Typos, rebuild static docs

10 files changed, 25 insertions, 10 deletions

diff --git a/ChangeLog b/ChangeLog
index 4c94b31..b236efe 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,15 @@
+commit 6f6575701d9b028af4b3b1b4b61c36d4989e2812
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-10-10 14:03:20 +0200
+
+    Add ORCID
+
+commit a33f1bbbf6f6121e8ad40284690a463733a00bc2
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-10-09 08:48:39 +0200
+
+    Write Step 2 input files on windows
+
 commit 311c4fbcc51ad727551da41569d64e6bc290c2b2
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2017-10-06 09:30:21 +0200
diff --git a/DESCRIPTION b/DESCRIPTION
index 163db20..64e0499 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,10 +2,10 @@ Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
 Version: 0.4-5
-Date: 2017-10-06
+Date: 2017-10-23
 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de",
                   role = c("aut", "cre", "cph"),
-                  comment = c(ORCID = "0000-0003-4371-6538")),
+                  comment = c(ORCID = "0000-0003-4371-6538"))
 Description: Utilities for simple calculations of predicted environmental
     concentrations ('PEC' values) and for dealing with data from some FOCUS
     pesticide fate modelling software packages.
diff --git a/R/PEC_sw_focus.R b/R/PEC_sw_focus.R
index e063ff3..e2c3e54 100644
--- a/R/PEC_sw_focus.R
+++ b/R/PEC_sw_focus.R
@@ -1,6 +1,6 @@
 #' Calculate PEC surface water at FOCUS Step 1
 #'
-#' This is reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
+#' This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
 #' authored by Michael Klein, in R. Note that results for multiple
 #' applications should be compared to the corresponding results for a
 #' single application. At current, this is not done automatically in
diff --git a/docs/authors.html b/docs/authors.html
index 4bec4d8..d2ef54f 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -74,7 +74,7 @@
     <ul class="list-unstyled">
       <li>
         <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright&nbsp;holder.
-        </p>
+        <br /><small>0000-0003-4371-6538</small></p>
       </li>
     </ul>
 
diff --git a/docs/index.html b/docs/index.html
index 7c7cca5..66f3304 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -85,7 +85,8 @@ this program. If not, see &lt;http:<span class="er">//</span>www.gnu.org/license
 <p>GPL</p>
 <h2>Developers</h2>
 <ul class="list-unstyled">
-<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li>
+<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <br><small>(0000-0003-4371-6538)</small>
+</li>
 </ul>
 </div>
 </div>
diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html
index 50651ae..2250795 100644
--- a/docs/reference/PEC_sw_focus.html
+++ b/docs/reference/PEC_sw_focus.html
@@ -72,7 +72,7 @@
     </div>
 
     
-    <p>This is reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
+    <p>This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
 authored by Michael Klein, in R. Note that results for multiple
 applications should be compared to the corresponding results for a
 single application. At current, this is not done automatically in
@@ -167,7 +167,7 @@ should be written</p></td>
     <tr>
       <th>overwrite</th>
       <td><p>Should an existing file a the location specified in
-<code>txt_file</code> be overwritten?</p></td>
+<code>txt_file</code> be overwritten? Only takes effect if append is FALSE.</p></td>
     </tr>
     <tr>
       <th>append</th>
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html
index f2df73a..b7dc4e6 100644
--- a/docs/reference/PELMO_runs.html
+++ b/docs/reference/PELMO_runs.html
@@ -190,7 +190,7 @@ 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;     218.452       0.788      55.054 </div><div class='input'>
+#&gt;     218.820       0.896      56.243 </div><div class='input'>
 <span class='co'># Demonstrate some results with metabolites.</span>
 <span class='no'>runs_2</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='fu'>list</span>(<span class='kw'>psm</span> <span class='kw'>=</span> <span class='st'>'Pesticide_D_1_May_every_other_year_mets'</span>,
                     <span class='kw'>win</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Cha"</span>, <span class='st'>"Ham"</span>, <span class='st'>"Kre"</span>)))
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 9973635..0fbae40 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -70,7 +70,7 @@
     <div class="page-header">
       <h1>
         Reference
-        <small>version&nbsp;0.4-3</small>
+        <small>version&nbsp;0.4-5</small>
       </h1>
     </div>
 
diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt
index e4c6dac..e0dddbf 100644
--- a/docs/reference/pesticide.txt
+++ b/docs/reference/pesticide.txt
@@ -1,3 +1,5 @@
 Active Substance	Compound	Comment	Mol mass a.i.	Mol mass met.	Water solubility	KOC assessed compound	KOC parent compound	DT50	Max. in Water	Max. in Soil asessed compound	App. Rate	Number of App.	Time between app.	App. Type	DT50 soil parent compound	DT50 soil	DT50 water	DT50 sediment	Region / Season	Interception class
 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/man/PEC_sw_focus.Rd b/man/PEC_sw_focus.Rd
index f953923..7ba5ae3 100644
--- a/man/PEC_sw_focus.Rd
+++ b/man/PEC_sw_focus.Rd
@@ -63,7 +63,7 @@ should be written}
 \item{append}{Should the input text file be appended?}
 }
 \description{
-This is reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
+This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
 authored by Michael Klein, in R. Note that results for multiple
 applications should be compared to the corresponding results for a
 single application. At current, this is not done automatically in