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authorJohannes Ranke <jranke@uni-bremen.de>2022-10-29 00:36:22 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2022-10-29 00:36:22 +0200
commit59566e315c5d05a0aa4a46ab80c5fda33c5c2f1e (patch)
tree91eb7671c50b2b5563a58344723304d159524f6d
parentf820bf5b91be0f589de16c3e3250f5f79672df75 (diff)
Update multistart docs
-rw-r--r--R/multistart.R4
-rw-r--r--_pkgdown.yml4
-rw-r--r--docs/dev/articles/web_only/multistart.html10
-rw-r--r--docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.pngbin59606 -> 59586 bytes
-rw-r--r--docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.pngbin55167 -> 55154 bytes
-rw-r--r--docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.pngbin21474 -> 21455 bytes
-rw-r--r--docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-6-1.pngbin54481 -> 54302 bytes
-rw-r--r--docs/dev/news/index.html4
-rw-r--r--docs/dev/pkgdown.yml2
-rw-r--r--docs/dev/reference/Rplot001.pngbin19755 -> 20021 bytes
-rw-r--r--docs/dev/reference/Rplot002.pngbin17365 -> 17243 bytes
-rw-r--r--docs/dev/reference/index.html8
-rw-r--r--docs/dev/reference/logLik.saem.mmkin.html2
-rw-r--r--docs/dev/reference/multistart-1.pngbin59284 -> 60852 bytes
-rw-r--r--docs/dev/reference/multistart-2.pngbin54871 -> 54922 bytes
-rw-r--r--docs/dev/reference/multistart.html9
-rw-r--r--docs/dev/reference/parplot.html172
-rw-r--r--docs/dev/reference/status.html171
-rw-r--r--docs/dev/reference/summary.mmkin.html17
-rw-r--r--docs/dev/sitemap.xml6
-rw-r--r--man/multistart.Rd4
21 files changed, 382 insertions, 31 deletions
diff --git a/R/multistart.R b/R/multistart.R
index 14683c11..61ef43dc 100644
--- a/R/multistart.R
+++ b/R/multistart.R
@@ -40,7 +40,7 @@
#' f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE)
#' f_saem_full <- saem(f_mmkin)
#' f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16)
-#' parplot(f_saem_full_multi, lpos = "bottomleft")
+#' parplot(f_saem_full_multi, lpos = "topleft")
#' illparms(f_saem_full)
#'
#' f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2")
@@ -50,9 +50,9 @@
#' # nodes, as it is referred to when updating the saem object on the nodes.
#' library(parallel)
#' cl <- makePSOCKcluster(12)
-#' clusterExport(cl, "f_mmkin")
#' f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cluster = cl)
#' parplot(f_saem_reduced_multi, lpos = "topright")
+#' stopCluster(cl)
#' }
multistart <- function(object, n = 50,
cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(),
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 6a357e05..cf9e292d 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -22,7 +22,7 @@ reference:
desc: Generic functions introduced by the package
contents:
- parms
- - convergence
+ - status
- illparms
- endpoints
- aw
@@ -63,7 +63,7 @@ reference:
- intervals.saem.mmkin
- multistart
- llhist
- - parhist
+ - parplot
- title: Datasets and known results
contents:
- focus_soil_moisture
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">&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><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">&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">"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(&gt;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>
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 e3baa59b..79543765 100644
--- 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
Binary files differ
diff --git 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
index d32e1214..4466d437 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
Binary files differ
diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png
index d72722f0..3dd36f91 100644
--- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png
+++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png
Binary files differ
diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-6-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-6-1.png
index f9b5aff2..3963e993 100644
--- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-6-1.png
+++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-6-1.png
Binary files differ
diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 029b6999..b509aca3 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -86,11 +86,11 @@
<div class="section level2">
<h2 class="page-header" data-toc-text="1.1.2" id="mkin-112">mkin 1.1.2<a class="anchor" aria-label="anchor" href="#mkin-112"></a></h2>
-<ul><li><p>‘R/multistart.R’: New method for testing multiple start parameters for hierarchical model fits, with diagnostic plotting functions ‘llhist’ and ‘parhist’.</p></li>
+<ul><li><p>‘R/multistart.R’: New method for testing multiple start parameters for hierarchical model fits, with diagnostic plotting functions ‘llhist’ and ‘parplot’.</p></li>
<li><p>‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.</p></li>
<li><p>‘R/saem.R’: Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported.</p></li>
<li><p>‘R/saem.R’: ‘logLik’ and ‘update’ methods for ‘saem.mmkin’ objects.</p></li>
-<li><p>‘R/convergence.R’: New generic to show convergence information with methods for ‘mmkin’ and ‘mhmkin’ objects.</p></li>
+<li><p>‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’ and ‘mhmkin’ objects.</p></li>
<li><p>‘R/illparms.R’: New generic to show ill-defined parameters with methods for ‘mkinfit’, ‘mmkin’, ‘saem.mmkin’ and ‘mhmkin’ objects.</p></li>
<li><p>‘R/summary.mmkin.R’: Summary method for mmkin objects.</p></li>
</ul></div>
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index 2bb496a8..12a9b003 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -12,7 +12,7 @@ articles:
compiled_models: web_only/compiled_models.html
dimethenamid_2018: web_only/dimethenamid_2018.html
multistart: web_only/multistart.html
-last_built: 2022-10-26T08:33Z
+last_built: 2022-10-28T21:37Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index f7b4238e..6841f086 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 018559d0..11f6a1cd 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 3d9d40b7..0fac6842 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -114,9 +114,9 @@ degradation models and one or more error models</p></td>
</td>
<td><p>Extract model parameters</p></td>
</tr><tr><td>
- <p><code><a href="convergence.html">convergence()</a></code> <code><a href="convergence.html">print(<i>&lt;convergence.mmkin&gt;</i>)</a></code> </p>
+ <p><code><a href="status.html">status()</a></code> <code><a href="status.html">print(<i>&lt;status.mmkin&gt;</i>)</a></code> <code><a href="status.html">print(<i>&lt;status.mhmkin&gt;</i>)</a></code> </p>
</td>
- <td><p>Method to get convergence information</p></td>
+ <td><p>Method to get status information for fit array objects</p></td>
</tr><tr><td>
<p><code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i>&lt;illparms.mmkin&gt;</i>)</a></code> <code><a href="illparms.html">print(<i>&lt;illparms.mhmkin&gt;</i>)</a></code> </p>
</td>
@@ -253,9 +253,9 @@ degradation models and one or more error models</p></td>
</td>
<td><p>Plot the distribution of log likelihoods from multistart objects</p></td>
</tr><tr><td>
- <p><code><a href="parhist.html">parhist()</a></code> </p>
+ <p><code><a href="parplot.html">parplot()</a></code> </p>
</td>
- <td><p>Plot parameter distributions from multistart objects</p></td>
+ <td><p>Plot parameter variability of multistart objects</p></td>
</tr></tbody><tbody><tr><th colspan="2">
<h2 id="datasets-and-known-results">Datasets and known results <a href="#datasets-and-known-results" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p>
diff --git a/docs/dev/reference/logLik.saem.mmkin.html b/docs/dev/reference/logLik.saem.mmkin.html
index 9694232c..99b3b906 100644
--- a/docs/dev/reference/logLik.saem.mmkin.html
+++ b/docs/dev/reference/logLik.saem.mmkin.html
@@ -91,7 +91,7 @@
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span>
-<span><span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, method <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="st">"lin"</span>, <span class="st">"is"</span>, <span class="st">"gq"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, method <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="st">"is"</span>, <span class="st">"lin"</span>, <span class="st">"gq"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
diff --git a/docs/dev/reference/multistart-1.png b/docs/dev/reference/multistart-1.png
index 25362568..7fc24a04 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 cf8c097e..7553a51a 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 c874bf50..176d40c0 100644
--- a/docs/dev/reference/multistart.html
+++ b/docs/dev/reference/multistart.html
@@ -175,7 +175,7 @@ doi: 10.1186/s12859-021-04373-4.</p>
</div>
<div id="see-also">
<h2>See also</h2>
- <div class="dont-index"><p><a href="parhist.html">parhist</a>, <a href="llhist.html">llhist</a></p></div>
+ <div class="dont-index"><p><a href="parplot.html">parplot</a>, <a href="llhist.html">llhist</a></p></div>
</div>
<div id="ref-examples">
@@ -195,7 +195,7 @@ doi: 10.1186/s12859-021-04373-4.</p>
<span class="r-in"><span><span class="va">f_mmkin</span> <span class="op">&lt;-</span> <span class="fu"><a href="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="r-in"><span><span class="va">f_saem_full</span> <span class="op">&lt;-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">f_saem_full_multi</span> <span class="op">&lt;-</span> <span class="fu">multistart</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="r-in"><span><span class="fu"><a href="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">"bottomleft"</span><span class="op">)</span></span></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_full_multi</span>, lpos <span class="op">=</span> <span class="st">"topleft"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="multistart-1.png" alt="" width="700" height="433"></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_full</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "sd(log_k2)"</span>
@@ -208,11 +208,10 @@ doi: 10.1186/s12859-021-04373-4.</p>
<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="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="fu"><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">clusterExport</a></span><span class="op">(</span><span class="va">cl</span>, <span class="st">"f_mmkin"</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in get(name, envir = envir):</span> object 'f_mmkin' not found</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-in"><span><span class="fu"><a href="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></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-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>
</div>
diff --git a/docs/dev/reference/parplot.html b/docs/dev/reference/parplot.html
new file mode 100644
index 00000000..38a93e27
--- /dev/null
+++ b/docs/dev/reference/parplot.html
@@ -0,0 +1,172 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Plot parameter variability of multistart objects — parplot • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Plot parameter variability of multistart objects — parplot"><meta property="og:description" content="Produces a boxplot with all parameters from the multiple runs, scaled
+either by the parameters of the run with the highest likelihood,
+or by their medians as proposed in the paper by Duchesne et al. (2021)."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
+ </ul></li>
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+
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+</div><!--/.navbar -->
+
+
+
+ </header><div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Plot parameter variability of multistart objects</h1>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parplot.R" class="external-link"><code>R/parplot.R</code></a></small>
+ <div class="hidden name"><code>parplot.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Produces a boxplot with all parameters from the multiple runs, scaled
+either by the parameters of the run with the highest likelihood,
+or by their medians as proposed in the paper by Duchesne et al. (2021).</p>
+ </div>
+
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">parplot</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for multistart.saem.mmkin</span></span>
+<span><span class="fu">parplot</span><span class="op">(</span></span>
+<span> <span class="va">object</span>,</span>
+<span> llmin <span class="op">=</span> <span class="op">-</span><span class="cn">Inf</span>,</span>
+<span> scale <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="st">"best"</span>, <span class="st">"median"</span><span class="op">)</span>,</span>
+<span> lpos <span class="op">=</span> <span class="st">"bottomleft"</span>,</span>
+<span> main <span class="op">=</span> <span class="st">""</span>,</span>
+<span> <span class="va">...</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>object</dt>
+<dd><p>The <a href="multistart.html">multistart</a> object</p></dd>
+
+
+<dt>...</dt>
+<dd><p>Passed to <a href="https://rdrr.io/r/graphics/boxplot.html" class="external-link">boxplot</a></p></dd>
+
+
+<dt>llmin</dt>
+<dd><p>The minimum likelihood of objects to be shown</p></dd>
+
+
+<dt>scale</dt>
+<dd><p>By default, scale parameters using the best available fit.
+If 'median', parameters are scaled using the median parameters from all fits.</p></dd>
+
+
+<dt>lpos</dt>
+<dd><p>Positioning of the legend.</p></dd>
+
+
+<dt>main</dt>
+<dd><p>Title of the plot</p></dd>
+
+</dl></div>
+ <div id="references">
+ <h2>References</h2>
+ <p>Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical
+identifiability in the frame of nonlinear mixed effects models: the example
+of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478.
+doi: 10.1186/s12859-021-04373-4.</p>
+ </div>
+ <div id="see-also">
+ <h2>See also</h2>
+ <div class="dont-index"><p><a href="multistart.html">multistart</a></p></div>
+ </div>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+ </nav></div>
+</div>
+
+
+ <footer><div class="copyright">
+ <p></p><p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
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+
+ </footer></div>
+
+
+
+
+
+
+ </body></html>
+
diff --git a/docs/dev/reference/status.html b/docs/dev/reference/status.html
new file mode 100644
index 00000000..778446b3
--- /dev/null
+++ b/docs/dev/reference/status.html
@@ -0,0 +1,171 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Method to get status information for fit array objects — status • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Method to get status information for fit array objects — status"><meta property="og:description" content="Method to get status information for fit array objects"><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+
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+ <div class="container template-reference-topic">
+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
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+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
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+ <div id="navbar" class="navbar-collapse collapse">
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+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu"><li>
+ <a href="../articles/mkin.html">Introduction to mkin</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
+ </ul></li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul><ul class="nav navbar-nav navbar-right"><li>
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+ <span class="fab fa-github fa-lg"></span>
+
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+</li>
+ </ul></div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header><div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Method to get status information for fit array objects</h1>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/status.R" class="external-link"><code>R/status.R</code></a></small>
+ <div class="hidden name"><code>status.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Method to get status information for fit array objects</p>
+ </div>
+
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">status</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mmkin</span></span>
+<span><span class="fu">status</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for status.mmkin</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mhmkin</span></span>
+<span><span class="fu">status</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for status.mhmkin</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>object</dt>
+<dd><p>The object to investigate</p></dd>
+
+
+<dt>...</dt>
+<dd><p>For potential future extensions</p></dd>
+
+
+<dt>x</dt>
+<dd><p>The object to be printed</p></dd>
+
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
+
+
+<p>An object with the same dimensions as the fit array
+suitable printing method.</p>
+ </div>
+
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">fits</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span></span></span>
+<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><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS A"</span> <span class="op">=</span> <span class="va">FOCUS_2006_A</span>,</span></span>
+<span class="r-in"><span> <span class="st">"FOCUS B"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">status</span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> dataset</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> model FOCUS A FOCUS B</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SFO OK OK </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> FOMC OK OK </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> OK: No warnings</span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+</code></pre></div>
+ </div>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+ </nav></div>
+</div>
+
+
+ <footer><div class="copyright">
+ <p></p><p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+</div>
+
+ </footer></div>
+
+
+
+
+
+
+ </body></html>
+
diff --git a/docs/dev/reference/summary.mmkin.html b/docs/dev/reference/summary.mmkin.html
index e440e4a9..145e3ba1 100644
--- a/docs/dev/reference/summary.mmkin.html
+++ b/docs/dev/reference/summary.mmkin.html
@@ -1,5 +1,5 @@
<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Summary method for class "mmkin" — summary.mmkin • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Summary method for class " mmkin summary.mmkin><meta property="og:description" content="Shows convergence information on the mkinfit objects contained in the object
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Summary method for class "mmkin" — summary.mmkin • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Summary method for class " mmkin summary.mmkin><meta property="og:description" content="Shows status information on the mkinfit objects contained in the object
and gives an overview of ill-defined parameters calculated by illparms."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -45,12 +45,15 @@ and gives an overview of ill-defined parameters calculated by illparms."><meta n
<a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
</li>
<li>
- <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
</li>
<li>
<a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
</li>
<li>
@@ -84,13 +87,13 @@ and gives an overview of ill-defined parameters calculated by illparms."><meta n
</div>
<div class="ref-description">
- <p>Shows convergence information on the <a href="mkinfit.html">mkinfit</a> objects contained in the object
+ <p>Shows status information on the <a href="mkinfit.html">mkinfit</a> objects contained in the object
and gives an overview of ill-defined parameters calculated by <a href="illparms.html">illparms</a>.</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span>
-<span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for summary.mmkin</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
@@ -127,11 +130,11 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms.
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS A"</span> <span class="op">=</span> <span class="va">FOCUS_2006_A</span>,</span></span>
<span class="r-in"><span> <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span>
-<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Error model: Constant variance </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 0.81 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 1.032 s</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Convergence:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Status:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> dataset</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> model FOCUS A FOCUS C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SFO OK OK </span>
diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml
index 86bf9185..2e2c4b14 100644
--- a/docs/dev/sitemap.xml
+++ b/docs/dev/sitemap.xml
@@ -244,6 +244,9 @@
<loc>https://pkgdown.jrwb.de/mkin/reference/parms.html</loc>
</url>
<url>
+ <loc>https://pkgdown.jrwb.de/mkin/reference/parplot.html</loc>
+ </url>
+ <url>
<loc>https://pkgdown.jrwb.de/mkin/reference/plot.mixed.mmkin.html</loc>
</url>
<url>
@@ -277,6 +280,9 @@
<loc>https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html</loc>
</url>
<url>
+ <loc>https://pkgdown.jrwb.de/mkin/reference/status.html</loc>
+ </url>
+ <url>
<loc>https://pkgdown.jrwb.de/mkin/reference/summary.mkinfit.html</loc>
</url>
<url>
diff --git a/man/multistart.Rd b/man/multistart.Rd
index 1f6773fe..5a5f7b44 100644
--- a/man/multistart.Rd
+++ b/man/multistart.Rd
@@ -77,7 +77,7 @@ dmta_ds[["Elliot 1"]] <- dmta_ds[["Elliot 2"]] <- NULL
f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE)
f_saem_full <- saem(f_mmkin)
f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16)
-parplot(f_saem_full_multi, lpos = "bottomleft")
+parplot(f_saem_full_multi, lpos = "topleft")
illparms(f_saem_full)
f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2")
@@ -87,9 +87,9 @@ illparms(f_saem_reduced)
# nodes, as it is referred to when updating the saem object on the nodes.
library(parallel)
cl <- makePSOCKcluster(12)
-clusterExport(cl, "f_mmkin")
f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cluster = cl)
parplot(f_saem_reduced_multi, lpos = "topright")
+stopCluster(cl)
}
}
\references{

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