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/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..3d660d3 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,66 +1,12 @@ - - - - - - - -Function reference • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Function reference • pfm - - - - + + -
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Reference

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General utility functions

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Functions that are independent of specific fate modelling areas

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General utility functions

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Functions that are independent of specific fate modelling areas

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geomean()

Calculate the geometric mean

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one_box()

Create a time series of decline data

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plot(<one_box>)

Plot time series of decline data

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sawtooth()

Create decline time series for multiple applications

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twa()

Calculate a time weighted average concentration

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max_twa()

The maximum time weighted average concentration for a moving window

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pfm_degradation()

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

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SFO_actual_twa()

Actual and maximum moving window time average concentrations for SFO kinetics

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FOMC_actual_twa()

Actual and maximum moving window time average concentrations for FOMC kinetics

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set_nd_nq() set_nd_nq_focus()

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

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reexports set_nd_nq set_nd_nq_focus

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Objects exported from other packages

TSCF()

Estimation of the transpiration stream concentration factor

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Predicted environmental concentrations in soil

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Predicted environmental concentrations in soil

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PEC_soil()

Calculate predicted environmental concentrations in soil

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PEC_soil_mets()

Calculate initial and accumulation PEC soil for a set of metabolites

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soil_scenario_data_EFSA_2015

Properties of the predefined scenarios from the EFSA guidance from 2015

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soil_scenario_data_EFSA_2017

Properties of the predefined scenarios from the EFSA guidance from 2017

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PEC_FOMC_accu_rel()

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

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EFSA_washoff_2017

Subset of EFSA crop washoff default values

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Predicted environmental concentrations in groundwater

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Predicted environmental concentrations in groundwater

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FOCUS_GW_scenarios_2012

A very small subset of the FOCUS Groundwater scenario definitions

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EFSA_GW_interception_2014

Subset of EFSA crop interception default values for groundwater modelling

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Predicted environmental concentrations in surface water

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Predicted environmental concentrations in surface water

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PEC_sw_drift()

Calculate predicted environmental concentrations in surface water due to drift

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drift_data_JKI

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

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PEC_sw_drainage_UK()

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

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PEC_sw_sed()

Calculate predicted environmental concentrations in sediment from surface water concentrations

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PEC_sw_focus()

Calculate PEC surface water at FOCUS Step 1

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chent_focus_sw()

Create a chemical compound object for FOCUS Step 1 calculations

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FOCUS_Step_12_scenarios

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

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PEC_sw_exposit_drainage()

Calculate PEC surface water due to drainage as in Exposit 3

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PEC_sw_exposit_runoff()

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

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perc_runoff_exposit

Runoff loss percentages as used in Exposit 3

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perc_runoff_reduction_exposit

Runoff reduction percentages as used in Exposit

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TOXSWA_cwa

R6 class for holding TOXSWA water concentration data and associated statistics

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read.TOXSWA_cwa()

Read TOXSWA surface water concentrations

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plot(<TOXSWA_cwa>)

Plot TOXSWA surface water concentrations

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Classifications and indicators

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Evaluating environmental fate properties

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Classifications and indicators

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Evaluating environmental fate properties

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SSLRC_mobility_classification()

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

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GUS() print(<GUS_result>)

Groundwater ubiquity score based on Gustafson (1989)

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Work with chent objects containing relevant information

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Work with chent objects containing relevant information

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

Retrieve endpoint information from the chyaml field of a chent object

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Utilities

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Utilities

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get_vertex()

Fit a parabola through three points

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