diff options
| -rw-r--r-- | pkg/DESCRIPTION | 6 | ||||
| -rw-r--r-- | pkg/NAMESPACE | 3 | ||||
| -rw-r--r-- | pkg/R/PEC_soil.R | 15 | ||||
| -rw-r--r-- | pkg/man/PEC_soil_product.Rd | 24 | ||||
| -rw-r--r-- | pkg/man/pfm_ai.Rd | 24 | ||||
| -rw-r--r-- | pkg/man/pfm_chent.Rd | 35 | ||||
| -rw-r--r-- | pkg/man/pfm_product.Rd | 26 | ||||
| -rw-r--r-- | pkg/tests/testthat/test_PEC_soil.R | 4 |
8 files changed, 43 insertions, 94 deletions
diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION index 247df20..39d3927 100644 --- a/pkg/DESCRIPTION +++ b/pkg/DESCRIPTION @@ -1,8 +1,8 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling -Version: 0.2-3.900 -Date: 2015-08-26 +Version: 0.2-4 +Date: 2015-09-11 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph")) Description: Utilities for simple calculations of predicted environmental @@ -10,7 +10,7 @@ Description: Utilities for simple calculations of predicted environmental fate modelling software packages. Depends: R6, mkin Imports: graphics -Suggests: testthat +Suggests: testthat, chents License: GPL LazyLoad: yes LazyData: yes diff --git a/pkg/NAMESPACE b/pkg/NAMESPACE index 2b7f1d6..a1c5df2 100644 --- a/pkg/NAMESPACE +++ b/pkg/NAMESPACE @@ -11,10 +11,7 @@ export(SFO_actual_twa) export(SSLRC_mobility_classification) export(TOXSWA_cwa) export(geomean) -export(pfm_ai) -export(pfm_chent) export(pfm_degradation) -export(pfm_product) export(read.TOXSWA_cwa) import(graphics) import(mkin) diff --git a/pkg/R/PEC_soil.R b/pkg/R/PEC_soil.R index 3c3ae15..fff1f20 100644 --- a/pkg/R/PEC_soil.R +++ b/pkg/R/PEC_soil.R @@ -44,12 +44,25 @@ PEC_soil <- function(rate, rate_units = "g/ha", interception = 0, return(PEC_soil) } +if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_type", "TP_identifier")) #' Calculate predicted environmental concentrations in soil for a product #' #' Calculates long term accumulation PEC values #' -#' @export +#' @param product An object of class pp +#' @param rate Application rate in units specified below +#' @param rate_units Defaults to g/ha +#' @param interception The fraction of the application rate that does not reach the soil +#' @param mixing_depth Mixing depth in cm +#' @param tillage_depth Periodic (see interval) deeper mixing in cm +#' @param interval Period of the deeper mixing, defaults to 365, which is a year if +#' rate units are in days +#' @param bulk_density Bulk density of the soil. Defaults to 1.5 kg/L, or 1500 kg/m3 +#' @param PEC_units Requested units for the calculated PEC. Only mg/kg currently supported +#' @return A data frame with compound names, and initial, plateau maximum, plateau minimum (background) +#' and long term maximum predicted concentrations in soil +#' @export PEC_soil_product #' @author Johannes Ranke PEC_soil_product <- function(product, rate, rate_units = "L/ha", interception = 0, mixing_depth = 5, tillage_depth = 20, diff --git a/pkg/man/PEC_soil_product.Rd b/pkg/man/PEC_soil_product.Rd index b708366..28cb5fd 100644 --- a/pkg/man/PEC_soil_product.Rd +++ b/pkg/man/PEC_soil_product.Rd @@ -8,6 +8,30 @@ PEC_soil_product(product, rate, rate_units = "L/ha", interception = 0, mixing_depth = 5, tillage_depth = 20, interval = 365, bulk_density = 1.5, PEC_units = "mg/kg") } +\arguments{ +\item{product}{An object of class pp} + +\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{tillage_depth}{Periodic (see interval) deeper mixing in cm} + +\item{interval}{Period of the deeper mixing, defaults to 365, which is a year if +rate units are in days} + +\item{bulk_density}{Bulk density of the soil. Defaults to 1.5 kg/L, or 1500 kg/m3} + +\item{PEC_units}{Requested units for the calculated PEC. Only mg/kg currently supported} +} +\value{ +A data frame with compound names, and initial, plateau maximum, plateau minimum (background) + and long term maximum predicted concentrations in soil +} \description{ Calculates long term accumulation PEC values } diff --git a/pkg/man/pfm_ai.Rd b/pkg/man/pfm_ai.Rd deleted file mode 100644 index 20c5acd..0000000 --- a/pkg/man/pfm_ai.Rd +++ /dev/null @@ -1,24 +0,0 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/pfm_chent.R -\docType{class} -\name{pfm_ai} -\alias{pfm_ai} -\title{R6 class for holding active ingredients} -\format{An \code{\link{R6Class}} generator object.} -\usage{ -pfm_ai -} -\description{ -An R6 class for holding information about active ingredients -} -\section{Fields}{ - -\describe{ -\item{\code{iso}}{ISO common name} -}} -\examples{ -atrazine <- pfm_ai("atrazine", smiles = "Clc1nc(nc(n1)NC(C)C)NCC", mw = 215.68) -print(atrazine) -} -\keyword{data} - diff --git a/pkg/man/pfm_chent.Rd b/pkg/man/pfm_chent.Rd deleted file mode 100644 index f72d038..0000000 --- a/pkg/man/pfm_chent.Rd +++ /dev/null @@ -1,35 +0,0 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/pfm_chent.R -\docType{class} -\name{pfm_chent} -\alias{pfm_chent} -\title{R6 class for holding a chemical entity} -\format{An \code{\link{R6Class}} generator object} -\usage{ -pfm_chent -} -\description{ -An R6 class for holding information about a chemical entity that is useful -for fate modelling -} -\section{Fields}{ - -\describe{ -\item{\code{acronym}}{Acronym for local use} - -\item{\code{smiles}}{SMILES code} - -\item{\code{mw}}{Molecular weight} - -\item{\code{main_source}}{Main source of information} - -\item{\code{transformations}}{} - -\item{\code{sorption_endpoints}}{} -}} -\examples{ -atrazine <- pfm_chent("atrazine", smiles = "Clc1nc(nc(n1)NC(C)C)NCC", mw = 215.68) -print(atrazine) -} -\keyword{data} - diff --git a/pkg/man/pfm_product.Rd b/pkg/man/pfm_product.Rd deleted file mode 100644 index 41ea4aa..0000000 --- a/pkg/man/pfm_product.Rd +++ /dev/null @@ -1,26 +0,0 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/pfm_chent.R -\docType{class} -\name{pfm_product} -\alias{pfm_product} -\title{R6 class for holding a product with at least one active ingredient} -\format{An \code{\link{R6Class}} generator object.} -\usage{ -pfm_product -} -\description{ -An R6 class for holding information about a product with at least one active ingredient -} -\section{Fields}{ - -\describe{ -\item{\code{name}}{The name of the product} - -\item{\code{ais}}{A list of active ingredients} - -\item{\code{concentrations}}{The concentration of the ais} - -\item{\code{concentration_units}}{Defaults to g/L} -}} -\keyword{data} - diff --git a/pkg/tests/testthat/test_PEC_soil.R b/pkg/tests/testthat/test_PEC_soil.R index 7901b69..27b2eb7 100644 --- a/pkg/tests/testthat/test_PEC_soil.R +++ b/pkg/tests/testthat/test_PEC_soil.R @@ -1,5 +1,5 @@ -library(mkin) -context("Setting up kinetic degradation models") +library(pfm) +context("Simple PEC soil calculations") test_that("PEC_soil calculates correctly", { # Application of 100 g/ha gives 0.133 mg/kg under default assumptions |