From 97d0465a296ef1f5ae4502f9374ae339c0a8148e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 12 Nov 2023 21:10:41 +0100 Subject: Update static docs --- docs/reference/index.html | 365 ++++++++++------------------------------------ 1 file changed, 73 insertions(+), 292 deletions(-) (limited to 'docs/reference/index.html') diff --git a/docs/reference/index.html b/docs/reference/index.html index fed30cc..e5af0b7 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,66 +1,12 @@ - - - - - - - -Function reference • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Function reference • pfm - - - - + + -
-
- -
- -
+

Reference

- - - - - - - - - - -
-

General utility functions

-

Functions that are independent of specific fate modelling areas

+ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+

General utility functions

+

Functions that are independent of specific fate modelling areas

+

geomean()

Calculate the geometric mean

+

one_box()

Create a time series of decline data

+

plot(<one_box>)

Plot time series of decline data

+

sawtooth()

Create decline time series for multiple applications

+

twa()

Calculate a time weighted average concentration

+

max_twa()

The maximum time weighted average concentration for a moving window

+

pfm_degradation()

Calculate a time course of relative concentrations based on an mkinmod model

+

SFO_actual_twa()

Actual and maximum moving window time average concentrations for SFO kinetics

+

FOMC_actual_twa()

Actual and maximum moving window time average concentrations for FOMC kinetics

-

set_nd_nq() set_nd_nq_focus()

-

Set non-detects and unquantified values in residue series without replicates

+
+

reexports set_nd_nq set_nd_nq_focus

+

Objects exported from other packages

TSCF()

Estimation of the transpiration stream concentration factor

-

Predicted environmental concentrations in soil

+
+

Predicted environmental concentrations in soil

+

PEC_soil()

Calculate predicted environmental concentrations in soil

+

PEC_soil_mets()

Calculate initial and accumulation PEC soil for a set of metabolites

+

soil_scenario_data_EFSA_2015

Properties of the predefined scenarios from the EFSA guidance from 2015

+

soil_scenario_data_EFSA_2017

Properties of the predefined scenarios from the EFSA guidance from 2017

+

PEC_FOMC_accu_rel()

Get the relative accumulation of an FOMC model over multiples of an interval

+

EFSA_washoff_2017

Subset of EFSA crop washoff default values

-

Predicted environmental concentrations in groundwater

+
+

Predicted environmental concentrations in groundwater

+

FOCUS_GW_scenarios_2012

A very small subset of the FOCUS Groundwater scenario definitions

+

EFSA_GW_interception_2014

Subset of EFSA crop interception default values for groundwater modelling

-

Predicted environmental concentrations in surface water

+
+

Predicted environmental concentrations in surface water

+

PEC_sw_drift()

Calculate predicted environmental concentrations in surface water due to drift

+

drift_data_JKI

Deposition from spray drift expressed as percent of the applied dose as published by the JKI

+

PEC_sw_drainage_UK()

Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method

+

PEC_sw_sed()

Calculate predicted environmental concentrations in sediment from surface water concentrations

+

PEC_sw_focus()

Calculate PEC surface water at FOCUS Step 1

+

chent_focus_sw()

Create a chemical compound object for FOCUS Step 1 calculations

+

FOCUS_Step_12_scenarios

Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator

+

PEC_sw_exposit_drainage()

Calculate PEC surface water due to drainage as in Exposit 3

+

PEC_sw_exposit_runoff()

Calculate PEC surface water due to runoff and erosion as in Exposit 3

+

perc_runoff_exposit

Runoff loss percentages as used in Exposit 3

+

perc_runoff_reduction_exposit

Runoff reduction percentages as used in Exposit

+

TOXSWA_cwa

R6 class for holding TOXSWA water concentration data and associated statistics

+

read.TOXSWA_cwa()

Read TOXSWA surface water concentrations

+

plot(<TOXSWA_cwa>)

Plot TOXSWA surface water concentrations

-

Classifications and indicators

-

Evaluating environmental fate properties

+
+

Classifications and indicators

+

Evaluating environmental fate properties

+

SSLRC_mobility_classification()

Determine the SSLRC mobility classification for a chemical substance from its Koc

+

GUS() print(<GUS_result>)

Groundwater ubiquity score based on Gustafson (1989)

-

Work with chent objects containing relevant information

+
+

Work with chent objects containing relevant information

+

endpoint() soil_DT50() soil_Kfoc() soil_N() soil_sorption()

Retrieve endpoint information from the chyaml field of a chent object

-

Utilities

+
+

Utilities

+

get_vertex()

Fit a parabola through three points

- +
+
-
-
-

Developed by Johannes Ranke.

+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.6.1.

+

Site built with pkgdown 2.0.7.

-
-
+
- - + + -- cgit v1.2.1 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/index.html | 517 +++++++++++++++++++++++++++------------------- 1 file changed, 301 insertions(+), 216 deletions(-) (limited to 'docs/reference/index.html') diff --git a/docs/reference/index.html b/docs/reference/index.html index e5af0b7..f41d356 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,241 +1,326 @@ -Function reference • pfmFunction reference • pfm + + Skip to contents -
-
-
-
-

Reference

+ +
+
+
+
+

Function reference

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-

General utility functions

-

Functions that are independent of specific fate modelling areas

-
-

geomean()

-

Calculate the geometric mean

-

one_box()

-

Create a time series of decline data

-

plot(<one_box>)

-

Plot time series of decline data

-

sawtooth()

-

Create decline time series for multiple applications

-

twa()

-

Calculate a time weighted average concentration

-

max_twa()

-

The maximum time weighted average concentration for a moving window

-

pfm_degradation()

-

Calculate a time course of relative concentrations based on an mkinmod model

-

SFO_actual_twa()

-

Actual and maximum moving window time average concentrations for SFO kinetics

-

FOMC_actual_twa()

-

Actual and maximum moving window time average concentrations for FOMC kinetics

-

reexports set_nd_nq set_nd_nq_focus

-

Objects exported from other packages

-

TSCF()

-

Estimation of the transpiration stream concentration factor

-

Predicted environmental concentrations in soil

-

-
-

PEC_soil()

-

Calculate predicted environmental concentrations in soil

-

PEC_soil_mets()

-

Calculate initial and accumulation PEC soil for a set of metabolites

-

soil_scenario_data_EFSA_2015

-

Properties of the predefined scenarios from the EFSA guidance from 2015

-

soil_scenario_data_EFSA_2017

-

Properties of the predefined scenarios from the EFSA guidance from 2017

-

PEC_FOMC_accu_rel()

-

Get the relative accumulation of an FOMC model over multiples of an interval

-

EFSA_washoff_2017

-

Subset of EFSA crop washoff default values

-

Predicted environmental concentrations in groundwater

-

-
-

FOCUS_GW_scenarios_2012

-

A very small subset of the FOCUS Groundwater scenario definitions

-

EFSA_GW_interception_2014

-

Subset of EFSA crop interception default values for groundwater modelling

-

Predicted environmental concentrations in surface water

-

-
-

PEC_sw_drift()

-

Calculate predicted environmental concentrations in surface water due to drift

-

drift_data_JKI

-

Deposition from spray drift expressed as percent of the applied dose as -published by the JKI

-

PEC_sw_drainage_UK()

-

Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method

-

PEC_sw_sed()

-

Calculate predicted environmental concentrations in sediment from surface -water concentrations

-

PEC_sw_focus()

-

Calculate PEC surface water at FOCUS Step 1

-

chent_focus_sw()

-

Create a chemical compound object for FOCUS Step 1 calculations

-

FOCUS_Step_12_scenarios

-

Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator

-

PEC_sw_exposit_drainage()

-

Calculate PEC surface water due to drainage as in Exposit 3

-

PEC_sw_exposit_runoff()

-

Calculate PEC surface water due to runoff and erosion as in Exposit 3

-

perc_runoff_exposit

-

Runoff loss percentages as used in Exposit 3

-

perc_runoff_reduction_exposit

-

Runoff reduction percentages as used in Exposit

-

TOXSWA_cwa

-

R6 class for holding TOXSWA water concentration data and associated statistics

-

read.TOXSWA_cwa()

-

Read TOXSWA surface water concentrations

-

plot(<TOXSWA_cwa>)

-

Plot TOXSWA surface water concentrations

-

Classifications and indicators

-

Evaluating environmental fate properties

-
-

SSLRC_mobility_classification()

-

Determine the SSLRC mobility classification for a chemical substance from its Koc

-

GUS() print(<GUS_result>)

-

Groundwater ubiquity score based on Gustafson (1989)

-

Work with chent objects containing relevant information

-

-
-

endpoint() soil_DT50() soil_Kfoc() soil_N() soil_sorption()

-

Retrieve endpoint information from the chyaml field of a chent object

-

Utilities

-

-
-

get_vertex()

-

Fit a parabola through three points

- - -
+
+

General utility functions

+ +

Functions that are independent of specific fate modelling areas

+ + +
+ + + + +
+ + geomean() +
+
Calculate the geometric mean
+
+ + one_box() +
+
Create a time series of decline data
+
+ + plot(<one_box>) +
+
Plot time series of decline data
+
+ + sawtooth() +
+
Create decline time series for multiple applications
+
+ + twa() +
+
Calculate a time weighted average concentration
+
+ + max_twa() +
+
The maximum time weighted average concentration for a moving window
+
+ + pfm_degradation() +
+
Calculate a time course of relative concentrations based on an mkinmod model
+
+ + SFO_actual_twa() +
+
Actual and maximum moving window time average concentrations for SFO kinetics
+
+ + FOMC_actual_twa() +
+
Actual and maximum moving window time average concentrations for FOMC kinetics
+
+ + reexports set_nd_nq set_nd_nq_focus +
+
Objects exported from other packages
+
+ + TSCF() +
+
Estimation of the transpiration stream concentration factor
+
+

Predicted environmental concentrations in soil

+ + + + +
+ + + + +
+ + PEC_soil() +
+
Calculate predicted environmental concentrations in soil
+
+ + PEC_soil_mets() +
+
Calculate initial and accumulation PEC soil for a set of metabolites
+
+ + soil_scenario_data_EFSA_2015 +
+
Properties of the predefined scenarios from the EFSA guidance from 2015
+
+ + soil_scenario_data_EFSA_2017 +
+
Properties of the predefined scenarios from the EFSA guidance from 2017
+
+ + PEC_FOMC_accu_rel() +
+
Get the relative accumulation of an FOMC model over multiples of an interval
+
+ + EFSA_washoff_2017 +
+
Subset of EFSA crop washoff default values
+
+

Predicted environmental concentrations in groundwater

+ + + + +
+ + + + +
+ + FOCUS_GW_scenarios_2012 +
+
A very small subset of the FOCUS Groundwater scenario definitions
+
+ + EFSA_GW_interception_2014 +
+
Subset of EFSA crop interception default values for groundwater modelling
+
+

Predicted environmental concentrations in surface water

+ + + + +
+ + + + +
+ + PEC_sw_drift() +
+
Calculate predicted environmental concentrations in surface water due to drift
+
+ + drift_data_JKI +
+
Deposition from spray drift expressed as percent of the applied dose as +published by the JKI
+
+ + PEC_sw_drainage_UK() +
+
Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method
+
+ + PEC_sw_sed() +
+
Calculate predicted environmental concentrations in sediment from surface +water concentrations
+
+ + PEC_sw_focus() +
+
Calculate PEC surface water at FOCUS Step 1
+
+ + chent_focus_sw() +
+
Create a chemical compound object for FOCUS Step 1 calculations
+
+ + FOCUS_Step_12_scenarios +
+
Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator
+
+ + PEC_sw_exposit_drainage() +
+
Calculate PEC surface water due to drainage as in Exposit 3
+
+ + PEC_sw_exposit_runoff() +
+
Calculate PEC surface water due to runoff and erosion as in Exposit 3
+
+ + perc_runoff_exposit +
+
Runoff loss percentages as used in Exposit 3
+
+ + perc_runoff_reduction_exposit +
+
Runoff reduction percentages as used in Exposit
+
+ + TOXSWA_cwa +
+
R6 class for holding TOXSWA water concentration data and associated statistics
+
+ + read.TOXSWA_cwa() +
+
Read TOXSWA surface water concentrations
+
+ + plot(<TOXSWA_cwa>) +
+
Plot TOXSWA surface water concentrations
+
+

Classifications and indicators

+ +

Evaluating environmental fate properties

+ + +
+ + + + +
+ + SSLRC_mobility_classification() +
+
Determine the SSLRC mobility classification for a chemical substance from its Koc
+
+ + GUS() print(<GUS_result>) +
+
Groundwater ubiquity score based on Gustafson (1989)
+
+

Work with chent objects containing relevant information

+ + + + +
+ + + + +
+ + endpoint() soil_DT50() soil_Kfoc() soil_N() soil_sorption() +
+
Retrieve endpoint information from the chyaml field of a chent object
+
+

Utilities

+ + + + +
+ + + +
+ + get_vertex() +
+
Fit a parabola through three points
+
+
-
- -- cgit v1.2.1