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diff --git a/docs/reference/index.md b/docs/reference/index.md new file mode 100644 index 0000000..089bd81 --- /dev/null +++ b/docs/reference/index.md @@ -0,0 +1,128 @@ +# Package index + +## General utility functions + +Functions that are independent of specific fate modelling areas + +- [`geomean()`](https://pkgdown.jrwb.de/pfm/reference/geomean.md) : + Calculate the geometric mean +- [`one_box()`](https://pkgdown.jrwb.de/pfm/reference/one_box.md) : + Create a time series of decline data +- [`plot(`*`<one_box>`*`)`](https://pkgdown.jrwb.de/pfm/reference/plot.one_box.md) + : Plot time series of decline data +- [`sawtooth()`](https://pkgdown.jrwb.de/pfm/reference/sawtooth.md) : + Create decline time series for multiple applications +- [`twa()`](https://pkgdown.jrwb.de/pfm/reference/twa.md) : Calculate a + time weighted average concentration +- [`max_twa()`](https://pkgdown.jrwb.de/pfm/reference/max_twa.md) : The + maximum time weighted average concentration for a moving window +- [`pfm_degradation()`](https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.md) + : Calculate a time course of relative concentrations based on an + mkinmod model +- [`SFO_actual_twa()`](https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.md) + : Actual and maximum moving window time average concentrations for SFO + kinetics +- [`FOMC_actual_twa()`](https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.md) + : Actual and maximum moving window time average concentrations for + FOMC kinetics +- [`reexports`](https://pkgdown.jrwb.de/pfm/reference/reexports.md) + [`set_nd_nq`](https://pkgdown.jrwb.de/pfm/reference/reexports.md) + [`set_nd_nq_focus`](https://pkgdown.jrwb.de/pfm/reference/reexports.md) + : Objects exported from other packages +- [`TSCF()`](https://pkgdown.jrwb.de/pfm/reference/TSCF.md) : Estimation + of the transpiration stream concentration factor + +## Predicted environmental concentrations in soil + +- [`PEC_soil()`](https://pkgdown.jrwb.de/pfm/reference/PEC_soil.md) : + Calculate predicted environmental concentrations in soil +- [`PEC_soil_mets()`](https://pkgdown.jrwb.de/pfm/reference/PEC_soil_mets.md) + : Calculate initial and accumulation PEC soil for a set of metabolites +- [`soil_scenario_data_EFSA_2015`](https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.md) + : Properties of the predefined scenarios from the EFSA guidance from + 2015 +- [`soil_scenario_data_EFSA_2017`](https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.md) + : Properties of the predefined scenarios from the EFSA guidance from + 2017 +- [`PEC_FOMC_accu_rel()`](https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.md) + : Get the relative accumulation of an FOMC model over multiples of an + interval +- [`EFSA_washoff_2017`](https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.md) + : Subset of EFSA crop washoff default values + +## Predicted environmental concentrations in groundwater + +- [`FOCUS_GW_scenarios_2012`](https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.md) + : A very small subset of the FOCUS Groundwater scenario definitions +- [`EFSA_GW_interception_2014`](https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.md) + : Subset of EFSA crop interception default values for groundwater + modelling + +## Predicted environmental concentrations in surface water + +- [`PEC_sw_drift()`](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.md) + : Calculate predicted environmental concentrations in surface water + due to drift +- [`drift_data_JKI`](https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.md) + : Deposition from spray drift expressed as percent of the applied dose + as published by the JKI +- [`drift_parameters_focus`](https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.md) + : Regression parameters for the Rautmann drift data +- [`drift_percentages_rautmann()`](https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.md) + : Calculate drift percentages based on Rautmann data +- [`PEC_sw_drainage_UK()`](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.md) + [`drainage_date_UK()`](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.md) + : Calculate initial predicted environmental concentrations in surface + water due to drainage using the UK method +- [`PEC_sw_sed()`](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.md) + : Calculate predicted environmental concentrations in sediment from + surface water concentrations +- [`PEC_sw_focus()`](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.md) + : Calculate PEC surface water at FOCUS Step 1 +- [`chent_focus_sw()`](https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.md) + : Create a chemical compound object for FOCUS Step 1 calculations +- [`FOCUS_Step_12_scenarios`](https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.md) + : Step 1/2 scenario data as distributed with the FOCUS Step 1/2 + calculator +- [`PEC_sw_exposit_drainage()`](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.md) + : Calculate PEC surface water due to drainage as in Exposit 3 +- [`PEC_sw_exposit_runoff()`](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.md) + : Calculate PEC surface water due to runoff and erosion as in Exposit + 3 +- [`perc_runoff_exposit`](https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.md) + : Runoff loss percentages as used in Exposit 3 +- [`perc_runoff_reduction_exposit`](https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.md) + : Runoff reduction percentages as used in Exposit +- [`TOXSWA_cwa`](https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.md) : + R6 class for holding TOXSWA water concentration data and associated + statistics +- [`read.TOXSWA_cwa()`](https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.md) + : Read TOXSWA surface water concentrations +- [`plot(`*`<TOXSWA_cwa>`*`)`](https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.md) + : Plot TOXSWA surface water concentrations + +## Classifications and indicators + +Evaluating environmental fate properties + +- [`SSLRC_mobility_classification()`](https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.md) + : Determine the SSLRC mobility classification for a chemical substance + from its Koc +- [`GUS()`](https://pkgdown.jrwb.de/pfm/reference/GUS.md) + [`print(`*`<GUS_result>`*`)`](https://pkgdown.jrwb.de/pfm/reference/GUS.md) + : Groundwater ubiquity score based on Gustafson (1989) + +## Work with chent objects containing relevant information + +- [`endpoint()`](https://pkgdown.jrwb.de/pfm/reference/endpoint.md) + [`soil_DT50()`](https://pkgdown.jrwb.de/pfm/reference/endpoint.md) + [`soil_Kfoc()`](https://pkgdown.jrwb.de/pfm/reference/endpoint.md) + [`soil_N()`](https://pkgdown.jrwb.de/pfm/reference/endpoint.md) + [`soil_sorption()`](https://pkgdown.jrwb.de/pfm/reference/endpoint.md) + : Retrieve endpoint information from the chyaml field of a chent + object + +## Utilities + +- [`get_vertex()`](https://pkgdown.jrwb.de/pfm/reference/get_vertex.md) + : Fit a parabola through three points |