chisq)</span></span> +<span><span class="co">## f_saem_reduced 9 663.67 661.80 -322.84 </span></span> +<span><span class="co">## best(f_saem_reduced_multi) 9 663.65 661.78 -322.82 0.0219 0 </span></span> +<span><span class="co">## f_saem_full 10 670.09 668.01 -325.05 0.0000 1 1</span></span> +<span><span class="co">## best(f_saem_full_multi) 10 665.61 663.52 -322.80 4.4870 0</span></span></code></pre> +<p>The reduced model results in lower AIC and BIC values, so it is +clearly preferable. Using multiple starting values gives a large +improvement in case of the full model, because it is less well-defined, +which impedes convergence. For the reduced model, using multiple +starting values only results in a small improvement of the model +fit.</p> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |