From aed160d7f0eaf5865e2bd9bf6c4b1c9d7b13d911 Mon Sep 17 00:00:00 2001 From: Ranke Johannes Date: Wed, 31 Jan 2024 13:16:17 +0100 Subject: Reorganise data generation - Use inst/data_generation for R code generating data as in some of my other packages - data/*.RData files were checked using https://github.com/jranke/dotfiles/blob/main/bin/rda_diff contents were not changed - Remove ChangeLog, the history is in the git logs - Update docs and some links contained therein - use \doi{} markup - Move logs to log directory --- docs/reference/endpoint.html | 295 ++++++++++++++++--------------------------- 1 file changed, 112 insertions(+), 183 deletions(-) (limited to 'docs/reference/endpoint.html') diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html index 39071ee..8ca3467 100644 --- a/docs/reference/endpoint.html +++ b/docs/reference/endpoint.html @@ -1,67 +1,15 @@ - - - - - - - -Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm - - - - - - - - - - - - - - + + -
-
- -
- -
+

Retrieve endpoint information from the chyaml field of a chent object

@@ -115,136 +49,131 @@ 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 +

+ 
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 +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

- +
+
+

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