From d81550d0cccae824cc748de48e7fd50ea8d8033a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Apr 2020 18:02:18 +0200 Subject: Make na.rm = FALSE the default for geomean() This makes more sense and is in line with mean() from base R. Adapt tests and update docs. --- docs/reference/endpoint.html | 62 ++++++++++++++++++++++++++------------------ 1 file changed, 37 insertions(+), 25 deletions(-) (limited to 'docs/reference/endpoint.html') diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html index 99e407c..39071ee 100644 --- a/docs/reference/endpoint.html +++ b/docs/reference/endpoint.html @@ -8,11 +8,13 @@ Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm + + @@ -32,8 +34,8 @@ - + + @@ -85,7 +88,6 @@ this function." /> Reference - @@ -107,32 +109,46 @@ this function." />
-

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)
+    
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)

-    
+soil_sorption(
+  chent,
+  values = c("Kfoc", "N"),
+  aggregators = c(Kfoc = geomean, Koc = geomean, N = mean),
+  signif = c(Kfoc = 3, N = 3),
+  raw = FALSE
+)
+

Arguments

@@ -185,7 +201,7 @@ about precision?

A named vector of aggregator functions to be used
- +

Value

The result from applying the aggregator function to @@ -193,25 +209,21 @@ about precision?

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