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authorJohannes Ranke <jranke@uni-bremen.de>2022-09-19 12:55:00 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2022-09-19 12:55:00 +0200
commit7a3f2ee22419608a8a634fd4d71d7176303b2f41 (patch)
tree292447a0f0f647253ac269074ba7b6ce4139c576 /docs/dev/articles/web_only
parent062a1be18677a4e83a64d23622b5214258d9bc7d (diff)
Improve parhist and llhist
In particular, adapt the display of parameter boxplots for saem fits using mkin transformations to the way used for saem fits using saemix transformations, i.e. always show parameters on the natural scale, and normalised them by dividing by the median from the multiple runs.
Diffstat (limited to 'docs/dev/articles/web_only')
-rw-r--r--docs/dev/articles/web_only/multistart.html6
-rw-r--r--docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-2-1.pngbin52067 -> 61772 bytes
-rw-r--r--docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.pngbin50142 -> 56540 bytes
-rw-r--r--docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.pngbin39793 -> 39866 bytes
4 files changed, 3 insertions, 3 deletions
diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html
index b3108120..f9b27a0c 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 16 September 2022 (rebuilt 2022-09-16)</h4>
+ <h4 data-toc-skip class="date">Last change 19 September 2022 (rebuilt 2022-09-19)</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>
@@ -135,13 +135,13 @@
<code class="sourceCode R"><span><span class="va">f_mmkin</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/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="va">f_saem_full</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span>
<span><span class="va">f_saem_full_multi</span> <span class="op">&lt;-</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>, lpos <span class="op">=</span> <span class="st">"bottomright"</span><span class="op">)</span></span></code></pre></div>
+<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>
<p><img src="multistart_files/figure-html/unnamed-chunk-2-1.png" width="700"></p>
<p>We see that not all variability parameters are identifiable, most problematic is the variance of k2. So we reduce the parameter distribution model by removing the intersoil variability for this parameter.</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">f_saem_reduced</span> <span class="op">&lt;-</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="va">f_saem_reduced_multi</span> <span class="op">&lt;-</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">"bottomright"</span><span class="op">)</span></span></code></pre></div>
+<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>
<p><img src="multistart_files/figure-html/unnamed-chunk-3-1.png" width="700"></p>
<p>We can also analyse the log-likelihoods obtained in the multiple runs:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
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index e30e56f0..18800fb9 100644
--- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-2-1.png
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diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
index 3ed0d546..908989e9 100644
--- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
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index 957c2457..e50177cc 100644
--- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
+++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
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