From b935273d651301b271e0cb66bf36c2bbc1d15b32 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 31 Jan 2019 01:40:24 +0100 Subject: Separate out PELMO utilities into rPELMO --- docs/reference/FOCUS_GW_scenarios_2012.html | 23 +-- docs/reference/FOCUS_Step_12_scenarios.html | 43 +++--- docs/reference/FOMC_actual_twa.html | 31 ++-- docs/reference/GUS.html | 34 ++--- docs/reference/PEC_FOMC_accu_rel.html | 23 +-- docs/reference/PEC_soil.html | 58 ++++---- docs/reference/PEC_soil_mets.html | 168 ++++++++++++++++++++++ docs/reference/PEC_sw_drainage_UK.html | 32 ++--- docs/reference/PEC_sw_drift.html | 30 ++-- docs/reference/PEC_sw_exposit_runoff.html | 25 ++-- docs/reference/PEC_sw_focus.html | 27 ++-- docs/reference/PEC_sw_sed.html | 29 ++-- docs/reference/SFO_actual_twa.html | 31 ++-- docs/reference/SSLRC_mobility_classification.html | 27 ++-- docs/reference/TOXSWA_cwa.html | 31 ++-- docs/reference/chent_focus_sw.html | 28 ++-- docs/reference/drift_data_JKI.html | 39 ++--- docs/reference/endpoint.html | 35 ++--- docs/reference/geomean.html | 31 ++-- docs/reference/get_vertex.html | 39 +++-- docs/reference/index.html | 92 +++++------- docs/reference/max_twa.html | 25 ++-- docs/reference/one_box.html | 40 +++--- docs/reference/perc_runoff_exposit.html | 25 ++-- docs/reference/perc_runoff_reduction_exposit.html | 25 ++-- docs/reference/pesticide.txt | 4 + docs/reference/pfm_degradation.html | 35 +++-- docs/reference/plot.TOXSWA_cwa.html | 43 +++--- docs/reference/plot.one_box.html | 33 ++--- docs/reference/read.TOXSWA_cwa.html | 35 +++-- docs/reference/sawtooth.html | 33 ++--- docs/reference/soil_scenario_data_EFSA_2015.html | 49 +++---- docs/reference/soil_scenario_data_EFSA_2017.html | 23 +-- docs/reference/twa.html | 25 ++-- 34 files changed, 730 insertions(+), 541 deletions(-) create mode 100644 docs/reference/PEC_soil_mets.html (limited to 'docs/reference') diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 65a6df2..d60f44f 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -1,6 +1,6 @@ - + @@ -9,17 +9,17 @@ A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012 • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> - + + - + @@ -9,17 +9,17 @@ Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ The text file is not included in the package as its licence is not clear." /> - + + - + @@ -9,17 +9,17 @@ Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Groundwater ubiquity score based on Gustafson (1989) — GUS • pfm - + - - + + - + - + @@ -40,7 +40,8 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> - + + - + @@ -9,17 +9,17 @@ Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Calculate predicted environmental concentrations in soil — PEC_soil • pfm - + - - + + - + - + @@ -42,7 +42,8 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> - + + + + + + + + + +Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets • pfm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Calculate initial and accumulation PEC soil for a set of metabolites

+ Source: R/PEC_soil.R + +
+ +
+ +

Calculate initial and accumulation PEC soil for a set of metabolites

+ +
+ + 
PEC_soil_mets(rate, mw_parent, mets, interval = 365, ...)
+ +

Arguments

+ + + + + + + + + + + + + + + + + + + + + + +
rate

Application rate in units specified below

mw_parent

The molecular weight of the parent compound

mets

A dataframe with metabolite identifiers as rownames +and columns "mw", "occ" and "DT50" holding their molecular weight, +maximum occurrence in soil and their soil DT50

interval

The interval for accumulation calculations

...

Further arguments are passed to PEC_soil

+ + +
+ +
+ +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown 1.3.0.

+
+
+
+ + + + + + diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html index 80dd7fa..b924c99 100644 --- a/docs/reference/PEC_sw_drainage_UK.html +++ b/docs/reference/PEC_sw_drainage_UK.html @@ -1,6 +1,6 @@ - + @@ -9,17 +9,17 @@ Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ published on the CRC website" /> - + + - + @@ -9,17 +9,17 @@ Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift • pfm - + - - + + - + - + @@ -40,7 +40,8 @@ with input via spray drift." /> - + + - + @@ -9,17 +9,17 @@ Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values - + + - + @@ -9,17 +9,17 @@ Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm - + - - + + - + - + @@ -44,7 +44,8 @@ to be used with the FOCUS calculator." /> - + + - + @@ -10,17 +10,17 @@ water concentrations — PEC_sw_sed • pfm - + - - + + - + - + @@ -41,7 +41,8 @@ PEC calculator" /> - + + - + @@ -9,17 +9,17 @@ Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ checked against the spreadsheet published on the CRC website" /> - + + - + @@ -9,17 +9,17 @@ R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> - + + - + @@ -9,17 +9,17 @@ Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -10,17 +10,17 @@ published by the JKI — drift_data_JKI • pfm - + - - + + - + - + @@ -41,7 +41,8 @@ published by the German Julius-Kühn Institute (JKI)." /> - + + - + @@ -9,17 +9,17 @@ Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm - + - - + + - + - + @@ -41,7 +41,8 @@ this function." /> - + + - + @@ -9,17 +9,17 @@ Calculate the geometric mean — geomean • pfm - + - - + + - + - + @@ -41,7 +41,8 @@ returns 0 if at least one element of the vector is 0." /> - + + - + @@ -9,17 +9,17 @@ Fit a parabola through three points — get_vertex • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ https://stackoverflow.com/a/717791" /> - + + - + @@ -9,17 +9,17 @@ Function reference • pfm - + - - + + - + - + @@ -35,7 +35,8 @@ - + + - + @@ -9,17 +9,17 @@ The maximum time weighted average concentration for a moving window — max_twa • pfm - + - - + + - + - + @@ -42,7 +42,8 @@ max_twa." /> - + + - + @@ -9,17 +9,17 @@ Create a time series of decline data — one_box • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ segment of a TOXSWA surface water body." /> - + + - + @@ -9,17 +9,17 @@ Plot time series of decline data — plot.one_box • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Read TOXSWA surface water concentrations — read.TOXSWA_cwa • pfm - + - - + + - + - + @@ -43,7 +43,8 @@ renamed to ConLiqWatLay in the out file." /> - + + - + @@ -9,17 +9,17 @@ Create decline time series for multiple applications — sawtooth • pfm - + - - + + - + - + @@ -40,7 +40,8 @@ times, with an interval i." /> - + + - + @@ -9,17 +9,17 @@ Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • pfm - + - - + + - + - + @@ -40,7 +40,8 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> - + + - + @@ -9,17 +9,17 @@ Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • pfm - + - - + + - + - + @@ -40,7 +40,8 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." /> - + + - + @@ -9,17 +9,17 @@ Calculate a time weighted average concentration — twa • pfm - + - - + + - + - + @@ -40,7 +40,8 @@ is after one window has passed." /> - + +