Reorganise repository using standard package layout

16 files changed, 0 insertions, 791 deletions

diff --git a/pkg/man/FOCUS_GW_scenarios_2012.Rd b/pkg/man/FOCUS_GW_scenarios_2012.Rd
deleted file mode 100644
index 3ae151b..0000000
--- a/pkg/man/FOCUS_GW_scenarios_2012.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% 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/pkg/man/GUS.Rd b/pkg/man/GUS.Rd
deleted file mode 100644
index f1f5f28..0000000
--- a/pkg/man/GUS.Rd
+++ /dev/null
@@ -1,81 +0,0 @@
-% 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/pkg/man/PEC_soil.Rd b/pkg/man/PEC_soil.Rd
deleted file mode 100644
index c0b5201..0000000
--- a/pkg/man/PEC_soil.Rd
+++ /dev/null
@@ -1,119 +0,0 @@
-% 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/pkg/man/PEC_sw_drainage_UK.Rd b/pkg/man/PEC_sw_drainage_UK.Rd
deleted file mode 100644
index cb64bde..0000000
--- a/pkg/man/PEC_sw_drainage_UK.Rd
+++ /dev/null
@@ -1,39 +0,0 @@
-% 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/pkg/man/PEC_sw_drift.Rd b/pkg/man/PEC_sw_drift.Rd
deleted file mode 100644
index 20fa921..0000000
--- a/pkg/man/PEC_sw_drift.Rd
+++ /dev/null
@@ -1,45 +0,0 @@
-% 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/pkg/man/PEC_sw_sed.Rd b/pkg/man/PEC_sw_sed.Rd
deleted file mode 100644
index 3140eb0..0000000
--- a/pkg/man/PEC_sw_sed.Rd
+++ /dev/null
@@ -1,42 +0,0 @@
-% 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/pkg/man/SFO_actual_twa.Rd b/pkg/man/SFO_actual_twa.Rd
deleted file mode 100644
index 573ea03..0000000
--- a/pkg/man/SFO_actual_twa.Rd
+++ /dev/null
@@ -1,29 +0,0 @@
-% 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/pkg/man/SSLRC_mobility_classification.Rd b/pkg/man/SSLRC_mobility_classification.Rd
deleted file mode 100644
index 04aa01d..0000000
--- a/pkg/man/SSLRC_mobility_classification.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% 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/pkg/man/TOXSWA_cwa.Rd b/pkg/man/TOXSWA_cwa.Rd
deleted file mode 100644
index de87510..0000000
--- a/pkg/man/TOXSWA_cwa.Rd
+++ /dev/null
@@ -1,58 +0,0 @@
-% 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/pkg/man/drift_data_JKI.Rd b/pkg/man/drift_data_JKI.Rd
deleted file mode 100644
index c193c0d..0000000
--- a/pkg/man/drift_data_JKI.Rd
+++ /dev/null
@@ -1,50 +0,0 @@
-% 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/pkg/man/endpoint.Rd b/pkg/man/endpoint.Rd
deleted file mode 100644
index fd16650..0000000
--- a/pkg/man/endpoint.Rd
+++ /dev/null
@@ -1,75 +0,0 @@
-% 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 \code{\link{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 \code{\link{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/pkg/man/geomean.Rd b/pkg/man/geomean.Rd
deleted file mode 100644
index ed82294..0000000
--- a/pkg/man/geomean.Rd
+++ /dev/null
@@ -1,31 +0,0 @@
-% 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/pkg/man/pfm_degradation.Rd b/pkg/man/pfm_degradation.Rd
deleted file mode 100644
index 9ab1d0a..0000000
--- a/pkg/man/pfm_degradation.Rd
+++ /dev/null
@@ -1,35 +0,0 @@
-% 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/pkg/man/plot.TOXSWA_cwa.Rd b/pkg/man/plot.TOXSWA_cwa.Rd
deleted file mode 100644
index b5f0163..0000000
--- a/pkg/man/plot.TOXSWA_cwa.Rd
+++ /dev/null
@@ -1,42 +0,0 @@
-% 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/pkg/man/read.TOXSWA_cwa.Rd b/pkg/man/read.TOXSWA_cwa.Rd
deleted file mode 100644
index 84ef3da..0000000
--- a/pkg/man/read.TOXSWA_cwa.Rd
+++ /dev/null
@@ -1,56 +0,0 @@
-% 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/pkg/man/soil_scenario_data_EFSA_2015.Rd b/pkg/man/soil_scenario_data_EFSA_2015.Rd
deleted file mode 100644
index b45af4a..0000000
--- a/pkg/man/soil_scenario_data_EFSA_2015.Rd
+++ /dev/null
@@ -1,46 +0,0 @@
-% 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}
-