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-rw-r--r--GNUmakefile2
-rw-r--r--README.html2
-rw-r--r--README.md6
-rw-r--r--docs/404.html2
-rw-r--r--docs/articles/index.html2
-rw-r--r--docs/authors.html2
-rw-r--r--docs/index.html4
-rw-r--r--docs/news/index.html9
-rw-r--r--docs/pkgdown.yml2
-rw-r--r--docs/reference/dimethenamid_2018.html47
-rw-r--r--docs/reference/endpoints.html2
-rw-r--r--docs/reference/index.html2
-rw-r--r--docs/reference/mixed.html2
-rw-r--r--docs/reference/mkinmod.html6
-rw-r--r--docs/reference/nlme.html2
-rw-r--r--docs/reference/nlme.mmkin.html2
-rw-r--r--docs/reference/plot.mixed.mmkin.html2
-rw-r--r--docs/reference/reexports.html2
18 files changed, 51 insertions, 47 deletions
diff --git a/GNUmakefile b/GNUmakefile
index 9056a0ec..39270cb3 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -114,7 +114,7 @@ pd_all: roxygen
git add -A
r-forge:
- git archive master > $(HOME)/git/mkin/mkin.tar;\
+ git archive main > $(HOME)/git/mkin/mkin.tar;\
cd $(RFDIR) && rm -r `ls` && tar -xf $(HOME)/git/mkin/mkin.tar;\
rm -r $(SDDIR)/*;\
cp -a docs/* $(SDDIR);\
diff --git a/README.html b/README.html
index 28683a23..68c11a37 100644
--- a/README.html
+++ b/README.html
@@ -421,7 +421,7 @@ pre code {
</div>
<div id="news" class="section level2">
<h2>News</h2>
-<p>There is a list of changes for the latest <a href="https://cran.r-project.org/package=mkin/news/news.html">CRAN release</a> and one for each github branch, e.g. <a href="https://github.com/jranke/mkin/blob/master/NEWS.md">the main branch</a>.</p>
+<p>There is a list of changes for the latest <a href="https://cran.r-project.org/package=mkin/news/news.html">CRAN release</a> and one for each github branch, e.g. <a href="https://github.com/jranke/mkin/blob/main/NEWS.md">the main branch</a>.</p>
</div>
<div id="credits-and-historical-remarks" class="section level2">
<h2>Credits and historical remarks</h2>
diff --git a/README.md b/README.md
index 6ee38e98..00223748 100644
--- a/README.md
+++ b/README.md
@@ -1,8 +1,8 @@
# mkin
[![](https://www.r-pkg.org/badges/version/mkin)](https://cran.r-project.org/package=mkin)
-[![Build Status](https://travis-ci.com/jranke/mkin.svg?branch=master)](https://app.travis-ci.com/github/jranke/mkin)
-[![codecov](https://codecov.io/github/jranke/mkin/branch/master/graphs/badge.svg)](https://codecov.io/github/jranke/mkin)
+[![Build Status](https://travis-ci.com/jranke/mkin.svg?branch=main)](https://app.travis-ci.com/github/jranke/mkin)
+[![codecov](https://codecov.io/github/jranke/mkin/branch/main/graphs/badge.svg)](https://codecov.io/github/jranke/mkin)
The R package **mkin** provides calculation routines for the analysis of
chemical degradation data, including <b>m</b>ulticompartment <b>kin</b>etics as
@@ -127,7 +127,7 @@ for installation instructions and a manual.
## News
There is a list of changes for the latest [CRAN release](https://cran.r-project.org/package=mkin/news/news.html)
-and one for each github branch, e.g. [the main branch](https://github.com/jranke/mkin/blob/master/NEWS.md).
+and one for each github branch, e.g. [the main branch](https://github.com/jranke/mkin/blob/main/NEWS.md).
## Credits and historical remarks
diff --git a/docs/404.html b/docs/404.html
index 86397bff..af049fc2 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
</span>
</div>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 8e05af32..a5852160 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -71,7 +71,7 @@
</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">1.0.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
</span>
</div>
diff --git a/docs/authors.html b/docs/authors.html
index 533ca458..878acf40 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -71,7 +71,7 @@
</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">1.0.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
</span>
</div>
diff --git a/docs/index.html b/docs/index.html
index 3e7ca59c..59d4f596 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -37,7 +37,7 @@
</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">1.0.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
</span>
</div>
@@ -258,7 +258,7 @@ Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic
<h2>Dev status</h2>
<ul class="list-unstyled">
<li><a href="https://cran.r-project.org/package=mkin"><img src="https://www.r-pkg.org/badges/version/mkin"></a></li>
-<li><a href="https://travis-ci.com/jranke/mkin"><img src="https://travis-ci.com/jranke/mkin.svg?branch=master" alt="Build Status"></a></li>
+<li><a href="https://app.travis-ci.com/github/jranke/mkin"><img src="https://travis-ci.com/jranke/mkin.svg?branch=master" alt="Build Status"></a></li>
<li><a href="https://codecov.io/github/jranke/mkin"><img src="https://codecov.io/github/jranke/mkin/branch/master/graphs/badge.svg" alt="codecov"></a></li>
</ul>
</div>
diff --git a/docs/news/index.html b/docs/news/index.html
index 0ac20352..75b701d2 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -71,7 +71,7 @@
</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">1.0.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
</span>
</div>
@@ -141,6 +141,13 @@
<small>Source: <a href='https://github.com/jranke/mkin/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
+ <div id="mkin-105-2021-09-15" class="section level1">
+<h1 class="page-header" data-toc-text="1.0.5">
+<a href="#mkin-105-2021-09-15" class="anchor"></a>mkin 1.0.5 (2021-09-15)</h1>
+<ul>
+<li>‘dimethenamid_2018’: Correct the data for the Borstel soil. The five observations from Staudenmaier (2013) that were previously stored as “Borstel 2” are actually just a subset of the 16 observations in “Borstel 1” which is now simply “Borstel”</li>
+</ul>
+</div>
<div id="mkin-104-2021-04-20" class="section level1">
<h1 class="page-header" data-toc-text="1.0.4">
<a href="#mkin-104-2021-04-20" class="anchor"></a>mkin 1.0.4 (2021-04-20)</h1>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 12ae2f05..c655c059 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: 2021-07-29T08:57Z
+last_built: 2021-10-01T11:50Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html
index 3b6ae721..542599da 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">1.0.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
</span>
</div>
@@ -162,13 +162,13 @@ constrained by data protection regulations.</p>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
- <p>An <a href='mkindsg.html'>mkindsg</a> object grouping eight datasets with some meta information</p>
+ <p>An <a href='mkindsg.html'>mkindsg</a> object grouping seven datasets with some meta information</p>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria (2018)
Renewal Assessment Report Dimethenamid-P Volume 3 - B.8 Environmental fate and behaviour
Rev. 2 - November 2017
-<a href='http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-5211'>http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-5211</a></p>
+<a href='https://open.efsa.europa.eu'>https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716</a></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The R code used to create this data object is installed with this package
@@ -177,33 +177,30 @@ specific pieces of information in the comments.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>dimethenamid_2018</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; &lt;mkindsg&gt; holding 8 mkinds objects
+</div><div class='output co'>#&gt; &lt;mkindsg&gt; holding 7 mkinds objects
#&gt; Title $title: Aerobic soil degradation data on dimethenamid-P from the EU assessment in 2018
#&gt; Occurrence of observed compounds $observed_n:
#&gt; DMTAP M23 M27 M31 DMTA
-#&gt; 4 7 7 7 4
+#&gt; 3 7 7 7 4
#&gt; Time normalisation factors $f_time_norm:
-#&gt; [1] 1.0000000 0.9706477 0.9706477 1.2284784 1.2284784 0.6233856 0.7678922
-#&gt; [8] 0.6733938
+#&gt; [1] 1.0000000 0.9706477 1.2284784 1.2284784 0.6233856 0.7678922 0.6733938
#&gt; Meta information $meta:
-#&gt; study usda_soil_type study_moisture_ref_type
-#&gt; Calke Unsworth 2014 Sandy loam pF2
-#&gt; Borstel 1 Staudenmaier 2013 Sand pF1
-#&gt; Borstel 2 Staudenmaier 2009 Sand pF1
-#&gt; Elliot 1 Wendt 1997 Clay loam pF2.5
-#&gt; Elliot 2 Wendt 1997 Clay loam pF2.5
-#&gt; Flaach König 1996 Sandy clay loam pF1
-#&gt; BBA 2.2 König 1995 Loamy sand pF1
-#&gt; BBA 2.3 König 1995 Sandy loam pF1
-#&gt; rel_moisture study_ref_moisture temperature
-#&gt; Calke 1.00 NA 20
-#&gt; Borstel 1 0.50 23.00 20
-#&gt; Borstel 2 0.50 23.00 20
-#&gt; Elliot 1 0.75 33.37 23
-#&gt; Elliot 2 0.75 33.37 23
-#&gt; Flaach 0.40 NA 20
-#&gt; BBA 2.2 0.40 NA 20
-#&gt; BBA 2.3 0.40 NA 20</div></pre>
+#&gt; study usda_soil_type study_moisture_ref_type rel_moisture
+#&gt; Calke Unsworth 2014 Sandy loam pF2 1.00
+#&gt; Borstel Staudenmaier 2009 Sand pF1 0.50
+#&gt; Elliot 1 Wendt 1997 Clay loam pF2.5 0.75
+#&gt; Elliot 2 Wendt 1997 Clay loam pF2.5 0.75
+#&gt; Flaach König 1996 Sandy clay loam pF1 0.40
+#&gt; BBA 2.2 König 1995 Loamy sand pF1 0.40
+#&gt; BBA 2.3 König 1995 Sandy loam pF1 0.40
+#&gt; study_ref_moisture temperature
+#&gt; Calke NA 20
+#&gt; Borstel 23.00 20
+#&gt; Elliot 1 33.37 23
+#&gt; Elliot 2 33.37 23
+#&gt; Flaach NA 20
+#&gt; BBA 2.2 NA 20
+#&gt; BBA 2.3 NA 20</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index a83276f3..bfe030b0 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." />
</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">1.0.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
</span>
</div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 36ef6367..ff7a4198 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -71,7 +71,7 @@
</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">1.0.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
</span>
</div>
diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html
index b4f8db16..b3bf35bf 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">1.0.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
</span>
</div>
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index cda53ce8..f9976c6b 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">1.0.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</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/RtmpQCjjOu/filef8c1f2031f4ea.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/Rtmp1acwPp/fileb9e34769fb8fe.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: 0x55555a59b978&gt;</div><div class='input'>
+#&gt; &lt;environment: 0x55555a720040&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/nlme.html b/docs/reference/nlme.html
index c6b43aab..6821bacf 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">1.0.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
</span>
</div>
diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html
index 03448606..b3052605 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">1.0.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
</span>
</div>
diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html
index b75fa6e6..090a644c 100644
--- a/docs/reference/plot.mixed.mmkin.html
+++ b/docs/reference/plot.mixed.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">1.0.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
</span>
</div>
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index c6d716a1..e195d8bf 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">1.0.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
</span>
</div>

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