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#' Retrieve endpoint information from the chyaml field of a chent object
#'
#' 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.
#'
#' 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.
#'
#' @import chents
#' @export
#' @param chent The \code{\link{chent}} object to get the information from
#' @param medium The medium for which information is sought
#' @param type The information type
#' @param lab_field If not NA, do we want laboratory or field endpoints
#' @param redox If not NA, are we looking for aerobic or anaerobic data
#' @param value The name of the value we want. The list given in the
#' usage section is not exclusive
#' @param aggregator The aggregator function. Can be mean,
#' \code{\link{geomean}}, or identity, for example.
#' @param raw Should the number(s) be returned as stored in the chent
#' object (could be a character value) to retain original information
#' about precision?
#' @param signif How many significant digits do we want
#' @return 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.
#'
endpoint <- function(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)
{
ep_list <- chent$chyaml[[medium]][[type]]
if (!is.na(lab_field[1])) {
ep_list <- ep_list[[lab_field]]
}
if (!is.na(redox[1])) {
ep_list <- ep_list[[redox]]
}
values <- ep_list$data[[value]]
if (raw) return(values)
else return(signif(aggregator(as.numeric(values)), signif))
}
#' @inheritParams endpoint
#' @rdname endpoint
#' @export
soil_DT50 <- function(chent, aggregator = geomean, signif = 3,
lab_field = "laboratory", value = "DT50ref",
redox = "aerobic", raw = FALSE) {
ep <- endpoint(chent, medium = "soil", type = "degradation",
lab_field = "laboratory", redox = redox,
signif = signif,
value = value, aggregator = aggregator, raw = raw)
return(ep)
}
#' @inheritParams endpoint
#' @rdname endpoint
#' @export
soil_Kfoc <- function(chent, aggregator = geomean, signif = 3,
value = "Kfoc", raw = FALSE) {
ep <- endpoint(chent, medium = "soil", type = "sorption",
signif = signif,
value = value, aggregator = aggregator, raw = raw)
return(ep)
}
#' @inheritParams endpoint
#' @rdname endpoint
#' @export
soil_N <- function(chent, aggregator = mean, signif = 3, raw = FALSE) {
ep <- endpoint(chent, medium = "soil", type = "sorption",
signif = signif,
value = "N", aggregator = aggregator, raw = raw)
return(ep)
}
#' @inheritParams endpoint
#' @rdname endpoint
#' @param values The values to be returned
#' @param aggregators A named vector of aggregator functions to be used
#' @export
soil_sorption <- function(chent, values = c("Kfoc", "N"),
aggregators = c(Kfoc = geomean, Koc = geomean, N = mean),
signif = c(Kfoc = 3, N = 3),
raw = FALSE) {
res <- sapply(values,
function(x) {
endpoint(chent, medium = "soil", type = "sorption",
signif = signif[[x]],
value = x, aggregator = aggregators[[x]], raw = raw)
}
)
return(res)
}
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