Reorganise repository using standard package layout

16 files changed, 791 insertions, 0 deletions

diff --git a/man/FOCUS_GW_scenarios_2012.Rd b/man/FOCUS_GW_scenarios_2012.Rd
new file mode 100644
index 0000000..3ae151b
--- /dev/null
+++ b/man/FOCUS_GW_scenarios_2012.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/FOCUS_GW_scenarios_2012.R
+\name{FOCUS_GW_scenarios_2012}
+\alias{FOCUS_GW_scenarios_2012}
+\title{A very small subset of the FOCUS Groundwater scenario defitions}
+\description{
+Currently, only a small subset of the soil definitions are provided.
+}
+\examples{
+FOCUS_GW_scenarios_2012
+}
+\references{
+FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. 
+ 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
new file mode 100644
index 0000000..f1f5f28
--- /dev/null
+++ b/man/GUS.Rd
@@ -0,0 +1,81 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/GUS.R
+\name{GUS}
+\alias{GUS}
+\alias{GUS.chent}
+\alias{GUS.numeric}
+\alias{print.GUS_result}
+\title{Groundwater ubiquity score based on Gustafson (1989)}
+\usage{
+GUS(...)
+
+\method{GUS}{numeric}(DT50, Koc, ...)
+
+\method{GUS}{chent}(chent, degradation_value = "DT50ref",
+  lab_field = "laboratory", redox = "aerobic", sorption_value = "Kfoc",
+  degradation_aggregator = geomean, sorption_aggregator = geomean, ...)
+
+\method{print}{GUS_result}(x, ..., digits = 1)
+}
+\arguments{
+\item{...}{Included in the generic to allow for further arguments later. Therefore
+this also had to be added to the specific methods.}
+
+\item{DT50}{Half-life of the chemical in soil. Should be a field
+half-life according to Gustafson (1989). However, leaching to the sub-soil
+can not completely be excluded in field dissipation experiments and Gustafson
+did not refer to any normalisation procedure, but says the field study should
+be conducted under use conditions.}
+
+\item{Koc}{The sorption constant normalised to organic carbon. Gustafson
+does not mention the nonlinearity of the sorption constant commonly
+found and usually described by Freundlich sorption, therefore it is 
+unclear at which reference concentration the Koc should be observed
+(and if the reference concentration would be in soil or in porewater).}
+
+\item{chent}{If a chent is given with appropriate information present in its
+chyaml field, this information is used, with defaults specified below.}
+
+\item{degradation_value}{Which of the available degradation values should 
+be used?}
+
+\item{lab_field}{Should laboratory or field half-lives be used? This
+defaults to lab in this implementation, in order to avoid
+double-accounting for mobility. If comparability with the original GUS
+values given by Gustafson (1989) is desired, non-normalised first-order
+field half-lives obtained under actual use conditions should be used.}
+
+\item{redox}{Aerobic or anaerobic degradation data}
+
+\item{sorption_value}{Which of the available sorption values should be used?
+Defaults to Kfoc as this is what is generally available from the European
+pesticide peer review process. These values generally use a reference
+concentration of 1 mg/L in porewater, that means they would be expected to
+be Koc values at a concentration of 1 mg/L in the water phase.}
+
+\item{degradation_aggregator}{Function for aggregating half-lives}
+
+\item{sorption_aggregator}{Function for aggregation Koc values}
+
+\item{x}{An object of class GUS_result to be printed}
+
+\item{digits}{The number of digits used in the print method}
+}
+\value{
+A list with the DT50 and Koc used as well as the resulting score
+  of class GUS_result
+}
+\description{
+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.
+}
+
diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd
new file mode 100644
index 0000000..c0b5201
--- /dev/null
+++ b/man/PEC_soil.Rd
@@ -0,0 +1,119 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PEC_soil.R
+\name{PEC_soil}
+\alias{PEC_soil}
+\title{Calculate predicted environmental concentrations in soil}
+\usage{
+PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5,
+  PEC_units = "mg/kg", PEC_pw_units = "mg/L", interval = NA,
+  n_periods = Inf, tillage_depth = 20, chent = NA, DT50 = NA,
+  Koc = NA, Kom = Koc/1.724, t_avg = 0, scenarios = c("default",
+  "EFSA_2015"), porewater = FALSE)
+}
+\arguments{
+\item{rate}{Application rate in units specified below}
+
+\item{rate_units}{Defaults to g/ha}
+
+\item{interception}{The fraction of the application rate that does not reach the soil}
+
+\item{mixing_depth}{Mixing depth in cm}
+
+\item{PEC_units}{Requested units for the calculated PEC. Only mg/kg currently supported}
+
+\item{PEC_pw_units}{Only mg/L currently supported}
+
+\item{interval}{Period of the deeper mixing, defaults to 365, which is a year if
+rate units are in days}
+
+\item{n_periods}{Number of periods to be considered for long term PEC calculations}
+
+\item{tillage_depth}{Periodic (see interval) deeper mixing in cm}
+
+\item{chent}{An optional chent object holding substance specific information. Can 
+also be a name for the substance as a character string}
+
+\item{DT50}{If specified, overrides soil DT50 endpoints from a chent object
+If DT50 is not specified here and not available from the chent object, zero
+degradation is assumed}
+
+\item{Koc}{If specified, overrides Koc endpoints from a chent object}
+
+\item{Kom}{Calculated from Koc by default, but can explicitly be specified
+as Kom here}
+
+\item{t_avg}{Averaging times for time weighted average concentrations}
+
+\item{scenarios}{If this is 'default', the DT50 will be used without correction
+and soil properties as specified in the REACH guidance (R.16, Table
+R.16-9) are used for porewater PEC calculations.  If this is "EFSA_2015",
+the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when
+'chents' is specified, the DegT50 with destination 'PECgw' will be used),
+and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also
+model and scenario adjustment factors from the EFSA guidance are used.}
+
+\item{porewater}{Should equilibrium porewater concentrations be estimated
+based on Kom and the organic carbon fraction of the soil instead of total
+soil concentrations?  Based on equation (7) given in the PPR panel opinion
+(EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015,
+p. 13).}
+}
+\value{
+The predicted concentration in soil
+}
+\description{
+This is a basic calculation of a contaminant concentration in bulk soil
+based on complete, instantaneous mixing. If an interval is given, an 
+attempt is made at calculating a long term maximum concentration using
+the concepts layed out for example in the PPR panel opinion (EFSA 2012).
+}
+\details{
+This assumes that the complete load to soil during the time specified by
+'interval' (typically 365 days) is dosed at once. As in the PPR panel
+opinion cited below (PPR panel 2012), only temperature correction using the
+Arrhenius equation is performed.
+
+Total soil and porewater PEC values for the scenarios as defined in the EFSA
+guidance (2015, p. 13) can easily be calculated.
+}
+\note{
+If temperature information is available in the selected scenarios, as
+  e.g. in the EFSA scenarios, the DT50 for groundwater modelling
+  (destination 'PECgw') is taken from the chent object, otherwise the DT50
+  with destination 'PECsoil'.
+}
+\examples{
+PEC_soil(100, interception = 0.25)
+
+# This is example 1 starting at p. 79 of the EFSA guidance (2015)
+PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
+               scenarios = "EFSA_2015")
+PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21),
+               Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE)
+
+# The following is from example 4 starting at p. 85 of the EFSA guidance (2015)
+# Metabolite M2
+# Calculate total and porewater soil concentrations for tier 1 scenarios
+# Relative molar mass is 100/300, formation fraction is 0.7 * 1
+results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
+                        scenarios = "EFSA_2015")
+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
+  selection and scenario parameterisation for predicting environmental
+  concentrations of plant protection products in soil. \emph{EFSA Journal}
+  \bold{10}(2) 2562, doi:10.2903/j.efsa.2012.2562
+
+  EFSA (European Food Safety Authority) (2015) EFSA guidance document for
+  predicting environmental concentrations of active substances of plant
+  protection products and transformation products of these active substances
+  in soil. \emph{EFSA Journal} \bold{13}(4) 4093
+  doi:10.2903/j.efsa.2015.4093
+}
+
diff --git a/man/PEC_sw_drainage_UK.Rd b/man/PEC_sw_drainage_UK.Rd
new file mode 100644
index 0000000..cb64bde
--- /dev/null
+++ b/man/PEC_sw_drainage_UK.Rd
@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PEC_sw_drainage_UK.R
+\name{PEC_sw_drainage_UK}
+\alias{PEC_sw_drainage_UK}
+\title{Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method}
+\usage{
+PEC_sw_drainage_UK(rate, interception = 0, Koc, latest_application = NULL,
+  soil_DT50 = NULL, model = NULL, model_parms = NULL)
+}
+\arguments{
+\item{rate}{Application rate in g/ha}
+
+\item{interception}{The fraction of the application rate that does not reach the soil}
+
+\item{Koc}{The sorption coefficient normalised to organic carbon in L/kg}
+
+\item{latest_application}{Latest application date, formatted as e.g. "01 July"}
+
+\item{soil_DT50}{Soil degradation half-life, if SFO kinetics are to be used}
+
+\item{model}{The soil degradation model to be used. Either one of "FOMC",
+"DFOP", "HS", or "IORE", or an mkinmod object}
+
+\item{model_parms}{A named numeric vector containing the model parameters}
+}
+\value{
+The predicted concentration in surface water in µg/L
+}
+\description{
+This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet
+published on the CRC website
+}
+\examples{
+PEC_sw_drainage_UK(150, Koc = 100)
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/man/PEC_sw_drift.Rd b/man/PEC_sw_drift.Rd
new file mode 100644
index 0000000..20fa921
--- /dev/null
+++ b/man/PEC_sw_drift.Rd
@@ -0,0 +1,45 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PEC_sw_drift.R
+\name{PEC_sw_drift}
+\alias{PEC_sw_drift}
+\title{Calculate predicted environmental concentrations in surface water due to drift}
+\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 = "µg/L")
+}
+\arguments{
+\item{rate}{Application rate in units specified below}
+
+\item{applications}{Number of applications for selection of drift percentile}
+
+\item{water_depth}{Depth of the water body in cm}
+
+\item{drift_percentages}{Percentage drift values for which to calculate PECsw.
+'drift_data' and 'distances' if not NULL.}
+
+\item{drift_data}{Source of drift percentage data}
+
+\item{crop}{Crop name (use German names for JKI data), defaults to "Ackerbau"}
+
+\item{distances}{The distances in m for which to get PEC values}
+
+\item{rate_units}{Defaults to g/ha}
+
+\item{PEC_units}{Requested units for the calculated PEC. Only µg/L currently supported}
+}
+\value{
+The predicted concentration in surface water
+}
+\description{
+This is a basic, vectorised form of a simple calculation of a contaminant
+concentration in surface water based on complete, instantaneous mixing
+with input via spray drift.
+}
+\examples{
+PEC_sw_drift(100)
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/man/PEC_sw_sed.Rd b/man/PEC_sw_sed.Rd
new file mode 100644
index 0000000..3140eb0
--- /dev/null
+++ b/man/PEC_sw_sed.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PEC_sw_sed.R
+\name{PEC_sw_sed}
+\alias{PEC_sw_sed}
+\title{Calculate predicted environmental concentrations in sediment from surface
+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("µg/kg", "mg/kg"))
+}
+\arguments{
+\item{PEC_sw}{Numeric vector or matrix of surface water concentrations in µg/L for
+which the corresponding sediment concentration is to be estimated}
+
+\item{percentage}{The percentage in sediment, used for the percentage method}
+
+\item{method}{The method used for the calculation}
+
+\item{sediment_depth}{Depth of the sediment layer}
+
+\item{water_depth}{Depth of the water body in cm}
+
+\item{sediment_density}{The density of the sediment in L/kg (equivalent to
+g/cm3)}
+
+\item{PEC_sed_units}{The units of the estimated sediment PEC value}
+}
+\value{
+The predicted concentration in sediment
+}
+\description{
+The method 'percentage' is equivalent to what is used in the CRD spreadsheet
+PEC calculator
+}
+\examples{
+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
new file mode 100644
index 0000000..573ea03
--- /dev/null
+++ b/man/SFO_actual_twa.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/SFO_actual_twa.R
+\name{SFO_actual_twa}
+\alias{SFO_actual_twa}
+\title{Actual and maximum moving window time average concentrations for SFO kinetics}
+\source{
+FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
+  Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, 
+  18 December 2014, p. 251
+}
+\usage{
+SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50,
+  100))
+}
+\arguments{
+\item{DT50}{The half-life.}
+
+\item{times}{The output times, and window sizes for time weighted average concentrations}
+}
+\description{
+Actual and maximum moving window time average concentrations for SFO kinetics
+}
+\examples{
+SFO_actual_twa(10)
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/man/SSLRC_mobility_classification.Rd b/man/SSLRC_mobility_classification.Rd
new file mode 100644
index 0000000..04aa01d
--- /dev/null
+++ b/man/SSLRC_mobility_classification.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/SSLRC_mobility_classification.R
+\name{SSLRC_mobility_classification}
+\alias{SSLRC_mobility_classification}
+\title{Determine the SSLRC mobility classification for a chemical substance from its Koc}
+\usage{
+SSLRC_mobility_classification(Koc)
+}
+\arguments{
+\item{Koc}{The sorption coefficient normalised to organic carbon in L/kg}
+}
+\value{
+A list containing the classification and the percentage of the
+  compound transported per 10 mm drain water
+}
+\description{
+This implements the method specified in the UK data requirements handbook and was 
+checked against the spreadsheet published on the CRC website
+}
+\examples{
+SSLRC_mobility_classification(100)
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd
new file mode 100644
index 0000000..de87510
--- /dev/null
+++ b/man/TOXSWA_cwa.Rd
@@ -0,0 +1,58 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/TOXSWA_cwa.R
+\docType{class}
+\name{TOXSWA_cwa}
+\alias{TOXSWA_cwa}
+\title{R6 class for holding TOXSWA cwa concentration data and associated statistics}
+\format{An \code{\link{R6Class}} generator object.}
+\usage{
+TOXSWA_cwa
+}
+\description{
+An R6 class for holding TOXSWA cwa concentration data and some associated statistics.
+Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}.
+}
+\section{Fields}{
+
+\describe{
+\item{\code{filename}}{Length one character vector.}
+
+\item{\code{basedir}}{Length one character vector.}
+
+\item{\code{segment}}{Length one integer, specifying for which segment the cwa data were read.}
+
+\item{\code{cwas}}{Dataframe holding the concentrations.}
+
+\item{\code{events}}{List of dataframes holding the event statistics for each threshold.}
+
+\item{\code{windows}}{Matrix of maximum time weighted average concentrations (TWAC_max)
+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{
+  \item{\code{get_events(threshold, total = FALSE)}}{
+        Populate a datataframe with event information for the specified threshold value
+        in µg/L. If \code{total = TRUE}, the total concentration including the amount
+        adsorbed to suspended matter will be used. The resulting dataframe is stored in the 
+        \code{events} field of the object.
+        }
+  \item{\code{moving_windows(windows, total = FALSE)}}{
+        Add to the \code{windows} field described above.
+        Again, if \code{total = TRUE}, the total concentration including the amount
+        adsorbed to suspended matter will be used.
+        }
+}
+}
+\examples{
+H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
+                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
+                                 zipfile = system.file("testdata/SwashProjects.zip",
+                                             package = "pfm"))
+H_sw_R1_stream$get_events(c(2, 10))
+H_sw_R1_stream$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
new file mode 100644
index 0000000..c193c0d
--- /dev/null
+++ b/man/drift_data_JKI.Rd
@@ -0,0 +1,50 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/drift_data_JKI.R
+\docType{data}
+\name{drift_data_JKI}
+\alias{drift_data_JKI}
+\title{Deposition from spray drift expressed as percent of the applied dose as
+published by the JKI}
+\format{A list currently containing matrices with spray drift percentage
+data for field crops (Ackerbau), and Pome/stone fruit, early and late
+(Obstbau frueh, spaet).}
+\source{
+JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved
+from
+http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html
+on 2015-06-11
+}
+\description{
+Deposition from spray drift expressed as percent of the applied dose as
+published by the German Julius-Kühn Institute (JKI).
+}
+\details{
+The data were extracted from the spreadsheet cited below using the R code
+given in the example section. The spreadsheet is not included in the package
+as its licence is not clear.
+}
+\examples{
+
+\dontrun{
+  # This is the code that was used to extract the data
+  library(readxl)
+  abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls"
+  JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet")
+  names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late")
+  drift_data_JKI <- list()
+
+  for (n in 1:8) {
+    drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2)
+    drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) 
+    dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]),
+                                            crop = JKI_crops)
+    drift_data_JKI[[n]] <- drift_data
+  }
+  save(drift_data_JKI, file = "data/drift_data_JKI.RData")
+}
+
+# And this is the resulting data
+drift_data_JKI
+}
+\keyword{datasets}
+
diff --git a/man/endpoint.Rd b/man/endpoint.Rd
new file mode 100644
index 0000000..0350a51
--- /dev/null
+++ b/man/endpoint.Rd
@@ -0,0 +1,75 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/endpoint.R
+\name{endpoint}
+\alias{endpoint}
+\alias{soil_DT50}
+\alias{soil_Kfoc}
+\alias{soil_N}
+\alias{soil_sorption}
+\title{Retrieve endpoint information from the chyaml field of a chent object}
+\usage{
+endpoint(chent, medium = "soil", type = c("degradation", "sorption"),
+  lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic",
+  "anaerobic"), value = c("DT50ref", "Kfoc", "N"), aggregator = geomean,
+  raw = FALSE, signif = 3)
+
+soil_DT50(chent, aggregator = geomean, signif = 3,
+  lab_field = "laboratory", value = "DT50ref", redox = "aerobic",
+  raw = FALSE)
+
+soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc",
+  raw = FALSE)
+
+soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)
+
+soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc =
+  geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3),
+  raw = FALSE)
+}
+\arguments{
+\item{chent}{The chent object to get the information from}
+
+\item{medium}{The medium for which information is sought}
+
+\item{type}{The information type}
+
+\item{lab_field}{If not NA, do we want laboratory or field endpoints}
+
+\item{redox}{If not NA, are we looking for aerobic or anaerobic data}
+
+\item{value}{The name of the value we want. The list given in the 
+usage section is not exclusive}
+
+\item{aggregator}{The aggregator function. Can be mean, 
+\code{\link{geomean}}, or identity, for example.}
+
+\item{raw}{Should the number(s) be returned as stored in the chent
+object (could be a character value) to retain original information
+about precision?}
+
+\item{signif}{How many significant digits do we want}
+
+\item{values}{The values to be returned}
+
+\item{aggregators}{A named vector of aggregator functions to be used}
+}
+\value{
+The result from applying the aggregator function to
+  the values converted to a numeric vector, rounded to the
+  given number of significant digits, or, if raw = TRUE,
+  the values as a character value, retaining any implicit
+  information on precision that may be present.
+}
+\description{
+R6 class objects of class chent represent chemical entities
+and can hold a list of information loaded from a chemical yaml file in their
+chyaml field. Such information is extracted and optionally aggregated by
+this function.
+}
+\details{
+The functions \code{soil_*} are functions to extract soil specific endpoints.
+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
new file mode 100644
index 0000000..ed82294
--- /dev/null
+++ b/man/geomean.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/geomean.R
+\name{geomean}
+\alias{geomean}
+\title{Calculate the geometric mean}
+\usage{
+geomean(x, na.rm = TRUE)
+}
+\arguments{
+\item{x}{Vector of numbers}
+
+\item{na.rm}{Should NA values be omitted?}
+}
+\value{
+The geometric mean
+}
+\description{
+Based on some posts in a thread on Stackoverflow
+\url{http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in}
+This function checks for negative values, removes NA values per default and
+returns 0 if at least one element of the vector is 0.
+}
+\examples{
+geomean(c(1, 3, 9))
+geomean(c(1, 3, NA, 9))
+\dontrun{geomean(c(1, -3, 9)) # returns an error}
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/man/pfm_degradation.Rd b/man/pfm_degradation.Rd
new file mode 100644
index 0000000..9ab1d0a
--- /dev/null
+++ b/man/pfm_degradation.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pfm_degradation.R
+\name{pfm_degradation}
+\alias{pfm_degradation}
+\title{Calculate a time course of relative concentrations based on an mkinmod model}
+\usage{
+pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink =
+  log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by =
+  step_days))
+}
+\arguments{
+\item{model}{The degradation model to be used. Either a parent only model like
+'SFO' or 'FOMC', or an mkinmod object}
+
+\item{DT50}{The half-life. This is only used when simple exponential decline
+is calculated (SFO model).}
+
+\item{parms}{The parameters used for the degradation model}
+
+\item{years}{For how many years should the degradation be predicted?}
+
+\item{step_days}{What step size in days should the output have?}
+
+\item{times}{The output times}
+}
+\description{
+Calculate a time course of relative concentrations based on an mkinmod model
+}
+\examples{
+head(pfm_degradation("SFO", DT50 = 10))
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/man/plot.TOXSWA_cwa.Rd b/man/plot.TOXSWA_cwa.Rd
new file mode 100644
index 0000000..b5f0163
--- /dev/null
+++ b/man/plot.TOXSWA_cwa.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/TOXSWA_cwa.R
+\name{plot.TOXSWA_cwa}
+\alias{plot.TOXSWA_cwa}
+\title{Plot TOXSWA surface water concentrations}
+\usage{
+\method{plot}{TOXSWA_cwa}(x, time_column = c("datetime", "t", "t_firstjan",
+  "t_rel_to_max"), xlab = "default", ylab = "default", add = FALSE,
+  total = FALSE, LC_TIME = "C", ...)
+}
+\arguments{
+\item{x}{The TOXSWA_cwa object to be plotted.}
+
+\item{time_column}{What should be used for the time axis. If "t_firstjan" is chosen,
+the time is given in days relative to the first of January in the first year.}
+
+\item{xlab, ylab}{Labels for x and y axis.}
+
+\item{add}{Should we add to an existing plot?}
+
+\item{total}{Should the total concentration in water be plotted, including substance sorbed
+to suspended matter?}
+
+\item{LC_TIME}{Specification of the locale used to format dates}
+
+\item{...}{Further arguments passed to \code{plot} if we are not adding to an existing plot}
+}
+\description{
+Plot TOXSWA hourly concentrations of a chemical substance in a specific
+segment of a TOXSWA surface water body.
+}
+\examples{
+H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
+                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
+                                 zipfile = system.file("testdata/SwashProjects.zip",
+                                             package = "pfm"))
+plot(H_sw_D4_pond)
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/man/read.TOXSWA_cwa.Rd b/man/read.TOXSWA_cwa.Rd
new file mode 100644
index 0000000..84ef3da
--- /dev/null
+++ b/man/read.TOXSWA_cwa.Rd
@@ -0,0 +1,56 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/TOXSWA_cwa.R
+\name{read.TOXSWA_cwa}
+\alias{read.TOXSWA_cwa}
+\title{Read TOXSWA surface water concentrations}
+\usage{
+read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last",
+  substance = "parent", total = FALSE, windows = NULL,
+  thresholds = NULL)
+}
+\arguments{
+\item{filename}{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).}
+
+\item{basedir}{The path to the directory where the cwa file resides.}
+
+\item{zipfile}{Optional path to a zip file containing the cwa file.}
+
+\item{segment}{The segment for which the data should be read. Either "last", or 
+the segment number.}
+
+\item{substance}{For TOXSWA 4 .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.}
+
+\item{total}{Set this to TRUE in order to read total concentrations as well. This is 
+only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa
+files. For .cwa files, the total concentration is always read as well.}
+
+\item{windows}{Numeric vector of width of moving windows in days, for calculating
+maximum time weighted average concentrations and areas under the curve.}
+
+\item{thresholds}{Numeric vector of threshold concentrations in µg/L for
+generating event statistics.}
+}
+\value{
+An instance of an R6 object of class
+\code{\link{TOXSWA_cwa}}.
+}
+\description{
+Read TOXSWA hourly concentrations of a chemical substance in a specific
+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).
+}
+\examples{
+H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
+                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
+                                 zipfile = system.file("testdata/SwashProjects.zip",
+                                                       package = "pfm"))
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/man/soil_scenario_data_EFSA_2015.Rd b/man/soil_scenario_data_EFSA_2015.Rd
new file mode 100644
index 0000000..b45af4a
--- /dev/null
+++ b/man/soil_scenario_data_EFSA_2015.Rd
@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/soil_scenario_data_EFSA_2015.R
+\docType{data}
+\name{soil_scenario_data_EFSA_2015}
+\alias{soil_scenario_data_EFSA_2015}
+\title{Properties of the predefined scenarios from the EFSA guidance from 2015}
+\format{A data frame with one row for each scenario. Row names are the scenario codes, 
+  e.g. CTN for the Northern scenario for the total concentration in soil. Columns are 
+  mostly self-explanatory. \code{rho} is the dry bulk density of the top soil.}
+\source{
+EFSA (European Food Safety Authority) (2015)
+EFSA guidance document for predicting environmental concentrations
+of active substances of plant protection products and transformation products of these
+active substances in soil. \emph{EFSA Journal} \bold{13}(4) 4093
+doi:10.2903/j.efsa.2015.4093
+}
+\description{
+Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the 
+concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the 
+scenario and model adjustment factors from p. 15 and p. 17 are included.
+}
+\examples{
+\dontrun{
+  # This is the code that was used to define the data
+  soil_scenario_data_EFSA_2015 <- data.frame(
+    Zone = rep(c("North", "Central", "South"), 2),
+    Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"),
+    T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8),
+    T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7),
+    Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"),
+    f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011),
+    theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347),
+    rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51),
+    f_sce = c(3, 2, 2, 2, 1.5, 1.5),
+    f_mod = c(2, 2, 2, 4, 4, 4),
+    stringsAsFactors = FALSE,
+    row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS")
+  )
+  save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData')
+}
+
+# And this is the resulting dataframe
+soil_scenario_data_EFSA_2015
+}
+\keyword{datasets}
+