Retrieve endpoint information from the chyaml field of a chent object

R6 class objects of class 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.

Usage

endpoint(
  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
)

soil_DT50(
  chent,
  aggregator = geomean,
  signif = 3,
  lab_field = "laboratory",
  value = "DT50ref",
  redox = "aerobic",
  raw = FALSE
)

soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", raw = FALSE)

soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)

soil_sorption(
  chent,
  values = c("Kfoc", "N"),
  aggregators = c(Kfoc = geomean, Koc = geomean, N = mean),
  signif = c(Kfoc = 3, N = 3),
  raw = FALSE
)

Arguments

chent: The chent object to get the information from
medium: The medium for which information is sought
type: The information type
lab_field: If not NA, do we want laboratory or field endpoints
redox: If not NA, are we looking for aerobic or anaerobic data
value: The name of the value we want. The list given in the usage section is not exclusive
aggregator: The aggregator function. Can be mean, geomean, or identity, for example.
raw: Should the number(s) be returned as stored in the chent object (could be a character value) to retain original information about precision?
signif: How many significant digits do we want
values: The values to be returned
aggregators: A named vector of aggregator functions to be used

Value

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.

Details

The functions soil_* are functions to extract soil specific endpoints. For the Freundlich exponent, the capital letter N is used in order to facilitate dealing with such data in R. In pesticide fate modelling, this exponent is often called 1/n.