aboutsummaryrefslogtreecommitdiff
path: root/docs/articles/web_only/multistart.html
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2023-05-19 17:08:43 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2023-05-19 17:10:16 +0200
commitcf54ccca37d27480dbf8d59eb027300518f7ad75 (patch)
tree81a9d5955f716a74822ecb65dc83daeeb7efbba6 /docs/articles/web_only/multistart.html
parentc931057ce8f05d3a0dfefea72b73903efb82e900 (diff)
Prepare release of v1.2.4v1.2.4
- Update DESCRIPTION - Update Makefile to document how to use R-patched - Remove markup from two URLs to avoid CRAN NOTE - Switch two vignettes from html_document to html_vignette to save space in the docs directory, also avoiding a CRAN NOTE - Complete rebuild of pkgdown docs for release
Diffstat (limited to 'docs/articles/web_only/multistart.html')
-rw-r--r--docs/articles/web_only/multistart.html28
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">&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>, 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">&lt;-</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">&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/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(&gt;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">

Contact - Imprint