diff options
| -rw-r--r-- | pkg/DESCRIPTION | 2 | ||||
| -rw-r--r-- | pkg/NAMESPACE | 1 | ||||
| -rw-r--r-- | pkg/R/PEC_sw_sed.R | 50 | ||||
| -rw-r--r-- | pkg/man/PEC_sw_sed.Rd | 42 | ||||
| -rw-r--r-- | pkg/tests/testthat/test_PEC_sed.R | 9 |
5 files changed, 103 insertions, 1 deletions
diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION index 9c4b276..39b8c20 100644 --- a/pkg/DESCRIPTION +++ b/pkg/DESCRIPTION @@ -2,7 +2,7 @@ Package: pfm Type: Package Title: Utilities for pesticide fate modelling Version: 0.2-1 -Date: 2015-06-11 +Date: 2015-06-12 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph")) Description: Utilities for simple PEC calculations and for dealing with data diff --git a/pkg/NAMESPACE b/pkg/NAMESPACE index 771739a..a1796f5 100644 --- a/pkg/NAMESPACE +++ b/pkg/NAMESPACE @@ -5,6 +5,7 @@ export(PEC_soil) export(PEC_sw_drainage_UK_ini) export(PEC_sw_drift) export(PEC_sw_drift_ini) +export(PEC_sw_sed) export(SFO_actual_twa) export(SSLRC_mobility_classification) export(TOXSWA_cwa) diff --git a/pkg/R/PEC_sw_sed.R b/pkg/R/PEC_sw_sed.R new file mode 100644 index 0000000..56396e8 --- /dev/null +++ b/pkg/R/PEC_sw_sed.R @@ -0,0 +1,50 @@ +# Copyright (C) 2015 Johannes Ranke +# Contact: jranke@uni-bremen.de +# This file is part of the R package pfm + +# This program is free software: you can redistribute it and/or modify it under +# the terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see <http://www.gnu.org/licenses/> + +#' Calculate initial predicted environmental concentrations in sediment from +#' surface water concentrations +#' +#' The method 'percentage' is equivalent to what is used in the CRD spreadsheet +#' PEC calculator +#' +#' @param PEC_sw Numeric vector or matrix of surface water concentrations in µg/L for +#' which the corresponding sediment concentration is to be estimated +#' @param percentage The percentage in sediment, used for the percentage method +#' @param method The method used for the calculation +#' @param sediment_depth Depth of the sediment layer +#' @param water_depth Depth of the water body in cm +#' @param sediment_density The density of the sediment in L/kg (equivalent to +#' g/cm3) +#' @param PEC_sed_units The units of the estimated sediment PEC value +#' @return The predicted concentration in sediment +#' @export +#' @author Johannes Ranke +#' @examples +#' PEC_sw_sed(PEC_sw_drift_ini(100, distances = 1), percentage = 50) +PEC_sw_sed <- function(PEC_sw, percentage = 100, method = "percentage", + sediment_depth = 5, water_depth = 30, + sediment_density = 1.3, + PEC_sed_units = c("\u00B5g/kg", "mg/kg")) +{ + method = match.arg(method) + PEC_sed_units = match.arg(PEC_sed_units) + if (method == "percentage") { + PEC_sed = PEC_sw * (percentage/100) * (water_depth / sediment_depth) * (1 / sediment_density) + if (PEC_sed_units == "mg/kg") PEC_sed <- PEC_sed / 1000 + } + return(PEC_sed) +} 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/tests/testthat/test_PEC_sed.R b/pkg/tests/testthat/test_PEC_sed.R new file mode 100644 index 0000000..d83be0f --- /dev/null +++ b/pkg/tests/testthat/test_PEC_sed.R @@ -0,0 +1,9 @@ +context("Simple PEC sediment calculations") + +test_that("PEC_sw_sed calculates correctly using the percentage method", { + # Application of 100 g/ha, 1 m spray drift distance (2.77% drift input), 50% in sediment, + # default assumptions of CRD spreadsheet (5 cm sediment depth, 1.3 kg/L sediment density) + # Reference value calculated with CRD spreadsheet + PEC_sw_100_1_m <- PEC_sw_drift_ini(100, distances = 1) + expect_equivalent(round(PEC_sw_sed(PEC_sw_100_1_m, percentage = 50), 3), 2.131) +}) |