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| author | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2026-06-22 18:01:11 +0200 |
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| committer | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2026-06-22 18:01:11 +0200 |
| commit | e0c130005ee7adbac9b832ea8157712419d51b7e (patch) | |
| tree | f5c188285ee3abd9edda16a6bb96b6142c80afba /docs/reference/endpoint.md | |
| parent | f8fdbc3237d12d5511058d2c0c40f3e99debe682 (diff) | |
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diff --git a/docs/reference/endpoint.md b/docs/reference/endpoint.md new file mode 100644 index 0000000..62eea9d --- /dev/null +++ b/docs/reference/endpoint.md @@ -0,0 +1,108 @@ +# 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 + +``` r +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`](https://pkgdown.jrwb.de/pfm/reference/geomean.md), 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. |
