From d66bd4aa0bf9c4d9b8793a4e308c9e80691b440f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 12 Nov 2023 21:40:01 +0100 Subject: Enable links to source, upgrade to bootstrap 5 --- docs/reference/endpoint.html | 342 +++++++++++++++++-------------------------- 1 file changed, 137 insertions(+), 205 deletions(-) (limited to 'docs/reference/endpoint.html') diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html index 39071ee..5e038b1 100644 --- a/docs/reference/endpoint.html +++ b/docs/reference/endpoint.html @@ -1,250 +1,182 @@ - - - - - - +Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm + Skip to contents + -Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm +
+
+
+

Retrieve endpoint information from the chyaml field of a chent object

+ Source: R/endpoint.R +
endpoint.Rd
+
- - +
+

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

+ 
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.

-
-
-
-

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 +

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 v1.2.3 From 4079a2c496aa4e8c6dc2a93afedcbedbf7a852b5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 12 Nov 2023 21:59:34 +0100 Subject: Enable markdown and rebuild docs --- DESCRIPTION | 1 + docs/pkgdown.yml | 2 +- docs/reference/EFSA_washoff_2017.html | 8 ++-- docs/reference/FOCUS_GW_scenarios_2012.html | 12 +++--- docs/reference/FOCUS_Step_12_scenarios.html | 6 +-- docs/reference/FOMC_actual_twa.html | 4 +- docs/reference/GUS.html | 6 +-- docs/reference/PEC_soil.html | 40 +++++++++--------- docs/reference/PEC_sw_drainage_UK.html | 10 ++--- docs/reference/PEC_sw_drift.html | 2 +- docs/reference/PEC_sw_exposit_drainage.html | 14 +++---- docs/reference/PEC_sw_exposit_runoff.html | 14 +++---- docs/reference/PEC_sw_focus.html | 28 ++++++------- docs/reference/SFO_actual_twa.html | 4 +- docs/reference/SSLRC_mobility_classification.html | 12 +++--- docs/reference/TOXSWA_cwa.html | 32 +++++++++++++-- docs/reference/TSCF-1.png | Bin 27659 -> 40587 bytes docs/reference/TSCF.html | 6 +-- docs/reference/endpoint.html | 12 +++--- docs/reference/max_twa.html | 8 ++-- docs/reference/perc_runoff_exposit.html | 14 +++---- docs/reference/perc_runoff_reduction_exposit.html | 8 ++-- docs/reference/soil_scenario_data_EFSA_2015.html | 26 ++++++------ docs/reference/soil_scenario_data_EFSA_2017.html | 26 ++++++------ docs/search.json | 2 +- man/EFSA_washoff_2017.Rd | 8 ++-- man/FOCUS_GW_scenarios_2012.Rd | 8 ++-- man/FOCUS_Step_12_scenarios.Rd | 6 +-- man/FOMC_actual_twa.Rd | 4 +- man/GUS.Rd | 6 +-- man/PEC_soil.Rd | 48 +++++++++++----------- man/PEC_sw_drainage_UK.Rd | 12 +++--- man/PEC_sw_drift.Rd | 2 +- man/PEC_sw_exposit_drainage.Rd | 14 +++---- man/PEC_sw_exposit_runoff.Rd | 14 +++---- man/PEC_sw_focus.Rd | 28 ++++++------- man/SFO_actual_twa.Rd | 4 +- man/SSLRC_mobility_classification.Rd | 14 +++---- man/TOXSWA_cwa.Rd | 6 +-- man/TSCF.Rd | 2 +- man/endpoint.Rd | 12 +++--- man/max_twa.Rd | 8 ++-- man/perc_runoff_exposit.Rd | 18 ++++---- man/perc_runoff_reduction_exposit.Rd | 14 +++---- man/soil_scenario_data_EFSA_2015.Rd | 18 ++++---- man/soil_scenario_data_EFSA_2017.Rd | 18 ++++---- 46 files changed, 290 insertions(+), 271 deletions(-) (limited to 'docs/reference/endpoint.html') diff --git a/DESCRIPTION b/DESCRIPTION index a12f90b..a159c56 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -27,4 +27,5 @@ LazyLoad: yes LazyData: yes Encoding: UTF-8 URL: https://pkgdown.jrwb.de/pfm, https://github.com/jranke/pfm +Roxygen: list(markdown = TRUE, r6 = TRUE) RoxygenNote: 7.2.3 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index eeed6da..6571239 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.17.1.1 pkgdown: 2.0.7 pkgdown_sha: ~ articles: {} -last_built: 2023-11-12T20:34Z +last_built: 2023-11-12T20:59Z urls: reference: https://pkgdown.jrwb.de/pfm/reference article: https://pkgdown.jrwb.de/pfm/articles diff --git a/docs/reference/EFSA_washoff_2017.html b/docs/reference/EFSA_washoff_2017.html index 1e292af..b424de9 100644 --- a/docs/reference/EFSA_washoff_2017.html +++ b/docs/reference/EFSA_washoff_2017.html @@ -54,10 +54,10 @@

Source

European Food Safety Authority (2017) EFSA guidance document for - predicting environmental concentrations of active substances of plant - protection products and transformation products of these active substances - in soil. EFSA Journal 15(10) 4982 - doi:10.2903/j.efsa.2017.4982

+predicting environmental concentrations of active substances of plant +protection products and transformation products of these active substances +in soil. EFSA Journal 15(10) 4982 +doi:10.2903/j.efsa.2017.4982

diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 84c2fac..2e9982b 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -1,6 +1,6 @@ -A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012 • pfmA very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012 • pfmProperties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • pfmProperties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • pfmProperties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • pfm