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-rw-r--r--docs/reference/PEC_soil.html2
-rw-r--r--docs/reference/PELMO_runs.html2
-rw-r--r--docs/reference/TOXSWA_cwa.html10
-rw-r--r--docs/reference/index.html2
-rw-r--r--docs/reference/pesticide.txt2
-rw-r--r--docs/reference/read.TOXSWA_cwa.html10
6 files changed, 16 insertions, 12 deletions
diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html
index feed9d5..5073067 100644
--- a/docs/reference/PEC_soil.html
+++ b/docs/reference/PEC_soil.html
@@ -150,7 +150,7 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012).</p>
<tr>
<th>interval</th>
<td><p>Period of the deeper mixing, defaults to 365, which is a year if
-rate units are in days</p></td>
+degradation rate units are in days</p></td>
</tr>
<tr>
<th>n_periods</th>
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html
index 1eac49b..5d53104 100644
--- a/docs/reference/PELMO_runs.html
+++ b/docs/reference/PELMO_runs.html
@@ -229,7 +229,7 @@ the period.plm file generated by the FOCUS PELMO GUI.</p>
#&gt;
#&gt; </div><div class='input'><span class='co'># We get exactly the same PECgw values (on Linux, calling PELMO using Wine).</span>
<span class='fu'>print</span>(<span class='no'>time_1</span>)</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.398 0.100 30.624 </div><div class='input'><span class='kw'>if</span>(!<span class='fu'>inherits</span>(<span class='fu'>try</span>(<span class='no'>cpuinfo</span> <span class='kw'>&lt;-</span> <span class='fu'>readLines</span>(<span class='st'>"/proc/cpuinfo"</span>)), <span class='st'>"try-error"</span>)) {
+#&gt; 0.384 0.095 30.954 </div><div class='input'><span class='kw'>if</span>(!<span class='fu'>inherits</span>(<span class='fu'>try</span>(<span class='no'>cpuinfo</span> <span class='kw'>&lt;-</span> <span class='fu'>readLines</span>(<span class='st'>"/proc/cpuinfo"</span>)), <span class='st'>"try-error"</span>)) {
<span class='fu'>cat</span>(<span class='fu'>gsub</span>(<span class='st'>"model name\t: "</span>, <span class='st'>"CPU model: "</span>, <span class='no'>cpuinfo</span>[<span class='fu'>grep</span>(<span class='st'>"model name"</span>, <span class='no'>cpuinfo</span>)[<span class='fl'>1</span>]]))
}</div><div class='output co'>#&gt; CPU model: AMD Ryzen 7 1700 Eight-Core Processor</div><div class='input'>
<span class='co'># Demonstrate some results with metabolites.</span>
diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html
index 3b11804..932e6ef 100644
--- a/docs/reference/TOXSWA_cwa.html
+++ b/docs/reference/TOXSWA_cwa.html
@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>R6 class for holding TOXSWA cwa concentration data and associated statistics — TOXSWA_cwa • pfm</title>
+<title>R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -30,9 +30,9 @@
-<meta property="og:title" content="R6 class for holding TOXSWA cwa concentration data and associated statistics — TOXSWA_cwa" />
+<meta property="og:title" content="R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa" />
-<meta property="og:description" content="An R6 class for holding TOXSWA cwa concentration data and some associated statistics.
+<meta property="og:description" content="An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics.
Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
<meta name="twitter:card" content="summary" />
@@ -98,14 +98,14 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>R6 class for holding TOXSWA cwa concentration data and associated statistics</h1>
+ <h1>R6 class for holding TOXSWA water concentration data and associated statistics</h1>
<small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/TOXSWA_cwa.R'><code>R/TOXSWA_cwa.R</code></a></small>
<div class="hidden name"><code>TOXSWA_cwa.Rd</code></div>
</div>
<div class="ref-description">
- <p>An R6 class for holding TOXSWA cwa concentration data and some associated statistics.
+ <p>An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics.
Usually, an instance of this class will be generated by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p>
</div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index c153b50..162298b 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -311,7 +311,7 @@ water concentrations</p></td>
<td>
<p><code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code> </p>
</td>
- <td><p>R6 class for holding TOXSWA cwa concentration data and associated statistics</p></td>
+ <td><p>R6 class for holding TOXSWA water concentration data and associated statistics</p></td>
</tr><tr>
<td>
diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt
index 85f103d..d4fd84e 100644
--- a/docs/reference/pesticide.txt
+++ b/docs/reference/pesticide.txt
@@ -35,3 +35,5 @@ Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Du
M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00
Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00
M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00
+Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00
+M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00
diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html
index 60e236a..aa18ec4 100644
--- a/docs/reference/read.TOXSWA_cwa.html
+++ b/docs/reference/read.TOXSWA_cwa.html
@@ -36,7 +36,8 @@
segment of a TOXSWA surface water body. Per default, the data for the last
segment are imported. As TOXSWA 4 reports the values at the end of the hour
(ConLiqWatLayCur) in its summary file, we use this value as well instead
-of the hourly averages (ConLiqWatLay)." />
+of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was
+renamed to ConLiqWatLay in the out file." />
<meta name="twitter:card" content="summary" />
@@ -112,7 +113,8 @@ of the hourly averages (ConLiqWatLay)." />
segment of a TOXSWA surface water body. Per default, the data for the last
segment are imported. As TOXSWA 4 reports the values at the end of the hour
(ConLiqWatLayCur) in its summary file, we use this value as well instead
-of the hourly averages (ConLiqWatLay).</p>
+of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was
+renamed to ConLiqWatLay in the out file.</p>
</div>
@@ -126,7 +128,7 @@ of the hourly averages (ConLiqWatLay).</p>
<tr>
<th>filename</th>
<td><p>The filename of the cwa file (TOXSWA 2.x.y or similar) or the
-out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).</p></td>
+out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.</p></td>
</tr>
<tr>
<th>basedir</th>
@@ -143,7 +145,7 @@ the segment number.</p></td>
</tr>
<tr>
<th>substance</th>
- <td><p>For TOXSWA 4 .out files, the default value "parent" leads
+ <td><p>For .out files, the default value "parent" leads
to reading concentrations of the parent compound. Alternatively, the substance
of interested can be selected by its code name.</p></td>
</tr>

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