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Diffstat (limited to 'docs/dev/articles/web_only/multistart.html')
| -rw-r--r-- | docs/dev/articles/web_only/multistart.html | 10 |
1 files changed, 5 insertions, 5 deletions
diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html index 275fc520..0c08905a 100644 --- a/docs/dev/articles/web_only/multistart.html +++ b/docs/dev/articles/web_only/multistart.html @@ -109,7 +109,7 @@ <h1 data-toc-skip>Short demo of the multistart method</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 26 September 2022 (rebuilt 2022-10-26)</h4> + <h4 data-toc-skip class="date">Last change 26 September 2022 (rebuilt 2022-10-28)</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> @@ -139,7 +139,7 @@ <p>We see that not all variability parameters are identifiable. The <code>illparms</code> function tells us that the confidence interval for the standard deviation of ‘log_k2’ includes zero. We check this assessment using multiple runs with different starting values.</p> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_saem_full_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_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="fu"><a href="../../reference/parhist.html">parhist</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span><span class="op">)</span></span></code></pre></div> +<span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span><span class="op">)</span></span></code></pre></div> <p><img src="multistart_files/figure-html/unnamed-chunk-3-1.png" width="700"></p> <p>This confirms that the variance of k2 is the most problematic 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"> @@ -148,7 +148,7 @@ <pre><code><span><span class="co">## character(0)</span></span></code></pre> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> <code class="sourceCode R"><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/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">"topright"</span><span class="op">)</span></span></code></pre></div> +<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><span class="op">)</span></span></code></pre></div> <p><img src="multistart_files/figure-html/unnamed-chunk-4-1.png" width="700"></p> <p>The results confirm that all remaining parameters can be determined with sufficient certainty.</p> <p>We can also analyse the log-likelihoods obtained in the multiple runs:</p> @@ -157,7 +157,7 @@ <p><img src="multistart_files/figure-html/unnamed-chunk-5-1.png" width="700"></p> <p>The parameter histograms can be further improved by excluding the result with the low likelihood.</p> <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="../../reference/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">"topright"</span>, llmin <span class="op">=</span> <span class="op">-</span><span class="fl">326</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> +<code class="sourceCode R"><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>, llmin <span class="op">=</span> <span class="op">-</span><span class="fl">326</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> <p><img src="multistart_files/figure-html/unnamed-chunk-6-1.png" width="700"></p> <p>We can use the <code>anova</code> method to compare the models, including a likelihood ratio test if the models are nested.</p> <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> @@ -165,7 +165,7 @@ <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 Chisq Df Pr(>Chisq)</span></span> -<span><span class="co">## best(f_saem_reduced_multi) 9 663.81 661.93 -322.90 </span></span> +<span><span class="co">## best(f_saem_reduced_multi) 9 663.64 661.77 -322.82 </span></span> <span><span class="co">## f_saem_full 10 668.27 666.19 -324.13 0 1 1</span></span></code></pre> <p>While AIC and BIC are lower for the reduced model, the likelihood ratio test does not indicate a significant difference between the fits.</p> </div> |