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diff --git a/docs/reference/PEC_sw_focus.md b/docs/reference/PEC_sw_focus.md new file mode 100644 index 0000000..aa87968 --- /dev/null +++ b/docs/reference/PEC_sw_focus.md @@ -0,0 +1,241 @@ +# Calculate PEC surface water at FOCUS Step 1 + +This is a reimplementation of the FOCUS Step 1 and 2 calculator version +3.2, authored by Michael Klein, in R. Note that results for multiple +applications should be compared to the corresponding results for a +single application. At current, this is not done automatically in this +implementation. Only Step 1 PECs are calculated. However, input files +can be generated that are suitable as input for the FOCUS calculator. + +## Usage + +``` r +PEC_sw_focus( + parent, + rate, + n = 1, + i = NA, + comment = "", + met = NULL, + f_drift = NA, + f_rd = 0.1, + scenario = FOCUS_Step_12_scenarios$names, + region = c("n", "s"), + season = c(NA, "of", "mm", "js"), + interception = c("no interception", "minimal crop cover", "average crop cover", + "full canopy"), + met_form_water = TRUE, + txt_file = "pesticide.txt", + overwrite = FALSE, + append = FALSE +) +``` + +## Arguments + +- parent: + + A list containing substance specific parameters, e.g. conveniently + generated by + [chent_focus_sw](https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.md). + +- rate: + + The application rate in g/ha. Overriden when applications are given + explicitly + +- n: + + The number of applications + +- i: + + The application interval + +- comment: + + A comment for the input file + +- met: + + A list containing metabolite specific parameters. e.g. conveniently + generated by + [chent_focus_sw](https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.md). + If not NULL, the PEC is calculated for this compound, not the parent. + +- f_drift: + + The fraction of the application rate reaching the waterbody via drift. + If NA, this is derived from the scenario name and the number of + applications via the drift data defined by the + [FOCUS_Step_12_scenarios](https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.md) + +- f_rd: + + The fraction of the amount applied reaching the waterbody via + runoff/drainage. At Step 1, it is assumed to be 10%, be it the parent + or a metabolite + +- scenario: + + The name of the scenario. Must be one of the scenario names given in + [FOCUS_Step_12_scenarios](https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.md) + +- region: + + 'n' for Northern Europe or 's' for Southern Europe. If NA, only Step 1 + PECsw are calculated + +- season: + + 'of' for October to February, 'mm' for March to May, and 'js' for June + to September. If NA, only step 1 PECsw are calculated + +- interception: + + One of 'no interception' (default), 'minimal crop cover', 'average + crop cover' or 'full canopy' + +- met_form_water: + + Should the metabolite formation in water be taken into account? This + can be switched off to check the influence and to compare with + previous versions of the Steps 12 calculator + +- txt_file: + + the name, and potentially the full path to the Steps.12 input text + file to which the specification of the run(s) should be written + +- overwrite: + + Should an existing file a the location specified in `txt_file` be + overwritten? Only takes effect if append is FALSE. + +- append: + + Should the input text file be appended, if it exists? + +## Note + +The formulas for input to the waterbody via runoff/drainage of the +parent and subsequent formation of the metabolite in water is not +documented in the model description coming with the calculator. As one +would expect, this appears to be (as we get the same results) calculated +by multiplying the application rate with the molar weight correction and +the formation fraction in water/sediment systems. + +Step 2 is not implemented. + +## References + +FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4). +FOrum for the Co-ordination of pesticde fate models and their USe. +http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf + +Website of the Steps 1 and 2 calculator at the Joint Research Center of +the European Union: http://esdac.jrc.ec.europa.eu/projects/stepsonetwo + +## Examples + +``` r +# Parent only +dummy_1 <- chent_focus_sw("Dummy 1", cwsat = 6000, DT50_ws = 6, Koc = 344.8) +PEC_sw_focus(dummy_1, 3000, f_drift = 0) +#> $f_drift +#> [1] 0 +#> +#> $eq_rate_drift_s +#> [1] 3000 +#> +#> $eq_rate_rd_s +#> [1] 3000 +#> +#> $eq_rate_rd_parent_s +#> [1] NA +#> +#> $input_drift_s +#> [1] 0 +#> +#> $input_rd_s +#> [1] 300 +#> +#> $f_rd_sw +#> [1] 0.6850566 +#> +#> $f_rd_sed +#> [1] 0.3149434 +#> +#> $PEC +#> type +#> Time PECsw TWAECsw PECsed TWAECsed +#> 0 6.850566e+02 NA 2.362075e+03 NA +#> 1 6.103161e+02 647.68635 2.104370e+03 2233.2225 +#> 2 5.437298e+02 612.03420 1.874780e+03 2110.2939 +#> 4 4.315586e+02 548.76030 1.488014e+03 1892.1255 +#> 7 3.051580e+02 469.88375 1.052185e+03 1620.1592 +#> 14 1.359325e+02 339.57370 4.686951e+02 1170.8501 +#> 21 6.055102e+01 257.45458 2.087799e+02 887.7034 +#> 28 2.697241e+01 203.47173 9.300089e+01 701.5705 +#> 42 5.352005e+00 140.10377 1.845371e+01 483.0778 +#> 50 2.123945e+00 118.24602 7.323361e+00 407.7123 +#> 100 6.585062e-03 59.30629 2.270529e-02 204.4881 +#> +#> $PEC_sw_max +#> [1] 685.0566 +#> +#> $PEC_sed_max +#> [1] 2362.075 +#> + +# Metabolite +new_dummy <- chent_focus_sw("New Dummy", mw = 250, Koc = 100) +M1 <- chent_focus_sw("M1", mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, + max_ws = 0, max_soil = 0.5) +PEC_sw_focus(new_dummy, 1000, scenario = "cereals, winter", met = M1) +#> $f_drift +#> [1] 0.02759 +#> +#> $eq_rate_drift_s +#> [1] 0 +#> +#> $eq_rate_rd_s +#> [1] 200 +#> +#> $eq_rate_rd_parent_s +#> [1] 0 +#> +#> $input_drift_s +#> [1] 0 +#> +#> $input_rd_s +#> [1] 20 +#> +#> $f_rd_sw +#> [1] 0.9375 +#> +#> $f_rd_sed +#> [1] 0.0625 +#> +#> $PEC +#> type +#> Time PECsw TWAECsw PECsed TWAECsed +#> 0 62.50000 NA 31.25000 NA +#> 1 62.06828 62.28414 31.03414 31.14207 +#> 2 61.63954 62.06890 30.81977 31.03445 +#> 4 60.79093 61.64158 30.39547 30.82079 +#> 7 59.53987 61.00800 29.76994 30.50400 +#> 14 56.71995 59.56326 28.35997 29.78163 +#> 21 54.03358 58.16414 27.01679 29.08207 +#> 28 51.47444 56.80902 25.73722 28.40451 +#> 42 46.71404 54.22460 23.35702 27.11230 +#> 50 44.19417 52.81945 22.09709 26.40973 +#> 100 31.25000 45.08422 15.62500 22.54211 +#> +#> $PEC_sw_max +#> [1] 62.5 +#> +#> $PEC_sed_max +#> [1] 31.25 +#> +``` |