aboutsummaryrefslogtreecommitdiff
path: root/docs
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2021-03-31 19:42:17 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2021-03-31 19:42:17 +0200
commit3a5463672c297b37c3c9135c8b144c48744c05d0 (patch)
treef28691df6359757133510ae44399ce71ecbfaa93 /docs
parent7bca4f58951c1c8cae63c4557102ae77a3aff616 (diff)
Bug fix in plot.mkinfit
In residual plots, use xlab and xlim if appropriate
Diffstat (limited to 'docs')
-rw-r--r--docs/articles/FOCUS_D.html16
-rw-r--r--docs/articles/FOCUS_D_files/figure-html/plot-1.pngbin79176 -> 79749 bytes
-rw-r--r--docs/articles/FOCUS_D_files/figure-html/plot_2-1.pngbin24025 -> 24279 bytes
-rw-r--r--docs/articles/FOCUS_D_files/header-attrs-2.7/header-attrs.js12
-rw-r--r--docs/articles/FOCUS_L.html62
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.pngbin42203 -> 42472 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.pngbin82006 -> 83163 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.pngbin32751 -> 33123 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.pngbin57939 -> 58647 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.pngbin35238 -> 35678 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.pngbin21999 -> 22090 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.pngbin35640 -> 36105 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.pngbin41399 -> 41395 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.pngbin40983 -> 40745 bytes
-rw-r--r--docs/articles/FOCUS_L_files/header-attrs-2.7/header-attrs.js12
-rw-r--r--docs/articles/mkin.html6
-rw-r--r--docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.pngbin89958 -> 89961 bytes
-rw-r--r--docs/articles/mkin_files/header-attrs-2.7/header-attrs.js12
-rw-r--r--docs/articles/twa.html6
-rw-r--r--docs/articles/twa_files/header-attrs-2.7/header-attrs.js12
-rw-r--r--docs/articles/web_only/FOCUS_Z.html6
-rw-r--r--docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.pngbin66640 -> 66566 bytes
-rw-r--r--docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.pngbin106038 -> 105728 bytes
-rw-r--r--docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.pngbin105042 -> 104598 bytes
-rw-r--r--docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.pngbin75626 -> 75131 bytes
-rw-r--r--docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.pngbin35744 -> 36162 bytes
-rw-r--r--docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.pngbin66640 -> 66566 bytes
-rw-r--r--docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.pngbin66424 -> 66341 bytes
-rw-r--r--docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.pngbin80520 -> 80289 bytes
-rw-r--r--docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.pngbin105149 -> 104958 bytes
-rw-r--r--docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.pngbin104479 -> 104309 bytes
-rw-r--r--docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.pngbin88890 -> 88640 bytes
-rw-r--r--docs/articles/web_only/FOCUS_Z_files/header-attrs-2.7/header-attrs.js12
-rw-r--r--docs/articles/web_only/NAFTA_examples.html6
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.pngbin78793 -> 79833 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.pngbin75470 -> 76357 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.pngbin80755 -> 81683 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.pngbin69885 -> 70857 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.pngbin77126 -> 78065 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.pngbin79693 -> 80776 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.pngbin75945 -> 76982 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.pngbin78004 -> 78986 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p16-1.pngbin93075 -> 94024 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.pngbin81521 -> 82684 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.pngbin79783 -> 80778 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.pngbin81974 -> 83064 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.pngbin101606 -> 102575 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.pngbin91429 -> 92480 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.pngbin77612 -> 78544 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.pngbin75129 -> 76187 bytes
-rw-r--r--docs/articles/web_only/NAFTA_examples_files/header-attrs-2.7/header-attrs.js12
-rw-r--r--docs/articles/web_only/benchmarks.html26
-rw-r--r--docs/articles/web_only/benchmarks_files/header-attrs-2.7/header-attrs.js12
-rw-r--r--docs/news/index.html2
-rw-r--r--docs/pkgdown.yml2
-rw-r--r--docs/reference/D24_2014.html2
-rw-r--r--docs/reference/Extract.mmkin.html2
-rw-r--r--docs/reference/Rplot001.pngbin27746 -> 1011 bytes
-rw-r--r--docs/reference/Rplot002.pngbin59394 -> 16524 bytes
-rw-r--r--docs/reference/Rplot003.pngbin15333 -> 15401 bytes
-rw-r--r--docs/reference/Rplot004.pngbin10647 -> 10689 bytes
-rw-r--r--docs/reference/Rplot005.pngbin19233 -> 19483 bytes
-rw-r--r--docs/reference/Rplot006.pngbin24545 -> 24302 bytes
-rw-r--r--docs/reference/Rplot007.pngbin24992 -> 25211 bytes
-rw-r--r--docs/reference/add_err-1.pngbin108676 -> 109666 bytes
-rw-r--r--docs/reference/add_err-2.pngbin63336 -> 63614 bytes
-rw-r--r--docs/reference/add_err-3.pngbin58909 -> 59316 bytes
-rw-r--r--docs/reference/add_err.html2
-rw-r--r--docs/reference/confint.mkinfit.html6
-rw-r--r--docs/reference/dimethenamid_2018.html2
-rw-r--r--docs/reference/experimental_data_for_UBA-1.pngbin102212 -> 102839 bytes
-rw-r--r--docs/reference/experimental_data_for_UBA.html2
-rw-r--r--docs/reference/f_time_norm_focus.html2
-rw-r--r--docs/reference/focus_soil_moisture.html2
-rw-r--r--docs/reference/logLik.mkinfit.html2
-rw-r--r--docs/reference/mccall81_245T-1.pngbin62537 -> 62564 bytes
-rw-r--r--docs/reference/mccall81_245T.html2
-rw-r--r--docs/reference/mixed-1.pngbin219866 -> 219876 bytes
-rw-r--r--docs/reference/mixed.html2
-rw-r--r--docs/reference/mkinds.html2
-rw-r--r--docs/reference/mkindsg.html2
-rw-r--r--docs/reference/mkinfit-1.pngbin65835 -> 66042 bytes
-rw-r--r--docs/reference/mkinfit.html28
-rw-r--r--docs/reference/mkinmod.html6
-rw-r--r--docs/reference/mkinpredict.html6
-rw-r--r--docs/reference/mkinresplot-1.pngbin23819 -> 23907 bytes
-rw-r--r--docs/reference/mkinresplot.html2
-rw-r--r--docs/reference/mmkin-1.pngbin110459 -> 111569 bytes
-rw-r--r--docs/reference/mmkin-2.pngbin107057 -> 108319 bytes
-rw-r--r--docs/reference/mmkin-3.pngbin96062 -> 96596 bytes
-rw-r--r--docs/reference/mmkin-4.pngbin67191 -> 67345 bytes
-rw-r--r--docs/reference/mmkin-5.pngbin64880 -> 65269 bytes
-rw-r--r--docs/reference/mmkin.html6
-rw-r--r--docs/reference/nlme-1.pngbin70133 -> 70276 bytes
-rw-r--r--docs/reference/nlme-2.pngbin94031 -> 94239 bytes
-rw-r--r--docs/reference/nlme.html2
-rw-r--r--docs/reference/nlme.mmkin-1.pngbin124677 -> 124827 bytes
-rw-r--r--docs/reference/nlme.mmkin-2.pngbin169523 -> 169698 bytes
-rw-r--r--docs/reference/nlme.mmkin-3.pngbin172692 -> 172809 bytes
-rw-r--r--docs/reference/nlme.mmkin.html2
-rw-r--r--docs/reference/parms.html2
-rw-r--r--docs/reference/plot.mkinfit-1.pngbin53151 -> 53333 bytes
-rw-r--r--docs/reference/plot.mkinfit-2.pngbin73254 -> 72971 bytes
-rw-r--r--docs/reference/plot.mkinfit-3.pngbin67810 -> 67908 bytes
-rw-r--r--docs/reference/plot.mkinfit-4.pngbin72295 -> 72505 bytes
-rw-r--r--docs/reference/plot.mkinfit-5.pngbin66560 -> 66973 bytes
-rw-r--r--docs/reference/plot.mkinfit-6.pngbin72717 -> 72699 bytes
-rw-r--r--docs/reference/plot.mkinfit-7.pngbin73553 -> 74240 bytes
-rw-r--r--docs/reference/plot.mkinfit.html2
-rw-r--r--docs/reference/plot.mmkin-1.pngbin48997 -> 49701 bytes
-rw-r--r--docs/reference/plot.mmkin-2.pngbin49376 -> 50025 bytes
-rw-r--r--docs/reference/plot.mmkin-3.pngbin46202 -> 46360 bytes
-rw-r--r--docs/reference/plot.mmkin-4.pngbin33057 -> 33389 bytes
-rw-r--r--docs/reference/plot.mmkin-5.pngbin57372 -> 58129 bytes
-rw-r--r--docs/reference/plot.mmkin.html2
-rw-r--r--docs/reference/reexports.html2
-rw-r--r--docs/reference/sigma_twocomp-1.pngbin43910 -> 43766 bytes
-rw-r--r--docs/reference/sigma_twocomp.html2
-rw-r--r--docs/reference/summary.nlme.mmkin.html12
-rw-r--r--docs/reference/transform_odeparms.html2
120 files changed, 213 insertions, 109 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 08acf58b..1bfba6e5 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -31,7 +31,7 @@
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
@@ -94,13 +94,13 @@
- </header><script src="FOCUS_D_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
+ </header><script src="FOCUS_D_files/header-attrs-2.7/header-attrs.js"></script><script src="FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">Last change 31 January 2019 (rebuilt 2021-02-15)</h4>
+ <h4 class="date">Last change 31 January 2019 (rebuilt 2021-03-31)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.rmd"><code>vignettes/FOCUS_D.rmd</code></a></small>
<div class="hidden name"><code>FOCUS_D.rmd</code></div>
@@ -185,10 +185,10 @@
<p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div>
-<pre><code>## mkin version used for fitting: 1.0.3
-## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 17:50:27 2021
-## Date of summary: Mon Feb 15 17:50:28 2021
+<pre><code>## mkin version used for fitting: 1.0.4
+## R version used for fitting: 4.0.4
+## Date of fit: Wed Mar 31 19:18:28 2021
+## Date of summary: Wed Mar 31 19:18:29 2021
##
## Equations:
## d_parent/dt = - k_parent * parent
@@ -196,7 +196,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 401 model solutions performed in 0.161 s
+## Fitted using 401 model solutions performed in 0.159 s
##
## Error model: Constant variance
##
diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png
index abf26715..c3a5d56e 100644
--- a/docs/articles/FOCUS_D_files/figure-html/plot-1.png
+++ b/docs/articles/FOCUS_D_files/figure-html/plot-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png
index f4937894..42e48dee 100644
--- a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png
+++ b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_D_files/header-attrs-2.7/header-attrs.js b/docs/articles/FOCUS_D_files/header-attrs-2.7/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/FOCUS_D_files/header-attrs-2.7/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+ var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+ var i, h, a;
+ for (i = 0; i < hs.length; i++) {
+ h = hs[i];
+ if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
+ a = h.attributes;
+ while (a.length > 0) h.removeAttribute(a[0].name);
+ }
+});
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index ab9739bc..7074816c 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -31,7 +31,7 @@
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
@@ -94,13 +94,13 @@
- </header><script src="FOCUS_L_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
+ </header><script src="FOCUS_L_files/header-attrs-2.7/header-attrs.js"></script><script src="FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">Last change 17 November 2016 (rebuilt 2021-02-15)</h4>
+ <h4 class="date">Last change 17 November 2016 (rebuilt 2021-03-31)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/FOCUS_L.rmd"><code>vignettes/FOCUS_L.rmd</code></a></small>
<div class="hidden name"><code>FOCUS_L.rmd</code></div>
@@ -126,10 +126,10 @@
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">m.L1.SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></code></pre></div>
-<pre><code>## mkin version used for fitting: 1.0.3
-## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 17:50:30 2021
-## Date of summary: Mon Feb 15 17:50:30 2021
+<pre><code>## mkin version used for fitting: 1.0.4
+## R version used for fitting: 4.0.4
+## Date of fit: Wed Mar 31 19:18:31 2021
+## Date of summary: Wed Mar 31 19:18:31 2021
##
## Equations:
## d_parent/dt = - k_parent * parent
@@ -232,10 +232,10 @@
<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
## doubtful</code></pre>
-<pre><code>## mkin version used for fitting: 1.0.3
-## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 17:50:31 2021
-## Date of summary: Mon Feb 15 17:50:31 2021
+<pre><code>## mkin version used for fitting: 1.0.4
+## R version used for fitting: 4.0.4
+## Date of fit: Wed Mar 31 19:18:32 2021
+## Date of summary: Wed Mar 31 19:18:32 2021
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -344,10 +344,10 @@
<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
-<pre><code>## mkin version used for fitting: 1.0.3
-## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 17:50:31 2021
-## Date of summary: Mon Feb 15 17:50:31 2021
+<pre><code>## mkin version used for fitting: 1.0.4
+## R version used for fitting: 4.0.4
+## Date of fit: Wed Mar 31 19:18:32 2021
+## Date of summary: Wed Mar 31 19:18:32 2021
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -425,10 +425,10 @@
<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p>
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
-<pre><code>## mkin version used for fitting: 1.0.3
-## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 17:50:32 2021
-## Date of summary: Mon Feb 15 17:50:32 2021
+<pre><code>## mkin version used for fitting: 1.0.4
+## R version used for fitting: 4.0.4
+## Date of fit: Wed Mar 31 19:18:33 2021
+## Date of summary: Wed Mar 31 19:18:33 2021
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -531,10 +531,10 @@
<p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p>
<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
-<pre><code>## mkin version used for fitting: 1.0.3
-## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 17:50:32 2021
-## Date of summary: Mon Feb 15 17:50:32 2021
+<pre><code>## mkin version used for fitting: 1.0.4
+## R version used for fitting: 4.0.4
+## Date of fit: Wed Mar 31 19:18:33 2021
+## Date of summary: Wed Mar 31 19:18:33 2021
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -644,10 +644,10 @@
<p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p>
<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
-<pre><code>## mkin version used for fitting: 1.0.3
-## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 17:50:33 2021
-## Date of summary: Mon Feb 15 17:50:33 2021
+<pre><code>## mkin version used for fitting: 1.0.4
+## R version used for fitting: 4.0.4
+## Date of fit: Wed Mar 31 19:18:34 2021
+## Date of summary: Wed Mar 31 19:18:34 2021
##
## Equations:
## d_parent/dt = - k_parent * parent
@@ -709,10 +709,10 @@
## parent 106 352</code></pre>
<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
-<pre><code>## mkin version used for fitting: 1.0.3
-## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 17:50:33 2021
-## Date of summary: Mon Feb 15 17:50:33 2021
+<pre><code>## mkin version used for fitting: 1.0.4
+## R version used for fitting: 4.0.4
+## Date of fit: Wed Mar 31 19:18:34 2021
+## Date of summary: Wed Mar 31 19:18:34 2021
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png
index e9c0b0a0..5f95a506 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png
index 3e03954d..82dc16c4 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png
index 8c9e8fd4..06082027 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png
index b3aa8334..75522f2f 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png
index 477829a5..145053fd 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png
index e8f21107..8fbe2159 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png
index c0e08884..b1840a39 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png
index 310b4f3b..f85a349f 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png
index 570f0026..a29ce1ff 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/header-attrs-2.7/header-attrs.js b/docs/articles/FOCUS_L_files/header-attrs-2.7/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/FOCUS_L_files/header-attrs-2.7/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+ var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+ var i, h, a;
+ for (i = 0; i < hs.length; i++) {
+ h = hs[i];
+ if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
+ a = h.attributes;
+ while (a.length > 0) h.removeAttribute(a[0].name);
+ }
+});
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 6dbb093d..a0fccc16 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -31,7 +31,7 @@
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
@@ -94,13 +94,13 @@
- </header><script src="mkin_files/header-attrs-2.6/header-attrs.js"></script><script src="mkin_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
+ </header><script src="mkin_files/header-attrs-2.7/header-attrs.js"></script><script src="mkin_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Introduction to mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">Last change 15 February 2021 (rebuilt 2021-02-15)</h4>
+ <h4 class="date">Last change 15 February 2021 (rebuilt 2021-03-31)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/mkin.rmd"><code>vignettes/mkin.rmd</code></a></small>
<div class="hidden name"><code>mkin.rmd</code></div>
diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
index bf38fdd7..8a182047 100644
--- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
+++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
Binary files differ
diff --git a/docs/articles/mkin_files/header-attrs-2.7/header-attrs.js b/docs/articles/mkin_files/header-attrs-2.7/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/mkin_files/header-attrs-2.7/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+ var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+ var i, h, a;
+ for (i = 0; i < hs.length; i++) {
+ h = hs[i];
+ if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
+ a = h.attributes;
+ while (a.length > 0) h.removeAttribute(a[0].name);
+ }
+});
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 2e3d2f96..167f60d3 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -31,7 +31,7 @@
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
@@ -94,13 +94,13 @@
- </header><script src="twa_files/header-attrs-2.6/header-attrs.js"></script><script src="twa_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
+ </header><script src="twa_files/header-attrs-2.7/header-attrs.js"></script><script src="twa_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Calculation of time weighted average concentrations with mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">Last change 18 September 2019 (rebuilt 2021-02-15)</h4>
+ <h4 class="date">Last change 18 September 2019 (rebuilt 2021-03-31)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/twa.rmd"><code>vignettes/twa.rmd</code></a></small>
<div class="hidden name"><code>twa.rmd</code></div>
diff --git a/docs/articles/twa_files/header-attrs-2.7/header-attrs.js b/docs/articles/twa_files/header-attrs-2.7/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/twa_files/header-attrs-2.7/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+ var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+ var i, h, a;
+ for (i = 0; i < hs.length; i++) {
+ h = hs[i];
+ if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
+ a = h.attributes;
+ while (a.length > 0) h.removeAttribute(a[0].name);
+ }
+});
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 57fc3545..e4a6cb52 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -31,7 +31,7 @@
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
@@ -94,13 +94,13 @@
- </header><script src="FOCUS_Z_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
+ </header><script src="FOCUS_Z_files/header-attrs-2.7/header-attrs.js"></script><script src="FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">Last change 16 January 2018 (rebuilt 2021-02-15)</h4>
+ <h4 class="date">Last change 16 January 2018 (rebuilt 2021-03-31)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/FOCUS_Z.rmd"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small>
<div class="hidden name"><code>FOCUS_Z.rmd</code></div>
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png
index 2213c446..2e70b207 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png
Binary files differ
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png
index 61b04d3a..4a205020 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png
Binary files differ
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png
index 409f1203..8b07d497 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png
Binary files differ
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png
index 4d6820cd..4765c9fe 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png
Binary files differ
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png
index 2e504961..e005446b 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png
Binary files differ
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png
index 2213c446..2e70b207 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png
Binary files differ
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png
index 7ab743af..f06ee667 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png
Binary files differ
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png
index 2e0dce77..b8e0e900 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png
Binary files differ
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png
index 458299c1..14dd7805 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png
Binary files differ
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png
index eb833066..414bc941 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png
Binary files differ
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png
index e7501cbb..0a83f8ea 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png
Binary files differ
diff --git a/docs/articles/web_only/FOCUS_Z_files/header-attrs-2.7/header-attrs.js b/docs/articles/web_only/FOCUS_Z_files/header-attrs-2.7/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/web_only/FOCUS_Z_files/header-attrs-2.7/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+ var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+ var i, h, a;
+ for (i = 0; i < hs.length; i++) {
+ h = hs[i];
+ if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
+ a = h.attributes;
+ while (a.length > 0) h.removeAttribute(a[0].name);
+ }
+});
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index e79375b3..65a71b56 100644
--- a/docs/articles/web_only/NAFTA_examples.html
+++ b/docs/articles/web_only/NAFTA_examples.html
@@ -31,7 +31,7 @@
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
@@ -94,13 +94,13 @@
- </header><script src="NAFTA_examples_files/header-attrs-2.6/header-attrs.js"></script><script src="NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
+ </header><script src="NAFTA_examples_files/header-attrs-2.7/header-attrs.js"></script><script src="NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">26 February 2019 (rebuilt 2021-02-15)</h4>
+ <h4 class="date">26 February 2019 (rebuilt 2021-03-31)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.rmd"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small>
<div class="hidden name"><code>NAFTA_examples.rmd</code></div>
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png
index f5420ce8..b1c874cc 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png
index 0ae4bd9f..9dfa26fb 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.png
index 57a48119..cdae6520 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png
index c42d45f0..57672896 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png
index 52dea51e..1e4995a8 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png
index ca1f29be..93bb7173 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png
index f69e6d3b..a2ee7966 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png
index 71fcd257..a40bd581 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png
index 820501a3..690c91ef 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png
index e264d2ea..c1284b83 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png
index e5b656a4..d40ad7e7 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png
index c9664c77..8c2ae01b 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png
index a81f814c..fbf566f7 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png
index 75d72e7c..1e137ddf 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png
index 3ce13a97..efc16dda 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png
index e2cf2f83..53addbd2 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png
Binary files differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.7/header-attrs.js b/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.7/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.7/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+ var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+ var i, h, a;
+ for (i = 0; i < hs.length; i++) {
+ h = hs[i];
+ if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
+ a = h.attributes;
+ while (a.length > 0) h.removeAttribute(a[0].name);
+ }
+});
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 9908c224..290906c1 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -31,7 +31,7 @@
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
@@ -94,13 +94,13 @@
- </header><script src="benchmarks_files/header-attrs-2.6/header-attrs.js"></script><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
+ </header><script src="benchmarks_files/header-attrs-2.7/header-attrs.js"></script><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Benchmark timings for mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">Last change 13 May 2020 (rebuilt 2021-02-15)</h4>
+ <h4 class="date">Last change 13 May 2020 (rebuilt 2021-03-31)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/benchmarks.rmd"><code>vignettes/web_only/benchmarks.rmd</code></a></small>
<div class="hidden name"><code>benchmarks.rmd</code></div>
@@ -232,6 +232,11 @@
<td align="right">1.881</td>
<td align="right">3.504</td>
</tr>
+<tr class="even">
+<td align="left">1.0.4</td>
+<td align="right">1.867</td>
+<td align="right">3.450</td>
+</tr>
</tbody>
</table>
</div>
@@ -301,6 +306,12 @@
<td align="right">6.344</td>
<td align="right">2.798</td>
</tr>
+<tr class="even">
+<td align="left">1.0.4</td>
+<td align="right">1.415</td>
+<td align="right">6.364</td>
+<td align="right">2.820</td>
+</tr>
</tbody>
</table>
</div>
@@ -400,6 +411,15 @@
<td align="right">1.923</td>
<td align="right">2.839</td>
</tr>
+<tr class="even">
+<td align="left">1.0.4</td>
+<td align="right">0.785</td>
+<td align="right">1.252</td>
+<td align="right">1.466</td>
+<td align="right">3.091</td>
+<td align="right">1.936</td>
+<td align="right">2.826</td>
+</tr>
</tbody>
</table>
</div>
diff --git a/docs/articles/web_only/benchmarks_files/header-attrs-2.7/header-attrs.js b/docs/articles/web_only/benchmarks_files/header-attrs-2.7/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/web_only/benchmarks_files/header-attrs-2.7/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+ var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+ var i, h, a;
+ for (i = 0; i < hs.length; i++) {
+ h = hs[i];
+ if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
+ a = h.attributes;
+ while (a.length > 0) h.removeAttribute(a[0].name);
+ }
+});
diff --git a/docs/news/index.html b/docs/news/index.html
index 3a52a093..fae6503a 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -145,8 +145,8 @@
<h1 class="page-header" data-toc-text="1.0.4">
<a href="#mkin-104-unreleased" class="anchor"></a>mkin 1.0.4 (Unreleased)</h1>
<ul>
-<li><p>‘plot.mixed.mmkin’: Reset graphical parameters on exit</p></li>
<li><p>All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters</p></li>
+<li><p>‘plot.mkinfit’: Use xlab and xlim for the residual plot if show_residuals is TRUE</p></li>
</ul>
</div>
<div id="mkin-103-2021-02-15" class="section level1">
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 49dceae1..df454e62 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
web_only/NAFTA_examples: NAFTA_examples.html
web_only/benchmarks: benchmarks.html
web_only/compiled_models: compiled_models.html
-last_built: 2021-02-24T14:04Z
+last_built: 2021-03-31T17:15Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/D24_2014.html b/docs/reference/D24_2014.html
index e2d47f1b..c59bfad6 100644
--- a/docs/reference/D24_2014.html
+++ b/docs/reference/D24_2014.html
@@ -77,7 +77,7 @@ constrained by data protection regulations." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 5a99cf1b..b1c73ba5 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -72,7 +72,7 @@
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
index 1cbcb153..17a35806 100644
--- a/docs/reference/Rplot001.png
+++ b/docs/reference/Rplot001.png
Binary files differ
diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
index 745d583d..808f1968 100644
--- a/docs/reference/Rplot002.png
+++ b/docs/reference/Rplot002.png
Binary files differ
diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png
index 19198739..97f650e2 100644
--- a/docs/reference/Rplot003.png
+++ b/docs/reference/Rplot003.png
Binary files differ
diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png
index 1028a9c4..21ad6783 100644
--- a/docs/reference/Rplot004.png
+++ b/docs/reference/Rplot004.png
Binary files differ
diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png
index aa844051..4828f5b2 100644
--- a/docs/reference/Rplot005.png
+++ b/docs/reference/Rplot005.png
Binary files differ
diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png
index 81525882..4aed2c87 100644
--- a/docs/reference/Rplot006.png
+++ b/docs/reference/Rplot006.png
Binary files differ
diff --git a/docs/reference/Rplot007.png b/docs/reference/Rplot007.png
index 10b7455a..3405a171 100644
--- a/docs/reference/Rplot007.png
+++ b/docs/reference/Rplot007.png
Binary files differ
diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png
index 9ba106db..70118923 100644
--- a/docs/reference/add_err-1.png
+++ b/docs/reference/add_err-1.png
Binary files differ
diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png
index 3088c40e..69b820c2 100644
--- a/docs/reference/add_err-2.png
+++ b/docs/reference/add_err-2.png
Binary files differ
diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png
index 493a761a..1de78fa7 100644
--- a/docs/reference/add_err-3.png
+++ b/docs/reference/add_err-3.png
Binary files differ
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index 6fbecd14..18ca517e 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -74,7 +74,7 @@ may depend on the predicted value and is specified as a standard deviation." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html
index 06e78459..e81e0c7b 100644
--- a/docs/reference/confint.mkinfit.html
+++ b/docs/reference/confint.mkinfit.html
@@ -79,7 +79,7 @@ method of Venzon and Moolgavkar (1988)." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
@@ -285,13 +285,13 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
<span class='va'>f_d_1</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; user system elapsed
-#&gt; 4.255 1.029 3.937 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span>
+#&gt; 3.871 0.000 3.871 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span>
<span class='co'># If we additionally exclude parent_0 (the confidence of which is often of</span>
<span class='co'># minor interest), we get a nice performance improvement if we use at least 4 cores</span>
<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile_no_parent_0</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>,
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"k_parent_sink"</span>, <span class='st'>"k_parent_m1"</span>, <span class='st'>"k_m1_sink"</span>, <span class='st'>"sigma"</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='va'>n_cores</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 1.469 0.092 0.911 </div><div class='input'><span class='va'>ci_profile</span>
+#&gt; 1.484 0.116 0.923 </div><div class='input'><span class='va'>ci_profile</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
#&gt; parent_0 96.456003640 1.027703e+02
#&gt; k_parent_sink 0.040762501 5.549764e-02
diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html
index 6845f74f..3b6ae721 100644
--- a/docs/reference/dimethenamid_2018.html
+++ b/docs/reference/dimethenamid_2018.html
@@ -77,7 +77,7 @@ constrained by data protection regulations." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png
index 33946ded..5527c07f 100644
--- a/docs/reference/experimental_data_for_UBA-1.png
+++ b/docs/reference/experimental_data_for_UBA-1.png
Binary files differ
diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html
index 77f75678..4da8d6c3 100644
--- a/docs/reference/experimental_data_for_UBA.html
+++ b/docs/reference/experimental_data_for_UBA.html
@@ -100,7 +100,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html
index aa494b27..a0899ac8 100644
--- a/docs/reference/f_time_norm_focus.html
+++ b/docs/reference/f_time_norm_focus.html
@@ -73,7 +73,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html
index 61f235db..bbacc554 100644
--- a/docs/reference/focus_soil_moisture.html
+++ b/docs/reference/focus_soil_moisture.html
@@ -73,7 +73,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index 9e5b4069..83fb4e48 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -76,7 +76,7 @@ the error model." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/mccall81_245T-1.png b/docs/reference/mccall81_245T-1.png
index 91fe060e..478462ae 100644
--- a/docs/reference/mccall81_245T-1.png
+++ b/docs/reference/mccall81_245T-1.png
Binary files differ
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index b7dca4a7..4f8d3fa0 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -74,7 +74,7 @@
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png
index 28a376f4..b9454c86 100644
--- a/docs/reference/mixed-1.png
+++ b/docs/reference/mixed-1.png
Binary files differ
diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html
index 23d955e3..b4f8db16 100644
--- a/docs/reference/mixed.html
+++ b/docs/reference/mixed.html
@@ -72,7 +72,7 @@
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index 5111a9e0..fe89012c 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -75,7 +75,7 @@ provided by this package come as mkinds objects nevertheless." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html
index 003e5e8f..a9686e4c 100644
--- a/docs/reference/mkindsg.html
+++ b/docs/reference/mkindsg.html
@@ -75,7 +75,7 @@ dataset if no data are supplied." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/mkinfit-1.png b/docs/reference/mkinfit-1.png
index de2a90a9..e1d0f2f4 100644
--- a/docs/reference/mkinfit-1.png
+++ b/docs/reference/mkinfit-1.png
Binary files differ
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 180f2ee7..2c162e49 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -80,7 +80,7 @@ likelihood function." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
@@ -431,10 +431,10 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
<span class='co'># Use shorthand notation for parent only degradation</span>
<span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; mkin version used for fitting: 1.0.3
-#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Feb 15 13:43:26 2021
-#&gt; Date of summary: Mon Feb 15 13:43:26 2021
+</div><div class='output co'>#&gt; mkin version used for fitting: 1.0.4
+#&gt; R version used for fitting: 4.0.4
+#&gt; Date of fit: Wed Mar 31 19:15:41 2021
+#&gt; Date of summary: Wed Mar 31 19:15:41 2021
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -574,10 +574,10 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
analytical <span class='op'>=</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>,
solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
-</div><div class='output co'>#&gt; test relative elapsed
-#&gt; 3 analytical 1.000 0.550
-#&gt; 1 deSolve_compiled 1.731 0.952
-#&gt; 2 eigen 2.662 1.464</div><div class='input'><span class='co'># }</span>
+</div><div class='output co'>#&gt; <span class='message'>Loading required package: rbenchmark</span></div><div class='output co'>#&gt; test relative elapsed
+#&gt; 3 analytical 1.000 0.547
+#&gt; 1 deSolve_compiled 1.717 0.939
+#&gt; 2 eigen 2.644 1.446</div><div class='input'><span class='co'># }</span>
<span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span>
<span class='co'># \dontrun{</span>
@@ -598,10 +598,10 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
#&gt; 2 6 -64.983 -1 0.3075 0.5792</div><div class='input'><span class='co'># Also, the missing standard error for log_beta and the t-tests for alpha</span>
<span class='co'># and beta indicate overparameterisation</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.FOMC_SFO.tc</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#&gt; <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#&gt; mkin version used for fitting: 1.0.3
-#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Feb 15 13:43:38 2021
-#&gt; Date of summary: Mon Feb 15 13:43:38 2021
+</div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#&gt; <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#&gt; mkin version used for fitting: 1.0.4
+#&gt; R version used for fitting: 4.0.4
+#&gt; Date of fit: Wed Mar 31 19:15:53 2021
+#&gt; Date of summary: Wed Mar 31 19:15:53 2021
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -610,7 +610,7 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 3729 model solutions performed in 2.802 s
+#&gt; Fitted using 3729 model solutions performed in 2.798 s
#&gt;
#&gt; Error model: Two-component variance function
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 4ce9468a..1e8ad60d 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -78,7 +78,7 @@ mkinmod." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
@@ -348,7 +348,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, full_name <span class='op'>=</span> <span class='st'>"Test compound"</span><span class='op'>)</span>,
m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, full_name <span class='op'>=</span> <span class='st'>"Metabolite M1"</span><span class='op'>)</span>,
name <span class='op'>=</span> <span class='st'>"SFO_SFO"</span>, dll_dir <span class='op'>=</span> <span class='va'>DLL_dir</span>, unload <span class='op'>=</span> <span class='cn'>TRUE</span>, overwrite <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Copied DLL from /tmp/RtmpiJ2M4Z/filee097a4a94a921.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span></div><div class='input'><span class='co'># Now we can save the model and restore it in a new session</span>
+</div><div class='output co'>#&gt; <span class='message'>Copied DLL from /tmp/Rtmp17EVw2/file269cfd5cc541a9.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span></div><div class='input'><span class='co'># Now we can save the model and restore it in a new session</span>
<span class='fu'><a href='https://rdrr.io/r/base/readRDS.html'>saveRDS</a></span><span class='op'>(</span><span class='va'>SFO_SFO.2</span>, file <span class='op'>=</span> <span class='st'>"~/SFO_SFO.rds"</span><span class='op'>)</span>
<span class='co'># Terminate the R session here if you would like to check, and then do</span>
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://pkgdown.jrwb.de/mkin/'>mkin</a></span><span class='op'>)</span>
@@ -397,7 +397,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
#&gt; })
#&gt; return(predicted)
#&gt; }
-#&gt; &lt;environment: 0x55555b0c2760&gt;</div><div class='input'>
+#&gt; &lt;environment: 0x55555c17ae90&gt;</div><div class='input'>
<span class='co'># If we have several parallel metabolites</span>
<span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
<span class='va'>m_synth_DFOP_par</span> <span class='op'>&lt;-</span> <span class='fu'>mkinmod</span><span class='op'>(</span>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 25e26419..5775ba62 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -74,7 +74,7 @@ kinetic parameters and initial values for the state variables." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
@@ -410,8 +410,8 @@ as these always return mapped output.</p></td>
</div><div class='output co'>#&gt; test relative elapsed
#&gt; 2 deSolve_compiled 1.0 0.005
#&gt; 4 analytical 1.0 0.005
-#&gt; 1 eigen 4.4 0.022
-#&gt; 3 deSolve 47.0 0.235</div><div class='input'>
+#&gt; 1 eigen 4.0 0.020
+#&gt; 3 deSolve 46.2 0.231</div><div class='input'>
<span class='co'># \dontrun{</span>
<span class='co'># Predict from a fitted model</span>
<span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png
index ffd34f6f..963aa5b7 100644
--- a/docs/reference/mkinresplot-1.png
+++ b/docs/reference/mkinresplot-1.png
Binary files differ
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index 04ff15b8..fe3150e7 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -75,7 +75,7 @@ argument show_residuals = TRUE." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png
index 0db3379f..26586ab9 100644
--- a/docs/reference/mmkin-1.png
+++ b/docs/reference/mmkin-1.png
Binary files differ
diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png
index 024a9892..dbcdd8ee 100644
--- a/docs/reference/mmkin-2.png
+++ b/docs/reference/mmkin-2.png
Binary files differ
diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png
index a23d7cb9..80245fc6 100644
--- a/docs/reference/mmkin-3.png
+++ b/docs/reference/mmkin-3.png
Binary files differ
diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png
index 89975db5..328aa564 100644
--- a/docs/reference/mmkin-4.png
+++ b/docs/reference/mmkin-4.png
Binary files differ
diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png
index a2f34983..9ce5e919 100644
--- a/docs/reference/mmkin-5.png
+++ b/docs/reference/mmkin-5.png
Binary files differ
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index c9800fe7..c73d14bf 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -75,7 +75,7 @@ datasets specified in its first two arguments." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
@@ -234,9 +234,9 @@ plotting.</p></div>
<span class='va'>time_default</span>
</div><div class='output co'>#&gt; user system elapsed
-#&gt; 4.630 0.415 1.717 </div><div class='input'><span class='va'>time_1</span>
+#&gt; 5.387 0.413 1.864 </div><div class='input'><span class='va'>time_1</span>
</div><div class='output co'>#&gt; user system elapsed
-#&gt; 5.694 0.000 5.694 </div><div class='input'>
+#&gt; 5.786 0.008 5.794 </div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png
index 728cc557..cca4ce0a 100644
--- a/docs/reference/nlme-1.png
+++ b/docs/reference/nlme-1.png
Binary files differ
diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png
index e8167455..c0d8e857 100644
--- a/docs/reference/nlme-2.png
+++ b/docs/reference/nlme-2.png
Binary files differ
diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html
index 7b0c6a97..c6b43aab 100644
--- a/docs/reference/nlme.html
+++ b/docs/reference/nlme.html
@@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png
index 9186c135..90ede880 100644
--- a/docs/reference/nlme.mmkin-1.png
+++ b/docs/reference/nlme.mmkin-1.png
Binary files differ
diff --git a/docs/reference/nlme.mmkin-2.png b/docs/reference/nlme.mmkin-2.png
index d395fe02..0d140fd1 100644
--- a/docs/reference/nlme.mmkin-2.png
+++ b/docs/reference/nlme.mmkin-2.png
Binary files differ
diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png
index 40518a59..8a60b52b 100644
--- a/docs/reference/nlme.mmkin-3.png
+++ b/docs/reference/nlme.mmkin-3.png
Binary files differ
diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html
index 189e34ef..03448606 100644
--- a/docs/reference/nlme.mmkin.html
+++ b/docs/reference/nlme.mmkin.html
@@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/parms.html b/docs/reference/parms.html
index e45d6a5c..b4346b13 100644
--- a/docs/reference/parms.html
+++ b/docs/reference/parms.html
@@ -74,7 +74,7 @@ considering the error structure that was assumed for the fit." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png
index e5da9f1c..54e5c46f 100644
--- a/docs/reference/plot.mkinfit-1.png
+++ b/docs/reference/plot.mkinfit-1.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png
index a11d1680..ff8418a3 100644
--- a/docs/reference/plot.mkinfit-2.png
+++ b/docs/reference/plot.mkinfit-2.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png
index c976d4b1..54f2b981 100644
--- a/docs/reference/plot.mkinfit-3.png
+++ b/docs/reference/plot.mkinfit-3.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png
index c8bc00fe..7a7bfc6c 100644
--- a/docs/reference/plot.mkinfit-4.png
+++ b/docs/reference/plot.mkinfit-4.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png
index 6631aa68..6a6741e7 100644
--- a/docs/reference/plot.mkinfit-5.png
+++ b/docs/reference/plot.mkinfit-5.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png
index 946b20c5..c4d0b9c7 100644
--- a/docs/reference/plot.mkinfit-6.png
+++ b/docs/reference/plot.mkinfit-6.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-7.png b/docs/reference/plot.mkinfit-7.png
index 10807ea8..802b00ef 100644
--- a/docs/reference/plot.mkinfit-7.png
+++ b/docs/reference/plot.mkinfit-7.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index b80c672d..ff6da93e 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -74,7 +74,7 @@ observed data together with the solution of the fitted model." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png
index 647dfb8a..d06d683c 100644
--- a/docs/reference/plot.mmkin-1.png
+++ b/docs/reference/plot.mmkin-1.png
Binary files differ
diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png
index 1bc1c9db..d3678aca 100644
--- a/docs/reference/plot.mmkin-2.png
+++ b/docs/reference/plot.mmkin-2.png
Binary files differ
diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png
index 50d6ffac..f84d5782 100644
--- a/docs/reference/plot.mmkin-3.png
+++ b/docs/reference/plot.mmkin-3.png
Binary files differ
diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png
index e049fa16..9919dacb 100644
--- a/docs/reference/plot.mmkin-4.png
+++ b/docs/reference/plot.mmkin-4.png
Binary files differ
diff --git a/docs/reference/plot.mmkin-5.png b/docs/reference/plot.mmkin-5.png
index 2421995b..945b863f 100644
--- a/docs/reference/plot.mmkin-5.png
+++ b/docs/reference/plot.mmkin-5.png
Binary files differ
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 20f9033d..3348e050 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -76,7 +76,7 @@ the fit of at least one model to the same dataset is shown." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 864c4ff9..c6d716a1 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -79,7 +79,7 @@ below to see their documentation.
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/sigma_twocomp-1.png b/docs/reference/sigma_twocomp-1.png
index 6e61684e..fddb86a7 100644
--- a/docs/reference/sigma_twocomp-1.png
+++ b/docs/reference/sigma_twocomp-1.png
Binary files differ
diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html
index 397582f0..1b4e45e4 100644
--- a/docs/reference/sigma_twocomp.html
+++ b/docs/reference/sigma_twocomp.html
@@ -73,7 +73,7 @@ dependence of the measured value \(y\):" />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html
index d6840425..8df9011d 100644
--- a/docs/reference/summary.nlme.mmkin.html
+++ b/docs/reference/summary.nlme.mmkin.html
@@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>
@@ -265,10 +265,10 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
#&gt; <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'><span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>f_nlme</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; nlme version used for fitting: 3.1.152
-#&gt; mkin version used for pre-fitting: 1.0.3
-#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Feb 15 13:46:13 2021
-#&gt; Date of summary: Mon Feb 15 13:46:13 2021
+#&gt; mkin version used for pre-fitting: 1.0.4
+#&gt; R version used for fitting: 4.0.4
+#&gt; Date of fit: Wed Mar 31 19:18:24 2021
+#&gt; Date of summary: Wed Mar 31 19:18:24 2021
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -278,7 +278,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 0.553 s using 4 iterations
+#&gt; Fitted in 0.537 s using 4 iterations
#&gt;
#&gt; Variance model: Two-component variance function
#&gt;
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index c3c756f6..bbaad91e 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -77,7 +77,7 @@ the ilr transformation is used." />
</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">1.0.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
</span>
</div>

Contact - Imprint