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/GUS.html | 287 ++++++++++++++++++------------------------------ 1 file changed, 109 insertions(+), 178 deletions(-) (limited to 'docs/reference/GUS.html') diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html index e371c1a..dfe3b80 100644 --- a/docs/reference/GUS.html +++ b/docs/reference/GUS.html @@ -1,66 +1,14 @@ - - - - - - - -Groundwater ubiquity score based on Gustafson (1989) — GUS • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Groundwater ubiquity score based on Gustafson (1989) — GUS • pfm - - - - - - - - - - - - - - + + -
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- -
- -
+

Groundwater ubiquity score based on Gustafson (1989)

@@ -113,139 +47,136 @@ the following equation $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$

- 
GUS(...)
-
-# S3 method for numeric
-GUS(DT50, Koc, ...)
-
-# S3 method for chent
-GUS(
-  chent,
-  degradation_value = "DT50ref",
-  lab_field = "laboratory",
-  redox = "aerobic",
-  sorption_value = "Kfoc",
-  degradation_aggregator = geomean,
-  sorption_aggregator = geomean,
-  ...
-)
-
-# S3 method for GUS_result
-print(x, ..., digits = 1)
- -

Arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
...

Included in the generic to allow for further arguments later. Therefore -this also had to be added to the specific methods.

DT50

Half-life of the chemical in soil. Should be a field +

+ 
GUS(...)
+
+# S3 method for numeric
+GUS(DT50, Koc, ...)
+
+# S3 method for chent
+GUS(
+  chent,
+  degradation_value = "DT50ref",
+  lab_field = "laboratory",
+  redox = "aerobic",
+  sorption_value = "Kfoc",
+  degradation_aggregator = geomean,
+  sorption_aggregator = geomean,
+  ...
+)
+
+# S3 method for GUS_result
+print(x, ..., digits = 1)
+
+ +
+

Arguments

+
...
+

Included in the generic to allow for further arguments later. Therefore +this also had to be added to the specific methods.

+ + +
DT50
+

Half-life of the chemical in soil. Should be a field half-life according to Gustafson (1989). However, leaching to the sub-soil can not completely be excluded in field dissipation experiments and Gustafson did not refer to any normalisation procedure, but says the field study should -be conducted under use conditions.

Koc

The sorption constant normalised to organic carbon. Gustafson +be conducted under use conditions.

+ + +
Koc
+

The sorption constant normalised to organic carbon. Gustafson does not mention the nonlinearity of the sorption constant commonly found and usually described by Freundlich sorption, therefore it is unclear at which reference concentration the Koc should be observed -(and if the reference concentration would be in soil or in porewater).

chent

If a chent is given with appropriate information present in its -chyaml field, this information is used, with defaults specified below.

degradation_value

Which of the available degradation values should -be used?

lab_field

Should laboratory or field half-lives be used? This +(and if the reference concentration would be in soil or in porewater).

+ + +
chent
+

If a chent is given with appropriate information present in its +chyaml field, this information is used, with defaults specified below.

+ + +
degradation_value
+

Which of the available degradation values should +be used?

+ + +
lab_field
+

Should laboratory or field half-lives be used? This defaults to lab in this implementation, in order to avoid double-accounting for mobility. If comparability with the original GUS values given by Gustafson (1989) is desired, non-normalised first-order -field half-lives obtained under actual use conditions should be used.

redox

Aerobic or anaerobic degradation data

sorption_value

Which of the available sorption values should be used? +field half-lives obtained under actual use conditions should be used.

+ + +
redox
+

Aerobic or anaerobic degradation data

+ + +
sorption_value
+

Which of the available sorption values should be used? Defaults to Kfoc as this is what is generally available from the European pesticide peer review process. These values generally use a reference concentration of 1 mg/L in porewater, that means they would be expected to -be Koc values at a concentration of 1 mg/L in the water phase.

degradation_aggregator

Function for aggregating half-lives

sorption_aggregator

Function for aggregation Koc values

x

An object of class GUS_result to be printed

digits

The number of digits used in the print method

- -

Value

- -

A list with the DT50 and Koc used as well as the resulting score - of class GUS_result

-

References

+be Koc values at a concentration of 1 mg/L in the water phase.

+ + +
degradation_aggregator
+

Function for aggregating half-lives

+ + +
sorption_aggregator
+

Function for aggregation Koc values

+ +
x
+

An object of class GUS_result to be printed

+ + +
digits
+

The number of digits used in the print method

+ +
+
+

Value

+ + +

A list with the DT50 and Koc used as well as the resulting score + of class GUS_result

+
+
+

References

Gustafson, David I. (1989) Groundwater ubiquity score: a simple method for assessing pesticide leachability. Environmental toxicology and chemistry 8(4) 339–57.

- -
- +

Author

Johannes Ranke

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