Reorganise repository using standard package layout

1 files changed, 0 insertions, 110 deletions

diff --git a/pkg/R/endpoint.R b/pkg/R/endpoint.R
deleted file mode 100644
index 314acd2..0000000
--- a/pkg/R/endpoint.R
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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)
-{
-  if (!is(chent, "chent")) {
-    stop("Please supply a chent object as created using the package 'chents' available from jrwb.de")
-  }
-  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)
-}