From a76221d87485029444c8e684022ca606a0c7e68d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 Jan 2017 22:41:01 +0100 Subject: Update static docs using pkgdown - Add _pkgdown.yml for a structured function/data reference - Make seealso links active - Make mkinfit calls quiet - Use pkgdown branch from pull request hadley/pkgdown#229 to have topics ordered --- docs/reference/endpoint.html | 170 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 170 insertions(+) create mode 100644 docs/reference/endpoint.html (limited to 'docs/reference/endpoint.html') diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html new file mode 100644 index 0000000..57a7652 --- /dev/null +++ b/docs/reference/endpoint.html @@ -0,0 +1,170 @@ + + + + + + + + +Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm + + + + + + + + + + + + + + + + + + + + + + + + +
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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.

+ + + 
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.

+ + +
+ +
+ + +
+ + + -- cgit v1.2.1