endpoint: Retrieve endpoint information from the chyaml field of a...

In jranke/pfm: Utilities for Pesticide Fate Modelling

Retrieve endpoint information from the chyaml field of a chent object

Description

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

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.

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.

jranke/pfm documentation built on Nov. 17, 2024, 6:42 a.m.