Changelog update and roxygen run

18 files changed, 19 insertions, 27 deletions

diff --git a/ChangeLog b/ChangeLog
index 20fd246..565282f 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,9 @@
+commit e51e063564bffcb75dbb6ab7a364704c8d8e992e
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2016-12-12 21:24:24 +0100
+
+    Fix reading .out for acronyms containing numbers
+
 commit 9124e0f7d673c65584c1b2f838a3b944ea89c31d
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2016-10-13 17:49:18 +0200
diff --git a/DESCRIPTION b/DESCRIPTION
index 5c3d779..2e8b886 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
 Version: 0.3-9
-Date: 2016-12-12
+Date: 2016-12-14
 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", 
                   role = c("aut", "cre", "cph"))
 Description: Utilities for simple calculations of predicted environmental
@@ -22,4 +22,4 @@ License: GPL
 LazyLoad: yes
 LazyData: yes
 Encoding: UTF-8
-RoxygenNote: 5.0.1
+RoxygenNote: 5.0.1.9000
diff --git a/man/FOCUS_GW_scenarios_2012.Rd b/man/FOCUS_GW_scenarios_2012.Rd
index 3ae151b..f2417d9 100644
--- a/man/FOCUS_GW_scenarios_2012.Rd
+++ b/man/FOCUS_GW_scenarios_2012.Rd
@@ -14,4 +14,3 @@ FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version
  FOrum for the Co-ordination of pesticde fate models and their USe. 
  http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf
 }
-
diff --git a/man/GUS.Rd b/man/GUS.Rd
index f1f5f28..edf61b6 100644
--- a/man/GUS.Rd
+++ b/man/GUS.Rd
@@ -2,8 +2,8 @@
 % Please edit documentation in R/GUS.R
 \name{GUS}
 \alias{GUS}
-\alias{GUS.chent}
 \alias{GUS.numeric}
+\alias{GUS.chent}
 \alias{print.GUS_result}
 \title{Groundwater ubiquity score based on Gustafson (1989)}
 \usage{
@@ -70,12 +70,11 @@ The groundwater ubiquity score GUS is calculated according to
 the following equation
 \deqn{GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})}{GUS = log10 DT50soil * (4 - log10 Koc)}
 }
-\author{
-Johannes Ranke
-}
 \references{
 Gustafson, David I. (1989) Groundwater ubiquity score: a simple
 method for assessing pesticide leachability. \emph{Environmental
 toxicology and chemistry} \bold{8}(4) 339–57.
 }
-
+\author{
+Johannes Ranke
+}
diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd
index c0b5201..dd780cf 100644
--- a/man/PEC_soil.Rd
+++ b/man/PEC_soil.Rd
@@ -100,9 +100,6 @@ results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_
 results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21),
                            Kom = 100, scenarios = "EFSA_2015", porewater = TRUE)
 }
-\author{
-Johannes Ranke
-}
 \references{
 EFSA Panel on Plant Protection Products and their Residues (2012)
   Scientific Opinion on the science behind the guidance for scenario
@@ -116,4 +113,6 @@ EFSA Panel on Plant Protection Products and their Residues (2012)
   in soil. \emph{EFSA Journal} \bold{13}(4) 4093
   doi:10.2903/j.efsa.2015.4093
 }
-
+\author{
+Johannes Ranke
+}
diff --git a/man/PEC_sw_drainage_UK.Rd b/man/PEC_sw_drainage_UK.Rd
index cb64bde..a968b94 100644
--- a/man/PEC_sw_drainage_UK.Rd
+++ b/man/PEC_sw_drainage_UK.Rd
@@ -36,4 +36,3 @@ PEC_sw_drainage_UK(150, Koc = 100)
 \author{
 Johannes Ranke
 }
-
diff --git a/man/PEC_sw_drift.Rd b/man/PEC_sw_drift.Rd
index ae27e82..f74cf67 100644
--- a/man/PEC_sw_drift.Rd
+++ b/man/PEC_sw_drift.Rd
@@ -6,7 +6,7 @@
 \usage{
 PEC_sw_drift(rate, applications = 1, water_depth = 30,
   drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau",
-  distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "<U+00B5>g/L")
+  distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")
 }
 \arguments{
 \item{rate}{Application rate in units specified below}
@@ -42,4 +42,3 @@ PEC_sw_drift(100)
 \author{
 Johannes Ranke
 }
-
diff --git a/man/PEC_sw_sed.Rd b/man/PEC_sw_sed.Rd
index d0e2ec6..1feb146 100644
--- a/man/PEC_sw_sed.Rd
+++ b/man/PEC_sw_sed.Rd
@@ -7,7 +7,7 @@ water concentrations}
 \usage{
 PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage",
   sediment_depth = 5, water_depth = 30, sediment_density = 1.3,
-  PEC_sed_units = c("<U+00B5>g/kg", "mg/kg"))
+  PEC_sed_units = c("µg/kg", "mg/kg"))
 }
 \arguments{
 \item{PEC_sw}{Numeric vector or matrix of surface water concentrations in µg/L for
@@ -39,4 +39,3 @@ PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50)
 \author{
 Johannes Ranke
 }
-
diff --git a/man/SFO_actual_twa.Rd b/man/SFO_actual_twa.Rd
index 573ea03..61f95aa 100644
--- a/man/SFO_actual_twa.Rd
+++ b/man/SFO_actual_twa.Rd
@@ -26,4 +26,3 @@ SFO_actual_twa(10)
 \author{
 Johannes Ranke
 }
-
diff --git a/man/SSLRC_mobility_classification.Rd b/man/SSLRC_mobility_classification.Rd
index 04aa01d..c7fd12d 100644
--- a/man/SSLRC_mobility_classification.Rd
+++ b/man/SSLRC_mobility_classification.Rd
@@ -23,4 +23,3 @@ SSLRC_mobility_classification(100)
 \author{
 Johannes Ranke
 }
-
diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd
index de87510..7935617 100644
--- a/man/TOXSWA_cwa.Rd
+++ b/man/TOXSWA_cwa.Rd
@@ -29,6 +29,7 @@ Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_
 and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) 
 for the requested moving window sizes in days.}
 }}
+
 \section{Methods}{
 
 \describe{
@@ -45,6 +46,7 @@ for the requested moving window sizes in days.}
         }
 }
 }
+
 \examples{
 H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
                                  basedir = "SwashProjects/project_H_sw/TOXSWA",
@@ -55,4 +57,3 @@ H_sw_R1_stream$moving_windows(c(7, 21))
 print(H_sw_R1_stream)
 }
 \keyword{data}
-
diff --git a/man/drift_data_JKI.Rd b/man/drift_data_JKI.Rd
index c193c0d..5597b66 100644
--- a/man/drift_data_JKI.Rd
+++ b/man/drift_data_JKI.Rd
@@ -47,4 +47,3 @@ as its licence is not clear.
 drift_data_JKI
 }
 \keyword{datasets}
-
diff --git a/man/endpoint.Rd b/man/endpoint.Rd
index 0350a51..9511083 100644
--- a/man/endpoint.Rd
+++ b/man/endpoint.Rd
@@ -72,4 +72,3 @@ For the Freundlich exponent, the capital letter \code{N} is used in order to
 facilitate dealing with such data in R. In pesticide fate modelling, this
 exponent is often called 1/n.
 }
-
diff --git a/man/geomean.Rd b/man/geomean.Rd
index ed82294..2887929 100644
--- a/man/geomean.Rd
+++ b/man/geomean.Rd
@@ -28,4 +28,3 @@ geomean(c(1, 3, NA, 9))
 \author{
 Johannes Ranke
 }
-
diff --git a/man/pfm_degradation.Rd b/man/pfm_degradation.Rd
index 9ab1d0a..0f3cc79 100644
--- a/man/pfm_degradation.Rd
+++ b/man/pfm_degradation.Rd
@@ -32,4 +32,3 @@ head(pfm_degradation("SFO", DT50 = 10))
 \author{
 Johannes Ranke
 }
-
diff --git a/man/plot.TOXSWA_cwa.Rd b/man/plot.TOXSWA_cwa.Rd
index b5f0163..4e81f91 100644
--- a/man/plot.TOXSWA_cwa.Rd
+++ b/man/plot.TOXSWA_cwa.Rd
@@ -39,4 +39,3 @@ plot(H_sw_D4_pond)
 \author{
 Johannes Ranke
 }
-
diff --git a/man/read.TOXSWA_cwa.Rd b/man/read.TOXSWA_cwa.Rd
index 84ef3da..f1d5908 100644
--- a/man/read.TOXSWA_cwa.Rd
+++ b/man/read.TOXSWA_cwa.Rd
@@ -53,4 +53,3 @@ H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
 \author{
 Johannes Ranke
 }
-
diff --git a/man/soil_scenario_data_EFSA_2015.Rd b/man/soil_scenario_data_EFSA_2015.Rd
index b45af4a..02c16dc 100644
--- a/man/soil_scenario_data_EFSA_2015.Rd
+++ b/man/soil_scenario_data_EFSA_2015.Rd
@@ -43,4 +43,3 @@ scenario and model adjustment factors from p. 15 and p. 17 are included.
 soil_scenario_data_EFSA_2015
 }
 \keyword{datasets}
-