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authorJohannes Ranke <jranke@uni-bremen.de>2023-04-17 19:39:09 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2023-04-17 19:39:09 +0200
commit004fce2520d6889d82226e21bc443426e81d93f2 (patch)
treea5b18bd357c506059ff2149f1c6602ea71df6d99 /docs/dev/reference
parent57ca408fda3fb8e42e0d5f3d9fc808d54268fa08 (diff)
Improve docs of multistart method
Diffstat (limited to 'docs/dev/reference')
-rw-r--r--docs/dev/reference/Rplot001.pngbin13993 -> 20512 bytes
-rw-r--r--docs/dev/reference/Rplot002.pngbin13470 -> 16766 bytes
-rw-r--r--docs/dev/reference/index.html5
-rw-r--r--docs/dev/reference/mkinpredict.html9
-rw-r--r--docs/dev/reference/multistart-1.pngbin66388 -> 63843 bytes
-rw-r--r--docs/dev/reference/multistart-2.pngbin56780 -> 52220 bytes
-rw-r--r--docs/dev/reference/multistart.html10
7 files changed, 9 insertions, 15 deletions
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index 5de2bdc7..278fd2e2 100644
--- a/docs/dev/reference/Rplot001.png
+++ b/docs/dev/reference/Rplot001.png
Binary files differ
diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png
index 556ca0a7..4b646f22 100644
--- a/docs/dev/reference/Rplot002.png
+++ b/docs/dev/reference/Rplot002.png
Binary files differ
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index 84bbbdc4..85dc7c6e 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -81,11 +81,6 @@
<li>
<a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
- <li class="divider">
- <li class="dropdown-header">Code coverage report</li>
- <li>
- <a href="../coverage/coverage.html"></a>
- </li>
</ul></li>
<li>
<a href="../news/index.html">News</a>
diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html
index 01c15a19..7d8e7c26 100644
--- a/docs/dev/reference/mkinpredict.html
+++ b/docs/dev/reference/mkinpredict.html
@@ -394,11 +394,12 @@ as these always return mapped output.</p></dd>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: rbenchmark</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> test relative elapsed</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled 1.0 0.002</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4 analytical 1.0 0.002</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 eigen 4.0 0.008</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3 deSolve 30.5 0.061</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled 1.00 0.004</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 eigen 4.00 0.016</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4 analytical 4.25 0.017</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3 deSolve 40.75 0.163</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
<span class="r-in"><span> <span class="co"># Predict from a fitted model</span></span></span>
diff --git a/docs/dev/reference/multistart-1.png b/docs/dev/reference/multistart-1.png
index c7937d67..ee0306d6 100644
--- a/docs/dev/reference/multistart-1.png
+++ b/docs/dev/reference/multistart-1.png
Binary files differ
diff --git a/docs/dev/reference/multistart-2.png b/docs/dev/reference/multistart-2.png
index e1983f12..69a178e3 100644
--- a/docs/dev/reference/multistart-2.png
+++ b/docs/dev/reference/multistart-2.png
Binary files differ
diff --git a/docs/dev/reference/multistart.html b/docs/dev/reference/multistart.html
index 3cdede7b..36767560 100644
--- a/docs/dev/reference/multistart.html
+++ b/docs/dev/reference/multistart.html
@@ -222,15 +222,13 @@ doi: 10.1186/s12859-021-04373-4.</p>
<span class="r-in"><span></span></span>
<span class="r-in"><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></span>
<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="co"># On Windows, we need to create a cluster first. When working with</span></span></span>
-<span class="r-in"><span><span class="co"># such a cluster, we need to export the mmkin object to the cluster</span></span></span>
-<span class="r-in"><span><span class="co"># nodes, as it is referred to when updating the saem object on the nodes.</span></span></span>
+<span class="r-in"><span><span class="co"># On Windows, we need to create a PSOCK cluster first and refer to it</span></span></span>
+<span class="r-in"><span><span class="co"># in the call to multistart()</span></span></span>
<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">parallel</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">cl</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makePSOCKcluster</a></span><span class="op">(</span><span class="fl">12</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">f_saem_reduced_multi</span> <span class="op">&lt;-</span> <span class="fu">multistart</span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cluster <span class="op">=</span> <span class="va">cl</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in checkForRemoteErrors(val):</span> 16 nodes produced errors; first error: unused argument (mc.preschedule = FALSE)</span>
-<span class="r-in"><span><span class="fu"><a href="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></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in parplot(f_saem_reduced_multi, lpos = "topright"):</span> object 'f_saem_reduced_multi' not found</span>
+<span class="r-in"><span><span class="fu"><a href="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></span>
+<span class="r-plt img"><img src="multistart-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

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