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diff --git a/docs/reference/PEC_soil.md b/docs/reference/PEC_soil.md new file mode 100644 index 0000000..d7666dc --- /dev/null +++ b/docs/reference/PEC_soil.md @@ -0,0 +1,261 @@ +# Calculate predicted environmental concentrations in soil + +This is a basic calculation of a contaminant concentration in bulk soil +based on complete, instantaneous mixing. If an interval is given, an +attempt is made at calculating a long term maximum concentration using +the concepts layed out in the PPR panel opinion (EFSA PPR panel 2012 and +in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017). + +## Usage + +``` r +PEC_soil( + rate, + rate_units = "g/ha", + interception = 0, + mixing_depth = 5, + PEC_units = "mg/kg", + PEC_pw_units = "mg/L", + interval = NA, + n_periods = Inf, + tillage_depth = 20, + leaching_depth = tillage_depth, + crop = "annual", + cultivation = FALSE, + chent = NA, + DT50 = NA, + FOMC = NA, + Koc = NA, + Kom = Koc/1.724, + t_avg = 0, + t_act = NULL, + scenarios = c("default", "EFSA_2017", "EFSA_2015"), + leaching = scenarios == "EFSA_2017", + porewater = FALSE +) +``` + +## Arguments + +- rate: + + Application rate in units specified below + +- rate_units: + + Defaults to g/ha + +- interception: + + The fraction of the application rate that does not reach the soil + +- mixing_depth: + + Mixing depth in cm + +- PEC_units: + + Requested units for the calculated PEC. Only mg/kg currently supported + +- PEC_pw_units: + + Only mg/L currently supported + +- interval: + + Period of the deeper mixing. The default is NA, i.e. no deeper mixing. + For annual deeper mixing, set this to 365 when degradation units are + in days + +- n_periods: + + Number of periods to be considered for long term PEC calculations + +- tillage_depth: + + Periodic (see interval) deeper mixing in cm + +- leaching_depth: + + EFSA (2017) uses the mixing depth (ecotoxicological evaluation depth) + to calculate leaching for annual crops where tillage takes place. By + default, losses from the layer down to the tillage depth are taken + into account in this implementation. + +- crop: + + Ignored for scenarios other than EFSA_2017. Only annual crops are + supported when these scenarios are used. Only crops with a single + cropping cycle per year are currently supported. + +- cultivation: + + Does mechanical cultivation in the sense of EFSA (2017) take place, + i.e. twice a year to a depth of 5 cm? Ignored for scenarios other than + EFSA_2017 + +- chent: + + An optional chent object holding substance specific information. Can + also be a name for the substance as a character string + +- DT50: + + If specified, overrides soil DT50 endpoints from a chent object If + DT50 is not specified here and not available from the chent object, + zero degradation is assumed + +- FOMC: + + If specified, it should be a named numeric vector containing the FOMC + parameters alpha and beta. This overrides any other degradation + endpoints, and the degradation during the interval and after the + maximum PEC is calculated using these parameters without temperature + correction + +- Koc: + + If specified, overrides Koc endpoints from a chent object + +- Kom: + + Calculated from Koc by default, but can explicitly be specified as Kom + here + +- t_avg: + + Averaging times for time weighted average concentrations + +- t_act: + + Time series for actual concentrations + +- scenarios: + + If this is 'default', a soil bulk density of 1.5 kg/L will be used. + The DT50 will be used without correction and soil properties as + specified in the REACH guidance (R.16, Table R.16-9) are used for + porewater PEC calculations. If this is "EFSA_2015", the DT50 is taken + to be a modelling half-life at 20°C and pF2 (for when 'chent' is + specified, the DegT50 with destination 'PECgw' will be used), and + corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also + model and scenario adjustment factors from the EFSA guidance are used. + +- leaching: + + Should leaching be taken into account? The default is FALSE, except + when the EFSA_2017 scenarios are used. + +- porewater: + + Should equilibrium porewater concentrations be estimated based on Kom + and the organic carbon fraction of the soil instead of total soil + concentrations? Based on equation (7) given in the PPR panel opinion + (EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance + (2015, p. 13). + +## Value + +The predicted concentration in soil + +## Details + +This assumes that the complete load to soil during the time specified by +'interval' (typically 365 days) is dosed at once. As in the PPR panel +opinion cited below (EFSA PPR panel 2012), only temperature correction +using the Arrhenius equation is performed. + +Total soil and porewater PEC values for the scenarios as defined in the +EFSA guidance (2017, p. 14/15) can easily be calculated. + +## Note + +While time weighted average (TWA) concentrations given in the examples +from the EFSA guidance from 2015 (p. 80) can be reproduced, this is not +true for the TWA concentrations given for the same example in the EFSA +guidance from 2017 (p. 92). + +According to the EFSA guidance (EFSA, 2017, p. 43), leaching should be +taken into account for the EFSA 2017 scenarios, using the evaluation +depth (here mixing depth) as the depth of the layer from which leaching +takes place. However, as the amount leaching below the evaluation depth +(often 5 cm) will partly be mixed back during tillage, the default in +this function is to use the tillage depth for the calculation of the +leaching rate. + +If temperature information is available in the selected scenarios, as +e.g. in the EFSA scenarios, the DT50 for groundwater modelling +(destination 'PECgw') is taken from the chent object, otherwise the DT50 +with destination 'PECsoil'. + +## References + +EFSA Panel on Plant Protection Products and their Residues (2012) +Scientific Opinion on the science behind the guidance for scenario +selection and scenario parameterisation for predicting environmental +concentrations of plant protection products in soil. *EFSA Journal* +**10**(2) 2562, doi:10.2903/j.efsa.2012.2562 + +EFSA (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 + +EFSA (European Food Safety Authority) (2015) 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* **13**(4) 4093 +doi:10.2903/j.efsa.2015.4093 + +## Author + +Johannes Ranke + +## Examples + +``` r +PEC_soil(100, interception = 0.25) +#> scenario +#> t_avg default +#> 0 0.1 + +# This is example 1 starting at p. 92 of the EFSA guidance (2017) +# Note that TWA concentrations differ from the ones given in the guidance +# for an unknown reason (the values from EFSA (2015) can be reproduced). +PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), + Kom = 1000, scenarios = "EFSA_2017") +#> scenario +#> t_avg CTN CTC CTS +#> 0 19.76834 13.8619 10.53795 +#> 21 19.59345 13.7169 10.39882 +PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), + Kom = 1000, scenarios = "EFSA_2017", porewater = TRUE) +#> scenario +#> t_avg CLN CLC CLS +#> 0 0.5541984 0.6779249 0.9816693 +#> 21 0.5484576 0.6693125 0.9609119 + +# This is example 1 starting at p. 79 of the EFSA guidance (2015) +PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), + scenarios = "EFSA_2015") +#> scenario +#> t_avg CTN CTC CTS +#> 0 21.96827 11.53750 9.145259 +#> 21 21.78517 11.40701 9.017370 +PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), + Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) +#> scenario +#> t_avg CLN CLC CLS +#> 0 0.7589401 0.6674322 0.9147861 +#> 21 0.7506036 0.6590345 0.8987279 + +# The following is from example 4 starting at p. 85 of the EFSA guidance (2015) +# Metabolite M2 +# Calculate total and porewater soil concentrations for tier 1 scenarios +# Relative molar mass is 100/300, formation fraction is 0.7 * 1 +results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), + scenarios = "EFSA_2015") +results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), + Kom = 100, scenarios = "EFSA_2015", porewater = TRUE) +``` |