pfm 0.3-1

Retrieve endpoint information from the chyaml field of a chent object

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 = rep(3, length(values)), 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.

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.

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.