Merge branch 'master' into pfm_chent

Conflicts:
	pkg/DESCRIPTION
	pkg/NAMESPACE

8 files changed, 302 insertions, 0 deletions

diff --git a/pkg/man/PEC_sw_drainage_UK_ini.Rd b/pkg/man/PEC_sw_drainage_UK_ini.Rd
new file mode 100644
index 0000000..1b2009d
--- /dev/null
+++ b/pkg/man/PEC_sw_drainage_UK_ini.Rd
@@ -0,0 +1,40 @@
+% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Please edit documentation in R/PEC_sw_drainage_UK.R
+\name{PEC_sw_drainage_UK_ini}
+\alias{PEC_sw_drainage_UK_ini}
+\title{Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method}
+\usage{
+PEC_sw_drainage_UK_ini(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 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_ini(150, Koc = 100)
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/pkg/man/PEC_sw_drift.Rd b/pkg/man/PEC_sw_drift.Rd
new file mode 100644
index 0000000..20299a5
--- /dev/null
+++ b/pkg/man/PEC_sw_drift.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2 (4.1.0.9001): 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_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_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_drift_ini.Rd b/pkg/man/PEC_sw_drift_ini.Rd
new file mode 100644
index 0000000..0bcbf97
--- /dev/null
+++ b/pkg/man/PEC_sw_drift_ini.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Please edit documentation in R/PEC_sw_drift_ini.R
+\name{PEC_sw_drift_ini}
+\alias{PEC_sw_drift_ini}
+\title{Calculate initial predicted environmental concentrations in surface water due to drift}
+\usage{
+PEC_sw_drift_ini(rate, applications = 1, water_depth = 30,
+  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_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_ini(100)
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/pkg/man/PEC_sw_sed.Rd b/pkg/man/PEC_sw_sed.Rd
new file mode 100644
index 0000000..ee496d1
--- /dev/null
+++ b/pkg/man/PEC_sw_sed.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Please edit documentation in R/PEC_sw_sed.R
+\name{PEC_sw_sed}
+\alias{PEC_sw_sed}
+\title{Calculate initial 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_ini(100, distances = 1), percentage = 50)
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/pkg/man/SFO_actual_twa.Rd b/pkg/man/SFO_actual_twa.Rd
new file mode 100644
index 0000000..967b60f
--- /dev/null
+++ b/pkg/man/SFO_actual_twa.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2 (4.1.0.9001): 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
new file mode 100644
index 0000000..62a345b
--- /dev/null
+++ b/pkg/man/SSLRC_mobility_classification.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2 (4.1.0.9001): 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/drift_data_JKI.Rd b/pkg/man/drift_data_JKI.Rd
new file mode 100644
index 0000000..a2bbb77
--- /dev/null
+++ b/pkg/man/drift_data_JKI.Rd
@@ -0,0 +1,46 @@
+% Generated by roxygen2 (4.1.0.9001): 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 früh, spät).}
+\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 früh", "Obstbau spät")
+  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")
+}
+}
+\keyword{datasets}
+
diff --git a/pkg/man/pfm_degradation.Rd b/pkg/man/pfm_degradation.Rd
new file mode 100644
index 0000000..b875434
--- /dev/null
+++ b/pkg/man/pfm_degradation.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2 (4.1.0.9001): 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{
+pfm_degradation("SFO", DT50 = 10)
+}
+\author{
+Johannes Ranke
+}
+