From 6acfd0dfb2670e3eeab6144c90586f28105583a8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 20 Jun 2018 14:53:02 +0200 Subject: Update static docs --- docs/authors.html | 2 +- docs/index.html | 2 +- docs/reference/FOCUS_GW_scenarios_2012.html | 2 +- docs/reference/FOCUS_PELMO_crop_sze_names.html | 2 +- docs/reference/FOCUS_PELMO_crops.html | 2 +- docs/reference/FOCUS_PELMO_location_codes.html | 2 +- docs/reference/FOCUS_Step_12_scenarios.html | 2 +- docs/reference/FOMC_actual_twa.html | 185 ++++++++++++++++++++++ docs/reference/GUS.html | 2 +- docs/reference/PEC_soil.html | 2 +- docs/reference/PEC_sw_drainage_UK.html | 2 +- docs/reference/PEC_sw_drift.html | 2 +- docs/reference/PEC_sw_exposit_runoff.html | 2 +- docs/reference/PEC_sw_focus.html | 2 +- docs/reference/PEC_sw_sed.html | 2 +- docs/reference/PELMO_path.html | 2 +- docs/reference/PELMO_runs.html | 4 +- docs/reference/SFO_actual_twa.html | 4 +- docs/reference/SSLRC_mobility_classification.html | 2 +- docs/reference/TOXSWA_cwa.html | 2 +- docs/reference/chent_focus_sw.html | 2 +- docs/reference/create_run_list.html | 2 +- docs/reference/drift_data_JKI.html | 2 +- docs/reference/endpoint.html | 2 +- docs/reference/focus_80th.html | 2 +- docs/reference/geomean.html | 2 +- docs/reference/get_flux.html | 2 +- docs/reference/get_interval.html | 2 +- docs/reference/index.html | 2 +- docs/reference/max_twa.html | 2 +- docs/reference/one_box.html | 2 +- docs/reference/perc_runoff_exposit.html | 2 +- docs/reference/perc_runoff_reduction_exposit.html | 2 +- docs/reference/pesticide.txt | 2 + docs/reference/pfm_degradation.html | 2 +- docs/reference/plot.TOXSWA_cwa.html | 2 +- docs/reference/plot.one_box.html | 2 +- docs/reference/read.TOXSWA_cwa.html | 2 +- docs/reference/sawtooth.html | 2 +- docs/reference/soil_scenario_data_EFSA_2015.html | 2 +- docs/reference/sum_periods.html | 2 +- docs/reference/twa.html | 2 +- 42 files changed, 229 insertions(+), 42 deletions(-) create mode 100644 docs/reference/FOMC_actual_twa.html diff --git a/docs/authors.html b/docs/authors.html index 0870c21..27e5e7c 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -58,7 +58,7 @@ pfm - 0.4.5 + 0.4.6 diff --git a/docs/index.html b/docs/index.html index 1558e8a..fc6e0f8 100644 --- a/docs/index.html +++ b/docs/index.html @@ -31,7 +31,7 @@ pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 3402035..1a9d513 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -62,7 +62,7 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/FOCUS_PELMO_crop_sze_names.html b/docs/reference/FOCUS_PELMO_crop_sze_names.html index 9297f2a..89348f6 100644 --- a/docs/reference/FOCUS_PELMO_crop_sze_names.html +++ b/docs/reference/FOCUS_PELMO_crop_sze_names.html @@ -64,7 +64,7 @@ files used for Beans (field) and Beans (vegetable) are the same." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/FOCUS_PELMO_crops.html b/docs/reference/FOCUS_PELMO_crops.html index 2393e41..16653d9 100644 --- a/docs/reference/FOCUS_PELMO_crops.html +++ b/docs/reference/FOCUS_PELMO_crops.html @@ -65,7 +65,7 @@ in the three letter code, i.e. 'Peas (animals)' has the code ape." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/FOCUS_PELMO_location_codes.html b/docs/reference/FOCUS_PELMO_location_codes.html index d601243..817d888 100644 --- a/docs/reference/FOCUS_PELMO_location_codes.html +++ b/docs/reference/FOCUS_PELMO_location_codes.html @@ -62,7 +62,7 @@ indexed by three letter acronyms." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index 294846d..9ceb79d 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -62,7 +62,7 @@ The text file is not included in the package as its licence is not clear." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/FOMC_actual_twa.html b/docs/reference/FOMC_actual_twa.html new file mode 100644 index 0000000..7a62183 --- /dev/null +++ b/docs/reference/FOMC_actual_twa.html @@ -0,0 +1,185 @@ + + + + + + + + +Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa • pfm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Actual and maximum moving window time average concentrations for FOMC kinetics

+ Source: R/FOMC_actual_twa.R + +
+ +
+ +

Actual and maximum moving window time average concentrations for FOMC kinetics

+ +
+ + 
FOMC_actual_twa(alpha = 1.0001, beta = 10, times = c(0, 1, 2, 4, 7, 14,
+  21, 28, 42, 50, 100))
+ +

Arguments

+ + + + + + + + + + + + + + +
alpha

Parameter of the FOMC model

beta

Parameter of the FOMC model

times

The output times, and window sizes for time weighted average concentrations

+ +

Source

+ +

FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation + Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, + 18 December 2014, p. 251

+ + +

Examples

+ 
FOMC_actual_twa(alpha = 1.0001, beta = 10)
#>         actual       twa
+#> 0   1.00000000       NaN
+#> 1   0.90908224 0.9530973
+#> 2   0.83331814 0.9115995
+#> 4   0.71426168 0.8411664
+#> 7   0.58820408 0.7580202
+#> 14  0.41663019 0.6253074
+#> 21  0.32254415 0.5387324
+#> 28  0.26312277 0.4767543
+#> 42  0.19227599 0.3925054
+#> 50  0.16663681 0.3583198
+#> 100 0.09088729 0.2397608
+
+ +
+ +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + + + + diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html index 3fa93c9..87714e0 100644 --- a/docs/reference/GUS.html +++ b/docs/reference/GUS.html @@ -63,7 +63,7 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index 65c8519..feed9d5 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -64,7 +64,7 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012)." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html index 6eb042e..91eeccb 100644 --- a/docs/reference/PEC_sw_drainage_UK.html +++ b/docs/reference/PEC_sw_drainage_UK.html @@ -62,7 +62,7 @@ published on the CRC website" /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html index fa9a968..02b641f 100644 --- a/docs/reference/PEC_sw_drift.html +++ b/docs/reference/PEC_sw_drift.html @@ -63,7 +63,7 @@ with input via spray drift." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html index 37ba843..2942ebb 100644 --- a/docs/reference/PEC_sw_exposit_runoff.html +++ b/docs/reference/PEC_sw_exposit_runoff.html @@ -62,7 +62,7 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index 5e66d25..535e82e 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -67,7 +67,7 @@ to be used with the FOCUS calculator." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html index 5dc6cea..532031b 100644 --- a/docs/reference/PEC_sw_sed.html +++ b/docs/reference/PEC_sw_sed.html @@ -64,7 +64,7 @@ PEC calculator" /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/PELMO_path.html b/docs/reference/PELMO_path.html index 12c9a0d..a678cb6 100644 --- a/docs/reference/PELMO_path.html +++ b/docs/reference/PELMO_path.html @@ -61,7 +61,7 @@ pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html index dc068c3..72e3c39 100644 --- a/docs/reference/PELMO_runs.html +++ b/docs/reference/PELMO_runs.html @@ -67,7 +67,7 @@ and run using wine." /> pfm - 0.4.5 + 0.4.6 @@ -229,7 +229,7 @@ the period.plm file generated by the FOCUS PELMO GUI.

#> #>
# We get exactly the same PECgw values (on Linux, calling PELMO using Wine). print(time_1)
#> User System verstrichen -#> 0.388 0.088 30.344
if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { +#> 0.390 0.084 30.914
if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]])) }
#> CPU model: AMD Ryzen 7 1700 Eight-Core Processor
# Demonstrate some results with metabolites. diff --git a/docs/reference/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html index e6fc526..e5b1e8a 100644 --- a/docs/reference/SFO_actual_twa.html +++ b/docs/reference/SFO_actual_twa.html @@ -61,7 +61,7 @@ pfm - 0.4.5 + 0.4.6
@@ -127,7 +127,7 @@

Source

FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation - Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, + Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, 18 December 2014, p. 251

diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html index 4e673bf..49b80e7 100644 --- a/docs/reference/SSLRC_mobility_classification.html +++ b/docs/reference/SSLRC_mobility_classification.html @@ -62,7 +62,7 @@ checked against the spreadsheet published on the CRC website" /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index a078e31..3b11804 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -62,7 +62,7 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html index 501f002..1683067 100644 --- a/docs/reference/chent_focus_sw.html +++ b/docs/reference/chent_focus_sw.html @@ -61,7 +61,7 @@ pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/create_run_list.html b/docs/reference/create_run_list.html index 02d2d0c..255aa1d 100644 --- a/docs/reference/create_run_list.html +++ b/docs/reference/create_run_list.html @@ -61,7 +61,7 @@ pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html index 9cee8fe..ada93e7 100644 --- a/docs/reference/drift_data_JKI.html +++ b/docs/reference/drift_data_JKI.html @@ -64,7 +64,7 @@ published by the German Julius-Kühn Institute (JKI)." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html index 2a36788..a078bd8 100644 --- a/docs/reference/endpoint.html +++ b/docs/reference/endpoint.html @@ -64,7 +64,7 @@ this function." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/focus_80th.html b/docs/reference/focus_80th.html index c15c73a..375e15a 100644 --- a/docs/reference/focus_80th.html +++ b/docs/reference/focus_80th.html @@ -64,7 +64,7 @@ values obtained by PELMO." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html index b8c2415..5673322 100644 --- a/docs/reference/geomean.html +++ b/docs/reference/geomean.html @@ -64,7 +64,7 @@ returns 0 if at least one element of the vector is 0." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/get_flux.html b/docs/reference/get_flux.html index 7e331ec..025b4ad 100644 --- a/docs/reference/get_flux.html +++ b/docs/reference/get_flux.html @@ -61,7 +61,7 @@ pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/get_interval.html b/docs/reference/get_interval.html index 2d1dc02..0cd69f3 100644 --- a/docs/reference/get_interval.html +++ b/docs/reference/get_interval.html @@ -61,7 +61,7 @@ pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/index.html b/docs/reference/index.html index 395b446..c153b50 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -58,7 +58,7 @@ pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html index 0875c46..6e5ee67 100644 --- a/docs/reference/max_twa.html +++ b/docs/reference/max_twa.html @@ -65,7 +65,7 @@ max_twa." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html index 1e793d0..9cd4d61 100644 --- a/docs/reference/one_box.html +++ b/docs/reference/one_box.html @@ -61,7 +61,7 @@ pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html index e24e0ad..e243efb 100644 --- a/docs/reference/perc_runoff_exposit.html +++ b/docs/reference/perc_runoff_exposit.html @@ -61,7 +61,7 @@ pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html index 69acbac..4e10a64 100644 --- a/docs/reference/perc_runoff_reduction_exposit.html +++ b/docs/reference/perc_runoff_reduction_exposit.html @@ -61,7 +61,7 @@ pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt index 42be741..0f03e9a 100644 --- a/docs/reference/pesticide.txt +++ b/docs/reference/pesticide.txt @@ -31,3 +31,5 @@ Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Du M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html index 899a0a4..e547ed1 100644 --- a/docs/reference/pfm_degradation.html +++ b/docs/reference/pfm_degradation.html @@ -61,7 +61,7 @@ pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html index cf5bdf9..8612bac 100644 --- a/docs/reference/plot.TOXSWA_cwa.html +++ b/docs/reference/plot.TOXSWA_cwa.html @@ -62,7 +62,7 @@ segment of a TOXSWA surface water body." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html index e4ffef4..a8f62d4 100644 --- a/docs/reference/plot.one_box.html +++ b/docs/reference/plot.one_box.html @@ -61,7 +61,7 @@ pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index d838794..60e236a 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -65,7 +65,7 @@ of the hourly averages (ConLiqWatLay)." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html index 6b2ce13..175e045 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.html @@ -63,7 +63,7 @@ times, with an interval i." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html index 77759b5..64c9c28 100644 --- a/docs/reference/soil_scenario_data_EFSA_2015.html +++ b/docs/reference/soil_scenario_data_EFSA_2015.html @@ -63,7 +63,7 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/sum_periods.html b/docs/reference/sum_periods.html index 96cbaf2..ec0c34b 100644 --- a/docs/reference/sum_periods.html +++ b/docs/reference/sum_periods.html @@ -61,7 +61,7 @@ pfm - 0.4.5 + 0.4.6 diff --git a/docs/reference/twa.html b/docs/reference/twa.html index 8f8e98f..da44f92 100644 --- a/docs/reference/twa.html +++ b/docs/reference/twa.html @@ -63,7 +63,7 @@ is after one window has passed." /> pfm - 0.4.5 + 0.4.6 -- cgit v1.2.1 From 6ca8bdb8636141fac592688a6794ae092f0bc85a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 20 Jun 2018 14:58:44 +0200 Subject: Advertise drat repo --- README.md | 14 +++++++++++--- docs/index.html | 6 +++++- docs/reference/PELMO_runs.html | 2 +- docs/reference/pesticide.txt | 2 ++ 4 files changed, 19 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index b4b2caa..68874f2 100644 --- a/README.md +++ b/README.md @@ -20,10 +20,18 @@ This means: ## Installation -You can install the package from [github](http://github.com/jranke/pfm), e.g. +The easiest way to install the package is probably to use +[drat](http://cran.r-project.org/package=drat): + +```r +install.packages("drat") +drat::addRepo("jranke") +install.packages("pfm") +``` + +Alternatively you can install the package using the `devtools` package. Using `quick = TRUE` skips docs, -multiple-architecture builds, demos, and vignettes, to make installation as -fast and painless as possible. +multiple-architecture builds, demos, and vignettes. ```r diff --git a/docs/index.html b/docs/index.html index fc6e0f8..b7f32cc 100644 --- a/docs/index.html +++ b/docs/index.html @@ -84,7 +84,11 @@ this program. If not, see <http:

Installation

-

You can install the package from github, e.g. using the devtools package. Using quick = TRUE skips docs, multiple-architecture builds, demos, and vignettes, to make installation as fast and painless as possible.

+

The easiest way to install the package is probably to use drat:

+
install.packages("drat")
+drat::addRepo("jranke")
+install.packages("pfm")
+

Alternatively you can install the package using the devtools package. Using quick = TRUE skips docs, multiple-architecture builds, demos, and vignettes.

library(devtools)
 install_github("jranke/pfm", quick = TRUE)
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html index 72e3c39..1eac49b 100644 --- a/docs/reference/PELMO_runs.html +++ b/docs/reference/PELMO_runs.html @@ -229,7 +229,7 @@ the period.plm file generated by the FOCUS PELMO GUI.

#> #>
# We get exactly the same PECgw values (on Linux, calling PELMO using Wine). print(time_1)
#> User System verstrichen -#> 0.390 0.084 30.914
if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { +#> 0.398 0.100 30.624
if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]])) }
#> CPU model: AMD Ryzen 7 1700 Eight-Core Processor
# Demonstrate some results with metabolites. diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt index 0f03e9a..85f103d 100644 --- a/docs/reference/pesticide.txt +++ b/docs/reference/pesticide.txt @@ -33,3 +33,5 @@ Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Du M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 -- cgit v1.2.1 From 8989a484b9b2d23463c95e0a3927e307ec0a5e64 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 4 Jul 2018 10:59:47 +0200 Subject: Some documentation updates Document that TOXSWA 5.5.3 is supported in the help files --- ChangeLog | 18 ++++++++++++++++++ DESCRIPTION | 2 +- R/PEC_soil.R | 4 ++-- R/TOXSWA_cwa.R | 11 ++++++----- README.html | 8 ++++++-- docs/reference/PEC_soil.html | 2 +- docs/reference/PELMO_runs.html | 2 +- docs/reference/TOXSWA_cwa.html | 10 +++++----- docs/reference/index.html | 2 +- docs/reference/pesticide.txt | 2 ++ docs/reference/read.TOXSWA_cwa.html | 10 ++++++---- man/PEC_soil.Rd | 2 +- man/TOXSWA_cwa.Rd | 4 ++-- man/read.TOXSWA_cwa.Rd | 7 ++++--- 14 files changed, 56 insertions(+), 28 deletions(-) diff --git a/ChangeLog b/ChangeLog index 926bcd6..2960fbe 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,21 @@ +commit 6ca8bdb8636141fac592688a6794ae092f0bc85a +Author: Johannes Ranke +Date: 2018-06-20 14:58:44 +0200 + + Advertise drat repo + +commit 6acfd0dfb2670e3eeab6144c90586f28105583a8 +Author: Johannes Ranke +Date: 2018-06-20 14:53:02 +0200 + + Update static docs + +commit cac29c8c1cc0f6004ef0cd63229cfb993a24496c +Author: Johannes Ranke +Date: 2018-06-11 16:27:22 +0200 + + Adapt to TOXSWA 5.5.3 + commit bd15236d5dedb4067bd29e58e655c5352aca1db4 Author: Johannes Ranke Date: 2018-06-08 16:20:40 +0200 diff --git a/DESCRIPTION b/DESCRIPTION index 0851224..c1d967f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling Version: 0.4-6 -Date: 2018-06-11 +Date: 2018-07-04 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-4371-6538")) diff --git a/R/PEC_soil.R b/R/PEC_soil.R index ea1cb71..15ccc90 100644 --- a/R/PEC_soil.R +++ b/R/PEC_soil.R @@ -1,4 +1,4 @@ -# Copyright (C) 2015 Johannes Ranke +# Copyright (C) 2015,2016,2018 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package pfm @@ -44,7 +44,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_typ #' @param interception The fraction of the application rate that does not reach the soil #' @param mixing_depth Mixing depth in cm #' @param interval Period of the deeper mixing, defaults to 365, which is a year if -#' rate units are in days +#' degradation rate units are in days #' @param n_periods Number of periods to be considered for long term PEC calculations #' @param PEC_units Requested units for the calculated PEC. Only mg/kg currently supported #' @param PEC_pw_units Only mg/L currently supported diff --git a/R/TOXSWA_cwa.R b/R/TOXSWA_cwa.R index 576c7d3..5b1e8f2 100644 --- a/R/TOXSWA_cwa.R +++ b/R/TOXSWA_cwa.R @@ -22,10 +22,11 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("cwa")) #' segment of a TOXSWA surface water body. Per default, the data for the last #' segment are imported. As TOXSWA 4 reports the values at the end of the hour #' (ConLiqWatLayCur) in its summary file, we use this value as well instead -#' of the hourly averages (ConLiqWatLay). +#' of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was +#' renamed to ConLiqWatLay in the out file. #' #' @param filename The filename of the cwa file (TOXSWA 2.x.y or similar) or the -#' out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar). +#' out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher. #' @param basedir The path to the directory where the cwa file resides. #' @param zipfile Optional path to a zip file containing the cwa file. #' @param segment The segment for which the data should be read. Either "last", or @@ -33,7 +34,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("cwa")) #' @param total Set this to TRUE in order to read total concentrations as well. This is #' only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa #' files. For .cwa files, the total concentration is always read as well. -#' @param substance For TOXSWA 4 .out files, the default value "parent" leads +#' @param substance For .out files, the default value "parent" leads #' to reading concentrations of the parent compound. Alternatively, the substance #' of interested can be selected by its code name. #' @param windows Numeric vector of width of moving windows in days, for calculating @@ -155,9 +156,9 @@ plot.TOXSWA_cwa <- function(x, time_column = c("datetime", "t", "t_firstjan", "t tmp <- Sys.setlocale("LC_TIME", lct) } -#' R6 class for holding TOXSWA cwa concentration data and associated statistics +#' R6 class for holding TOXSWA water concentration data and associated statistics #' -#' An R6 class for holding TOXSWA cwa concentration data and some associated statistics. +#' An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. #' Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. #' #' @docType class diff --git a/README.html b/README.html index 026f011..ef6dfca 100644 --- a/README.html +++ b/README.html @@ -15,7 +15,7 @@ - + @@ -138,7 +138,11 @@ You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>

Installation

-

You can install the package from github, e.g. using the devtools package. Using quick = TRUE skips docs, multiple-architecture builds, demos, and vignettes, to make installation as fast and painless as possible.

+

The easiest way to install the package is probably to use drat:

+
install.packages("drat")
+drat::addRepo("jranke")
+install.packages("pfm")
+

Alternatively you can install the package using the devtools package. Using quick = TRUE skips docs, multiple-architecture builds, demos, and vignettes.

library(devtools)
 install_github("jranke/pfm", quick = TRUE)
diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index feed9d5..5073067 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -150,7 +150,7 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012).

interval

Period of the deeper mixing, defaults to 365, which is a year if -rate units are in days

+degradation rate units are in days

n_periods diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html index 1eac49b..5d53104 100644 --- a/docs/reference/PELMO_runs.html +++ b/docs/reference/PELMO_runs.html @@ -229,7 +229,7 @@ the period.plm file generated by the FOCUS PELMO GUI.

#> #>
# We get exactly the same PECgw values (on Linux, calling PELMO using Wine). print(time_1)
#> User System verstrichen -#> 0.398 0.100 30.624
if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { +#> 0.384 0.095 30.954
if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]])) }
#> CPU model: AMD Ryzen 7 1700 Eight-Core Processor
# Demonstrate some results with metabolites. diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index 3b11804..932e6ef 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -6,7 +6,7 @@ -R6 class for holding TOXSWA cwa concentration data and associated statistics — TOXSWA_cwa • pfm +R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm @@ -30,9 +30,9 @@ - + - @@ -98,14 +98,14 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
-

R6 class for holding TOXSWA cwa concentration data and associated statistics

+

R6 class for holding TOXSWA water concentration data and associated statistics

Source: R/TOXSWA_cwa.R
-

An R6 class for holding TOXSWA cwa concentration data and some associated statistics. +

An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. Usually, an instance of this class will be generated by read.TOXSWA_cwa.

diff --git a/docs/reference/index.html b/docs/reference/index.html index c153b50..162298b 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -311,7 +311,7 @@ water concentrations

TOXSWA_cwa

-

R6 class for holding TOXSWA cwa concentration data and associated statistics

+

R6 class for holding TOXSWA water concentration data and associated statistics

diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt index 85f103d..d4fd84e 100644 --- a/docs/reference/pesticide.txt +++ b/docs/reference/pesticide.txt @@ -35,3 +35,5 @@ Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Du M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index 60e236a..aa18ec4 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -36,7 +36,8 @@ segment of a TOXSWA surface water body. Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour (ConLiqWatLayCur) in its summary file, we use this value as well instead -of the hourly averages (ConLiqWatLay)." /> +of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was +renamed to ConLiqWatLay in the out file." /> @@ -112,7 +113,8 @@ of the hourly averages (ConLiqWatLay)." /> segment of a TOXSWA surface water body. Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour (ConLiqWatLayCur) in its summary file, we use this value as well instead -of the hourly averages (ConLiqWatLay).

+of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was +renamed to ConLiqWatLay in the out file.

@@ -126,7 +128,7 @@ of the hourly averages (ConLiqWatLay).

filename

The filename of the cwa file (TOXSWA 2.x.y or similar) or the -out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).

+out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.

basedir @@ -143,7 +145,7 @@ the segment number.

substance -

For TOXSWA 4 .out files, the default value "parent" leads +

For .out files, the default value "parent" leads to reading concentrations of the parent compound. Alternatively, the substance of interested can be selected by its code name.

diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd index dd780cf..1491790 100644 --- a/man/PEC_soil.Rd +++ b/man/PEC_soil.Rd @@ -24,7 +24,7 @@ PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5, \item{PEC_pw_units}{Only mg/L currently supported} \item{interval}{Period of the deeper mixing, defaults to 365, which is a year if -rate units are in days} +degradation rate units are in days} \item{n_periods}{Number of periods to be considered for long term PEC calculations} diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd index 3152c6e..f073180 100644 --- a/man/TOXSWA_cwa.Rd +++ b/man/TOXSWA_cwa.Rd @@ -3,13 +3,13 @@ \docType{class} \name{TOXSWA_cwa} \alias{TOXSWA_cwa} -\title{R6 class for holding TOXSWA cwa concentration data and associated statistics} +\title{R6 class for holding TOXSWA water concentration data and associated statistics} \format{An \code{\link{R6Class}} generator object.} \usage{ TOXSWA_cwa } \description{ -An R6 class for holding TOXSWA cwa concentration data and some associated statistics. +An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. } \section{Fields}{ diff --git a/man/read.TOXSWA_cwa.Rd b/man/read.TOXSWA_cwa.Rd index 2541c9b..c76fdbd 100644 --- a/man/read.TOXSWA_cwa.Rd +++ b/man/read.TOXSWA_cwa.Rd @@ -10,7 +10,7 @@ read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", } \arguments{ \item{filename}{The filename of the cwa file (TOXSWA 2.x.y or similar) or the -out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).} +out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.} \item{basedir}{The path to the directory where the cwa file resides.} @@ -19,7 +19,7 @@ out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).} \item{segment}{The segment for which the data should be read. Either "last", or the segment number.} -\item{substance}{For TOXSWA 4 .out files, the default value "parent" leads +\item{substance}{For .out files, the default value "parent" leads to reading concentrations of the parent compound. Alternatively, the substance of interested can be selected by its code name.} @@ -42,7 +42,8 @@ Read TOXSWA hourly concentrations of a chemical substance in a specific segment of a TOXSWA surface water body. Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour (ConLiqWatLayCur) in its summary file, we use this value as well instead -of the hourly averages (ConLiqWatLay). +of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was +renamed to ConLiqWatLay in the out file. } \examples{ H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", -- cgit v1.2.1 From c4c3ca282c6aadca82e392692ae4100fec1dd834 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 10 Jul 2018 16:46:47 +0200 Subject: .out file from TOXSWA 5.5.3 for testing --- inst/testdata/SwashProjects_TOXSWA_553.zip | Bin 0 -> 2395548 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 inst/testdata/SwashProjects_TOXSWA_553.zip diff --git a/inst/testdata/SwashProjects_TOXSWA_553.zip b/inst/testdata/SwashProjects_TOXSWA_553.zip new file mode 100644 index 0000000..b32c3e9 Binary files /dev/null and b/inst/testdata/SwashProjects_TOXSWA_553.zip differ -- cgit v1.2.1 From cb3695dd434b3a3273217fb22c5ffb86065ae96d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 10 Jul 2018 17:57:33 +0200 Subject: EFSA PEC soil guidance from 2017 - Implement the new guidance as well as possible - Maintenance work addressing CRAN checks --- .Rbuildignore | 1 + ChangeLog | 14 +++ DESCRIPTION | 4 +- GNUmakefile | 2 +- R/PEC_soil.R | 213 +++++++++++++++++++++++++------- R/PEC_sw_exposit_runoff.R | 1 + R/soil_scenario_data_EFSA_2015.R | 8 +- R/soil_scenario_data_EFSA_2017.R | 20 +++ README.html | 2 +- README.md | 2 +- build.log | 3 +- data/soil_scenario_data_EFSA_2017.RData | Bin 0 -> 582 bytes man/PEC_soil.Rd | 59 +++++++-- man/perc_runoff_exposit.Rd | 1 + man/soil_scenario_data_EFSA_2015.Rd | 8 +- man/soil_scenario_data_EFSA_2017.Rd | 25 ++++ test.log | 38 +++--- tests/testthat/test_PEC_soil.R | 68 +++++++--- tests/testthat/test_PELMO.R | 10 +- tests/testthat/test_TOXSWA.R | 49 +++++--- 20 files changed, 407 insertions(+), 121 deletions(-) create mode 100644 R/soil_scenario_data_EFSA_2017.R create mode 100644 data/soil_scenario_data_EFSA_2017.RData create mode 100644 man/soil_scenario_data_EFSA_2017.Rd diff --git a/.Rbuildignore b/.Rbuildignore index cbcae93..b6fc8e9 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -4,6 +4,7 @@ ^README.html$ ^build.log$ ^test.log$ +^test.R$ ^inst/extdata/Tabelle\ der\ Abdrifteckwerte.xls$ ^inst/extdata/FOCUS_Step_12_scenarios.txt$ ^_pkgdown.yml$ diff --git a/ChangeLog b/ChangeLog index 2960fbe..e9c2e8a 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,17 @@ +commit c4c3ca282c6aadca82e392692ae4100fec1dd834 +Author: Johannes Ranke +Date: 2018-07-10 16:46:47 +0200 + + .out file from TOXSWA 5.5.3 for testing + +commit 8989a484b9b2d23463c95e0a3927e307ec0a5e64 +Author: Johannes Ranke +Date: 2018-07-04 10:59:47 +0200 + + Some documentation updates + + Document that TOXSWA 5.5.3 is supported in the help files + commit 6ca8bdb8636141fac592688a6794ae092f0bc85a Author: Johannes Ranke Date: 2018-06-20 14:58:44 +0200 diff --git a/DESCRIPTION b/DESCRIPTION index c1d967f..c7ea8a9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling -Version: 0.4-6 -Date: 2018-07-04 +Version: 0.5.1 +Date: 2018-07-10 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-4371-6538")) diff --git a/GNUmakefile b/GNUmakefile index a6b575c..c10c13a 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -57,7 +57,7 @@ winbin: $(WINBIN) test: build @echo "Running testthat tests..." - "$(R_HOME)/bin/Rscript" -e 'devtools::test()' 2>&1 | tee test.log + NOT_CRAN=true "$(R_HOME)/bin/Rscript" -e 'devtools::test()' 2>&1 | tee test.log @echo "DONE." quickcheck: build diff --git a/R/PEC_soil.R b/R/PEC_soil.R index 15ccc90..1227f6a 100644 --- a/R/PEC_soil.R +++ b/R/PEC_soil.R @@ -17,23 +17,34 @@ # Register global variables if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_type", "TP_identifier", - "soil_scenario_data_EFSA_2015")) + "soil_scenario_data_EFSA_2015", + "soil_scenario_data_EFSA_2017", "bottom")) #' 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 +#' 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 for example in the PPR panel opinion (EFSA 2012). -#' +#' 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). +#' #' 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 (PPR panel 2012), only temperature correction using the -#' Arrhenius equation is performed. -#' +#' 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 (2015, p. 13) can easily be calculated. -#' +#' 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) are be reproduced, this is not +#' true for the TWA concentrations given for the same example in the EFSA guidance +#' from 2017 (p. 92). +#' @note 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. #' @note 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 @@ -49,7 +60,17 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_typ #' @param PEC_units Requested units for the calculated PEC. Only mg/kg currently supported #' @param PEC_pw_units Only mg/L currently supported #' @param tillage_depth Periodic (see interval) deeper mixing in cm -#' @param chent An optional chent object holding substance specific information. Can +#' @param 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. +#' @param 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 +#' @param 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. +#' @param chent An optional chent object holding substance specific information. Can #' also be a name for the substance as a character string #' @param 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 @@ -65,6 +86,8 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_typ #' 'chents' 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. +#' @param leaching Should leaching be taken into account? The default is FALSE, +#' except when the EFSA_2017 scenarios are used. #' @param 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 @@ -76,23 +99,38 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_typ #' selection and scenario parameterisation for predicting environmental #' concentrations of plant protection products in soil. \emph{EFSA Journal} #' \bold{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. \emph{EFSA Journal} \bold{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. \emph{EFSA Journal} \bold{13}(4) 4093 #' doi:10.2903/j.efsa.2015.4093 +#' #' @author Johannes Ranke #' @export #' @examples #' PEC_soil(100, interception = 0.25) #' +#' # 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") +#' PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), +#' Kom = 1000, scenarios = "EFSA_2017", porewater = TRUE) +#' #' # 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") #' PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), #' Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) -#' +#' #' # 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 @@ -103,34 +141,97 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_typ #' Kom = 100, scenarios = "EFSA_2015", porewater = TRUE) PEC_soil <- function(rate, rate_units = "g/ha", interception = 0, - mixing_depth = 5, + mixing_depth = 5, PEC_units = "mg/kg", PEC_pw_units = "mg/L", interval = NA, n_periods = Inf, - tillage_depth = 20, - chent = NA, - DT50 = NA, + tillage_depth = 20, + leaching_depth = tillage_depth, + crop = "annual", + cultivation = FALSE, + chent = NA, + DT50 = NA, Koc = NA, Kom = Koc / 1.724, t_avg = 0, - scenarios = c("default", "EFSA_2015"), + scenarios = c("default", "EFSA_2017", "EFSA_2015"), + leaching = scenarios == "EFSA_2017", porewater = FALSE) { + # Comments with equation numbers in parentheses refer to + # the numbering in the EFSA guidance from 2017, appendix A rate_to_soil = (1 - interception) * rate rate_units = match.arg(rate_units) PEC_units = match.arg(PEC_units) scenarios = match.arg(scenarios) - sce <- switch(scenarios, + if (scenarios == "EFSA_2017") { + if (crop != "annual") stop("Only annual crops are currently supported") + if (cultivation) stop("Permanent crops with mechanical cultivation are currently not supported") + } + sce <- switch(scenarios, default = data.frame(rho = 1.5, T_arr = NA, theta_fc = 0.2, f_om = 1.724 * 0.02, f_sce = 1, f_mod = 1, row.names = "default"), - EFSA_2015 = if (porewater) soil_scenario_data_EFSA_2015[4:6, ] - else soil_scenario_data_EFSA_2015[1:3, ] + EFSA_2015 = if (porewater) soil_scenario_data_EFSA_2015[4:6, ] + else soil_scenario_data_EFSA_2015[1:3, ], + EFSA_2017 = if (porewater) soil_scenario_data_EFSA_2017[4:6, ] + else soil_scenario_data_EFSA_2017[1:3, ] ) n_sce = nrow(sce) soil_volume = 100 * 100 * (mixing_depth/100) # in m3 soil_mass = soil_volume * sce$rho * 1000 # in kg + # In EFSA (2017), f_om is depth dependent for permanent crops + # For annual crops, the correction factor is 1 (uniform f_om is + # assumed) + mixing_depth_string <- paste(mixing_depth, "cm") + tillage_depth_string <- paste(tillage_depth, "cm") + if (scenarios == "EFSA_2017" & crop != "annual") { + # Correction factors f_f_om with depth according to EFSA 2017, p. 15 + f_f_om_depth = data.frame( + depth = c("0-5", "5-10", "10-20", "20-30"), + bottom = c(5, 10, 20, 30), + thickness = c(5, 5, 10, 10), + f_f_om_no_cultivation = c(1.95, 1.30, 0.76, 0.62), + f_f_om_cultivation = c(1.50, 1.20, 0.90, 0.75)) + # Averages for the 0-5 cm and 0-20 cm layers + f_f_om_layer = data.frame( + layer = c("0-5", "0-20"), + f_f_om_no_cultivation = c(1.95, (5 * 1.95 + 5 * 1.3 + 10 * 0.76)/20), + f_f_om_cultivation = c(1.50, (5 * 1.5 + 5 * 1.2 + 10 * 0.9)/20)) + # The resulting mean value for 0-20 cm and no cultivation of 1.1925 is + # consistent with the value of 1.19 given in Table B.4 on p. 54 of the + # 2017 EFSA guidance + + f_f_om_average <- function(depth, cultivation) { + rownames(f_f_om_layer) = paste(f_f_om_layer$layer, "cm") + if (depth %in% c(5, 20)) { + if (cultivation) { + return(f_f_om_layer[paste0("0-", depth, " cm"), "f_f_om_cultivation"]) + } else { + return(f_f_om_layer[paste0("0-", depth, " cm"), "f_f_om_no_cultivation"]) + } + } else { + stop("Depths other than 5 and 20 cm are not supported when using EFSA 2017 scenarios for permanent crops") + } + } + + # For the loss via leaching, the equilibrium and therefore the f_om at the + # bottom of the layer is probably most relevant. Unfortunately this is not + # clarified in the guidance. + f_f_om_bottom <- function(depth, cultivation) { + bottom_depth <- depth # rename to avoid confusion when subsetting + if (cultivation) { + f_f_om <- subset(f_f_om_depth, bottom == bottom_depth)$f_f_om_cultivation + } else { + f_f_om <- subset(f_f_om_depth, bottom == bottom_depth)$f_f_om_no_cultivation + } + return(f_f_om) + } + } else { + f_f_om_average <- f_f_om_bottom <- function(depth, cultivation) 1 + } + # The following is C_T,ini from EFSA 2012, p. 22, but potentially with interception > 0 - PEC_soil_ini = rate_to_soil * 1000 / soil_mass # in mg/kg + PEC_soil_ini = rate_to_soil * 1000 / soil_mass # in mg/kg (A1) # Decide which DT50 to take, or set degradation to zero if no DT50 available if (is.na(DT50) & is(chent, "chent")) { @@ -142,26 +243,56 @@ PEC_soil <- function(rate, rate_units = "g/ha", interception = 0, if (length(DT50) > 1) stop("More than one PECsoil DT50 in chent object") if (length(DT50) == 0) DT50 <- Inf } - k = log(2)/DT50 + k_ref = log(2)/DT50 # (A5) # Temperature correction of degradation (accumulation) if (all(is.na(sce$T_arr))) { # No temperature correction f_T = 1 } else { # Temperature correction as in EFSA 2012 p. 23 - f_T = ifelse(sce$T_arr == 0, - 0, - exp(- (65.4 / 0.008314) * (1/(sce$T_arr + 273.15) - 1/293.15))) + f_T = ifelse(sce$T_arr == 0, + 0, # (A4b) + exp(- (65.4 / 0.008314) * (1/(sce$T_arr + 273.15) - 1/293.15))) # (A4a) } - # X is the fraction left after one period (EFSA guidance p. 23) - X = exp(- k * f_T * interval) - + # Define Kom if needed + if (leaching | porewater) { + # If Kom is not specified, try to get K(f)oc + if (is.na(Kom)) { + # If Koc not specified, try to get K(f)oc from chent + if (is.na(Koc) & is(chent, "chent")) { + Koc <- soil_Kfoc(chent) + } else { + stop("No Kom information specified") + } + Kom <- Koc / 1.724 + } + } + + if (leaching) { + leaching_depth_string <- paste(leaching_depth, "cm") + f_q <- c("1 cm" = 0.8, "2.5 cm" = 0.75, "5 cm" = 0.7, "20 cm" = 0.5) # EFSA 2017 p. 54 + if (leaching_depth_string %in% names(f_q)) { + q_mm_year = f_q[leaching_depth_string] * sce$prec # Irrigation at tier 1? I have not found values for Tier 1 + q_dm_day = q_mm_year / (100 * 365) + leaching_depth_dm <- leaching_depth / 10 + + k_leach = q_dm_day/(leaching_depth_dm * (sce$theta_fc + sce$rho * f_f_om_average(leaching_depth, cultivation) * sce$f_om * Kom)) + } else { + stop("Leaching can not be calculated, because f_q for this leaching depth is undefined") + } + } else { + k_leach = 0 + } + + # X is the fraction left after one period (EFSA 2017 guidance p. 23) + X = exp(- (k_ref * f_T + k_leach) * interval) # (A3) + # f_accu is the fraction left after n periods (X + X^2 + ...) - f_accu = 0 + f_accu = 0 if (!is.na(interval)) { if (n_periods == Inf) { - f_accu = X/(1 - X) + f_accu = X/(1 - X) # part of (A2) } else { for (i in 1:n_periods) { f_accu = f_accu + X^i @@ -171,25 +302,14 @@ PEC_soil <- function(rate, rate_units = "g/ha", interception = 0, f_tillage = mixing_depth / tillage_depth - PEC_background = f_accu * f_tillage * PEC_soil_ini + PEC_background = f_accu * f_tillage * PEC_soil_ini # (A2) - PEC_soil = (1 + f_accu * f_tillage) * PEC_soil_ini + PEC_soil = PEC_soil_ini + PEC_background # (A6) # Get porewater PEC if requested if (porewater) { - # If Kom is not specified, try to get K(f)oc - if (is.na(Kom)) { - # If Koc not specified, try to get K(f)oc from chent - if (is.na(Koc) & is(chent, "chent")) { - Koc <- soil_Kfoc(chent) - } - Kom <- Koc / 1.724 - } - - if (is.na(Kom)) stop("No Kom information specified") - - PEC_soil = PEC_soil/((sce$theta_fc/sce$rho) + sce$f_om * Kom) + PEC_soil = PEC_soil/((sce$theta_fc/sce$rho) + f_f_om_average(mixing_depth, cultivation) * sce$f_om * Kom) # (A7) } # Scenario adjustment factors @@ -200,14 +320,15 @@ PEC_soil <- function(rate, rate_units = "g/ha", interception = 0, result <- matrix(NA, ncol = n_sce, nrow = length(t_avg), dimnames = list(t_avg = t_avg, scenario = rownames(sce))) - + result[1, ] <- PEC_soil_sce_mod for (i in seq_along(t_avg)) { t_av_i <- t_avg[i] + k_avg <- f_T * k_ref # Leaching not taken into account, EFSA 2017 p. 43 if (t_av_i > 0) { # Equation 10 from p. 24 (EFSA 2015) - result[i, ] <- PEC_soil_sce_mod/(t_av_i * f_T * k) * (1 - exp(- f_T * k * t_av_i)) + result[i, ] <- PEC_soil_sce_mod/(t_av_i * k_avg) * (1 - exp(- k_avg * t_av_i)) # (A8) } } diff --git a/R/PEC_sw_exposit_runoff.R b/R/PEC_sw_exposit_runoff.R index f56b8f8..733f621 100644 --- a/R/PEC_sw_exposit_runoff.R +++ b/R/PEC_sw_exposit_runoff.R @@ -6,6 +6,7 @@ #' @format A data frame with percentage values for the dissolved fraction and the fraction #' bound to eroding particles, with Koc classes used as row names #' \describe{ +#' \item{Koc_lower_bound}{The lower bound of the Koc class} #' \item{dissolved}{The percentage of the applied substance transferred to an #' adjacent water body in the dissolved phase} #' \item{bound}{The percentage of the applied substance transferred to an diff --git a/R/soil_scenario_data_EFSA_2015.R b/R/soil_scenario_data_EFSA_2015.R index fb096bc..660cafe 100644 --- a/R/soil_scenario_data_EFSA_2015.R +++ b/R/soil_scenario_data_EFSA_2015.R @@ -10,10 +10,10 @@ #' e.g. CTN for the Northern scenario for the total concentration in soil. Columns are #' mostly self-explanatory. \code{rho} is the dry bulk density of the top soil. #' @source 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. \emph{EFSA Journal} \bold{13}(4) 4093 -#' doi:10.2903/j.efsa.2015.4093 +#' EFSA guidance document for predicting environmental concentrations +#' of active substances of plant protection products and transformation products of these +#' active substances in soil. \emph{EFSA Journal} \bold{13}(4) 4093 +#' doi:10.2903/j.efsa.2015.4093 #' @keywords datasets #' @examples #' \dontrun{ diff --git a/R/soil_scenario_data_EFSA_2017.R b/R/soil_scenario_data_EFSA_2017.R new file mode 100644 index 0000000..79ee15f --- /dev/null +++ b/R/soil_scenario_data_EFSA_2017.R @@ -0,0 +1,20 @@ +#' Properties of the predefined scenarios from the EFSA guidance from 2017 +#' +#' Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the +#' concentration in soil as given in the EFSA guidance (2017, p. 14/15). Also, the +#' scenario and model adjustment factors from p. 16 and p. 18 are included. +#' +#' @name soil_scenario_data_EFSA_2017 +#' @docType data +#' @format A data frame with one row for each scenario. Row names are the scenario codes, +#' e.g. CTN for the Northern scenario for the total concentration in soil. Columns are +#' mostly self-explanatory. \code{rho} is the dry bulk density of the top soil. +#' @source 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. \emph{EFSA Journal} \bold{15}(10) 4982 +#' doi:10.2903/j.efsa.2017.4982 +#' @keywords datasets +#' @examples +#' soil_scenario_data_EFSA_2017 +NULL diff --git a/README.html b/README.html index ef6dfca..77a9d18 100644 --- a/README.html +++ b/README.html @@ -138,7 +138,7 @@ You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>

Installation

-

The easiest way to install the package is probably to use drat:

+

The easiest way to install the package is probably to use drat:

install.packages("drat")
 drat::addRepo("jranke")
 install.packages("pfm")
diff --git a/README.md b/README.md index 68874f2..ab34018 100644 --- a/README.md +++ b/README.md @@ -21,7 +21,7 @@ This means: ## Installation The easiest way to install the package is probably to use -[drat](http://cran.r-project.org/package=drat): +[drat](https://cran.r-project.org/package=drat): ```r install.packages("drat") diff --git a/build.log b/build.log index ea12067..e77bb21 100644 --- a/build.log +++ b/build.log @@ -3,6 +3,7 @@ * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories +Removed empty directory ‘pfm/inst/testdata/SwashProjects/Project_1/MACRO’ * looking to see if a ‘data/datalist’ file should be added -* building ‘pfm_0.4-6.tar.gz’ +* building ‘pfm_0.5.1.tar.gz’ diff --git a/data/soil_scenario_data_EFSA_2017.RData b/data/soil_scenario_data_EFSA_2017.RData new file mode 100644 index 0000000..ff8f045 Binary files /dev/null and b/data/soil_scenario_data_EFSA_2017.RData differ diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd index 1491790..f9e82e8 100644 --- a/man/PEC_soil.Rd +++ b/man/PEC_soil.Rd @@ -6,9 +6,11 @@ \usage{ 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, chent = NA, DT50 = NA, + n_periods = Inf, tillage_depth = 20, leaching_depth = tillage_depth, + crop = "annual", cultivation = FALSE, chent = NA, DT50 = NA, Koc = NA, Kom = Koc/1.724, t_avg = 0, scenarios = c("default", - "EFSA_2015"), porewater = FALSE) + "EFSA_2017", "EFSA_2015"), leaching = scenarios == "EFSA_2017", + porewater = FALSE) } \arguments{ \item{rate}{Application rate in units specified below} @@ -30,7 +32,20 @@ degradation rate units are in days} \item{tillage_depth}{Periodic (see interval) deeper mixing in cm} -\item{chent}{An optional chent object holding substance specific information. Can +\item{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.} + +\item{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.} + +\item{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} + +\item{chent}{An optional chent object holding substance specific information. Can also be a name for the substance as a character string} \item{DT50}{If specified, overrides soil DT50 endpoints from a chent object @@ -52,6 +67,9 @@ the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also model and scenario adjustment factors from the EFSA guidance are used.} +\item{leaching}{Should leaching be taken into account? The default is FALSE, +except when the EFSA_2017 scenarios are used.} + \item{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 @@ -63,20 +81,33 @@ The predicted concentration in soil } \description{ This is a basic calculation of a contaminant concentration in bulk soil -based on complete, instantaneous mixing. If an interval is given, an +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 for example in the PPR panel opinion (EFSA 2012). +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). } \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 (PPR panel 2012), only temperature correction using the +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 (2015, p. 13) can easily be calculated. +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) are 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 @@ -85,6 +116,14 @@ If temperature information is available in the selected scenarios, as \examples{ PEC_soil(100, interception = 0.25) +# 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") +PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), + Kom = 1000, scenarios = "EFSA_2017", porewater = TRUE) + # 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") @@ -107,6 +146,12 @@ EFSA Panel on Plant Protection Products and their Residues (2012) concentrations of plant protection products in soil. \emph{EFSA Journal} \bold{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. \emph{EFSA Journal} \bold{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 diff --git a/man/perc_runoff_exposit.Rd b/man/perc_runoff_exposit.Rd index 4f460e4..bdc36e8 100644 --- a/man/perc_runoff_exposit.Rd +++ b/man/perc_runoff_exposit.Rd @@ -6,6 +6,7 @@ \format{A data frame with percentage values for the dissolved fraction and the fraction bound to eroding particles, with Koc classes used as row names \describe{ + \item{Koc_lower_bound}{The lower bound of the Koc class} \item{dissolved}{The percentage of the applied substance transferred to an adjacent water body in the dissolved phase} \item{bound}{The percentage of the applied substance transferred to an diff --git a/man/soil_scenario_data_EFSA_2015.Rd b/man/soil_scenario_data_EFSA_2015.Rd index 02c16dc..64c00a8 100644 --- a/man/soil_scenario_data_EFSA_2015.Rd +++ b/man/soil_scenario_data_EFSA_2015.Rd @@ -9,10 +9,10 @@ mostly self-explanatory. \code{rho} is the dry bulk density of the top soil.} \source{ 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. \emph{EFSA Journal} \bold{13}(4) 4093 -doi:10.2903/j.efsa.2015.4093 + EFSA guidance document for predicting environmental concentrations + of active substances of plant protection products and transformation products of these + active substances in soil. \emph{EFSA Journal} \bold{13}(4) 4093 + doi:10.2903/j.efsa.2015.4093 } \description{ Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the diff --git a/man/soil_scenario_data_EFSA_2017.Rd b/man/soil_scenario_data_EFSA_2017.Rd new file mode 100644 index 0000000..aeaacac --- /dev/null +++ b/man/soil_scenario_data_EFSA_2017.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/soil_scenario_data_EFSA_2017.R +\docType{data} +\name{soil_scenario_data_EFSA_2017} +\alias{soil_scenario_data_EFSA_2017} +\title{Properties of the predefined scenarios from the EFSA guidance from 2017} +\format{A data frame with one row for each scenario. Row names are the scenario codes, + e.g. CTN for the Northern scenario for the total concentration in soil. Columns are + mostly self-explanatory. \code{rho} is the dry bulk density of the top soil.} +\source{ +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. \emph{EFSA Journal} \bold{15}(10) 4982 + doi:10.2903/j.efsa.2017.4982 +} +\description{ +Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the +concentration in soil as given in the EFSA guidance (2017, p. 14/15). Also, the +scenario and model adjustment factors from p. 16 and p. 18 are included. +} +\examples{ +soil_scenario_data_EFSA_2017 +} +\keyword{datasets} diff --git a/test.log b/test.log index 2692d54..f16336b 100644 --- a/test.log +++ b/test.log @@ -2,23 +2,25 @@ Loading pfm Loading required package: testthat Loading required package: R6 Loading required package: mkin -Loading required package: minpack.lm -Loading required package: rootSolve -Loading required package: inline -Loading required package: methods -Loading required package: parallel Testing pfm -Exposit runoff calculations: ... -Geometric mean calculation: ...... -Check max_twa for parent mkinfit models against analytical solutions: . -Simple PEC sediment calculations: . -Simple PEC soil calculations: ........... -Simple PEC surface water calculations with drift entry: .. -Create PELMO runs from psm files and execute them: ........................................................................................................................................................................................................................... -Actual and time weighted average concentrations for SFO kinetics: . -FOCUS Step 1 calculations: ......... -FOCUS Steps 12 input files: ........ -Read and analyse TOXSWA cwa files: ....... -UK drainage PEC calculations: ............ +✔ | OK F W S | Context + ⠏ | 0 | Exposit runoff calculations ⠋ | 1 | Exposit runoff calculations ⠙ | 2 | Exposit runoff calculations ⠹ | 3 | Exposit runoff calculations ✔ | 3 | Exposit runoff calculations + ⠏ | 0 | Geometric mean calculation ⠋ | 1 | Geometric mean calculation ⠙ | 2 | Geometric mean calculation ⠹ | 3 | Geometric mean calculation ⠸ | 4 | Geometric mean calculation ⠼ | 5 | Geometric mean calculation ⠴ | 6 | Geometric mean calculation ✔ | 6 | Geometric mean calculation + ⠏ | 0 | Check max_twa for parent mkinfit models against analytical solutions ⠋ | 1 | Check max_twa for parent mkinfit models against analytical solutions ✔ | 1 | Check max_twa for parent mkinfit models against analytical solutions [1.0 s] + ⠏ | 0 | Simple PEC sediment calculations ⠋ | 1 | Simple PEC sediment calculations ✔ | 1 | Simple PEC sediment calculations + ⠏ | 0 | Simple PEC soil calculations ⠋ | 1 | Simple PEC soil calculations ⠙ | 2 | Simple PEC soil calculations ⠹ | 3 | Simple PEC soil calculations ⠸ | 4 | Simple PEC soil calculations ⠼ | 5 | Simple PEC soil calculations ⠴ | 6 | Simple PEC soil calculations ⠦ | 7 | Simple PEC soil calculations ⠧ | 8 | Simple PEC soil calculations ⠇ | 9 | Simple PEC soil calculations ⠏ | 10 | Simple PEC soil calculations ⠋ | 11 | Simple PEC soil calculations ⠙ | 12 | Simple PEC soil calculations ⠹ | 13 | Simple PEC soil calculations ✔ | 13 | Simple PEC soil calculations + ⠏ | 0 | Simple PEC surface water calculations with drift entry ⠋ | 1 | Simple PEC surface water calculations with drift entry ⠙ | 2 | Simple PEC surface water calculations with drift entry ✔ | 2 | Simple PEC surface water calculations with drift entry + ⠏ | 0 | Create PELMO runs from psm files and execute them ⠋ | 1 | Create PELMO runs from psm files and execute them ⠙ | 2 | Create PELMO runs from psm files and execute them ⠹ | 3 | Create PELMO runs from psm files and execute them ⠸ | 4 | Create PELMO runs from psm files and execute them ⠼ | 5 | Create PELMO runs from psm files and execute them ⠴ | 6 | Create PELMO runs from psm files and execute them ⠦ | 7 | Create PELMO runs from psm files and execute them ⠧ | 8 | Create PELMO runs from psm files and execute them ⠇ | 9 | Create PELMO runs from psm files and execute them ⠏ | 10 | Create PELMO runs from psm files and execute them ⠋ | 11 | Create PELMO runs from psm files and execute them ⠙ | 12 | Create PELMO runs from psm files and execute them ⠹ | 13 | Create PELMO runs from psm files and execute them ⠸ | 14 | Create PELMO runs from psm files and execute them ⠼ | 15 | Create PELMO runs from psm files and execute them ⠴ | 16 | Create PELMO runs from psm files and execute them ⠦ | 17 | Create PELMO runs from psm files and execute them ⠧ | 18 | Create PELMO runs from psm files and execute them ⠇ | 19 | Create PELMO runs from psm files and execute them ⠏ | 20 | Create PELMO runs from psm files and execute them ⠋ | 21 | Create PELMO runs from psm files and execute them ⠙ | 22 | Create PELMO runs from psm files and execute them ⠹ | 23 | Create PELMO runs from psm files and execute them ⠸ | 24 | Create PELMO runs from psm files and execute them ⠼ | 25 | Create PELMO runs from psm files and execute them ⠴ | 26 | Create PELMO runs from psm files and execute them ⠦ | 27 | Create PELMO runs from psm files and execute them ⠧ | 28 | Create PELMO runs from psm files and execute them ⠇ | 29 | Create PELMO runs from psm files and execute them ⠏ | 30 | Create PELMO runs from psm files and execute them ⠋ | 31 | Create PELMO runs from psm files and execute them ⠙ | 32 | Create PELMO runs from psm files and execute them ⠹ | 33 | Create PELMO runs from psm files and execute them ⠸ | 34 | Create PELMO runs from psm files and execute them ⠼ | 35 | Create PELMO runs from psm files and execute them ⠴ | 36 | Create PELMO runs from psm files and execute them ⠦ | 37 | Create PELMO runs from psm files and execute them ⠧ | 38 | Create PELMO runs from psm files and execute them ⠇ | 39 | Create PELMO runs from psm files and execute them ⠏ | 40 | Create PELMO runs from psm files and execute them ⠋ | 41 | Create PELMO runs from psm files and execute them ⠙ | 42 | Create PELMO runs from psm files and execute them ⠹ | 43 | Create PELMO runs from psm files and execute them ⠸ | 44 | Create PELMO runs from psm files and execute them ⠼ | 45 | Create PELMO runs from psm files and execute them ⠴ | 46 | Create PELMO runs from psm files and execute them ⠦ | 47 | Create PELMO runs from psm files and execute them ⠧ | 48 | Create PELMO runs from psm files and execute them ⠇ | 49 | Create PELMO runs from psm files and execute them ⠏ | 50 | Create PELMO runs from psm files and execute them ⠋ | 51 | Create PELMO runs from psm files and execute them ⠙ | 52 | Create PELMO runs from psm files and execute them ⠹ | 53 | Create PELMO runs from psm files and execute them ⠸ | 54 | Create PELMO runs from psm files and execute them ⠼ | 55 | Create PELMO runs from psm files and execute them ⠴ | 56 | Create PELMO runs from psm files and execute them ⠦ | 57 | Create PELMO runs from psm files and execute them ⠧ | 58 | Create PELMO runs from psm files and execute them ⠇ | 59 | Create PELMO runs from psm files and execute them ⠏ | 60 | Create PELMO runs from psm files and execute them ⠋ | 61 | Create PELMO runs from psm files and execute them ⠙ | 62 | Create PELMO runs from psm files and execute them ⠹ | 63 | Create PELMO runs from psm files and execute them ⠸ | 64 | Create PELMO runs from psm files and execute them ⠼ | 65 | Create PELMO runs from psm files and execute them ⠴ | 66 | Create PELMO runs from psm files and execute them ⠦ | 67 | Create PELMO runs from psm files and execute them ⠧ | 68 | Create PELMO runs from psm files and execute them ⠇ | 69 | Create PELMO runs from psm files and execute them ⠏ | 70 | Create PELMO runs from psm files and execute them ⠋ | 71 | Create PELMO runs from psm files and execute them ⠙ | 72 | Create PELMO runs from psm files and execute them ⠹ | 73 | Create PELMO runs from psm files and execute them ⠸ | 74 | Create PELMO runs from psm files and execute them ⠼ | 75 | Create PELMO runs from psm files and execute them ⠴ | 76 | Create PELMO runs from psm files and execute them ⠦ | 77 | Create PELMO runs from psm files and execute them ⠧ | 78 | Create PELMO runs from psm files and execute them ⠇ | 79 | Create PELMO runs from psm files and execute them ⠏ | 80 | Create PELMO runs from psm files and execute them ⠋ | 81 | Create PELMO runs from psm files and execute them ⠙ | 82 | Create PELMO runs from psm files and execute them ⠹ | 83 | Create PELMO runs from psm files and execute them ⠸ | 84 | Create PELMO runs from psm files and execute them ⠼ | 85 | Create PELMO runs from psm files and execute them ⠴ | 86 | Create PELMO runs from psm files and execute them ⠦ | 87 | Create PELMO runs from psm files and execute them ⠧ | 88 | Create PELMO runs from psm files and execute them ⠇ | 89 | Create PELMO runs from psm files and execute them ⠏ | 90 | Create PELMO runs from psm files and execute them ⠋ | 91 | Create PELMO runs from psm files and execute them ⠙ | 92 | Create PELMO runs from psm files and execute them ⠹ | 93 | Create PELMO runs from psm files and execute them ⠸ | 94 | Create PELMO runs from psm files and execute them ⠼ | 95 | Create PELMO runs from psm files and execute them ⠴ | 96 | Create PELMO runs from psm files and execute them ⠦ | 97 | Create PELMO runs from psm files and execute them ⠧ | 98 | Create PELMO runs from psm files and execute them ⠇ | 99 | Create PELMO runs from psm files and execute them ⠏ | 100 | Create PELMO runs from psm files and execute them ⠋ | 101 | Create PELMO runs from psm files and execute them ⠙ | 102 | Create PELMO runs from psm files and execute them ⠹ | 103 | Create PELMO runs from psm files and execute them ⠸ | 104 | Create PELMO runs from psm files and execute them ⠼ | 105 | Create PELMO runs from psm files and execute them ⠴ | 106 | Create PELMO runs from psm files and execute them ⠦ | 107 | Create PELMO runs from psm files and execute them ⠧ | 108 | Create PELMO runs from psm files and execute them ⠇ | 109 | Create PELMO runs from psm files and execute them ⠏ | 110 | Create PELMO runs from psm files and execute them ⠋ | 111 | Create PELMO runs from psm files and execute them ⠙ | 112 | Create PELMO runs from psm files and execute them ⠹ | 113 | Create PELMO runs from psm files and execute them ⠸ | 114 | Create PELMO runs from psm files and execute them ⠼ | 115 | Create PELMO runs from psm files and execute them ⠴ | 116 | Create PELMO runs from psm files and execute them ⠦ | 117 | Create PELMO runs from psm files and execute them ⠧ | 118 | Create PELMO runs from psm files and execute them ⠇ | 119 | Create PELMO runs from psm files and execute them ⠏ | 120 | Create PELMO runs from psm files and execute them ⠋ | 121 | Create PELMO runs from psm files and execute them ⠙ | 122 | Create PELMO runs from psm files and execute them ⠹ | 123 | Create PELMO runs from psm files and execute them ⠸ | 124 | Create PELMO runs from psm files and execute them ⠼ | 125 | Create PELMO runs from psm files and execute them ⠴ | 126 | Create PELMO runs from psm files and execute them ⠦ | 127 | Create PELMO runs from psm files and execute them ⠧ | 128 | Create PELMO runs from psm files and execute them ⠇ | 129 | Create PELMO runs from psm files and execute them ⠏ | 130 | Create PELMO runs from psm files and execute them ⠋ | 131 | Create PELMO runs from psm files and execute them ⠙ | 132 | Create PELMO runs from psm files and execute them ⠹ | 133 | Create PELMO runs from psm files and execute them ⠸ | 134 | Create PELMO runs from psm files and execute them ⠼ | 135 | Create PELMO runs from psm files and execute them ⠴ | 136 | Create PELMO runs from psm files and execute them ⠦ | 137 | Create PELMO runs from psm files and execute them ⠧ | 138 | Create PELMO runs from psm files and execute them ⠇ | 139 | Create PELMO runs from psm files and execute them ⠏ | 140 | Create PELMO runs from psm files and execute them ⠋ | 141 | Create PELMO runs from psm files and execute them ⠙ | 142 | Create PELMO runs from psm files and execute them ⠹ | 143 | Create PELMO runs from psm files and execute them ⠸ | 144 | Create PELMO runs from psm files and execute them ⠼ | 145 | Create PELMO runs from psm files and execute them ⠴ | 146 | Create PELMO runs from psm files and execute them ⠦ | 147 | Create PELMO runs from psm files and execute them ⠧ | 148 | Create PELMO runs from psm files and execute them ⠇ | 149 | Create PELMO runs from psm files and execute them ⠏ | 150 | Create PELMO runs from psm files and execute them ⠋ | 151 | Create PELMO runs from psm files and execute them ⠙ | 152 | Create PELMO runs from psm files and execute them ⠹ | 153 | Create PELMO runs from psm files and execute them ⠸ | 154 | Create PELMO runs from psm files and execute them ⠼ | 155 | Create PELMO runs from psm files and execute them ⠴ | 156 | Create PELMO runs from psm files and execute them ⠦ | 157 | Create PELMO runs from psm files and execute them ⠧ | 158 | Create PELMO runs from psm files and execute them ⠇ | 159 | Create PELMO runs from psm files and execute them ⠏ | 160 | Create PELMO runs from psm files and execute them ⠋ | 161 | Create PELMO runs from psm files and execute them ⠙ | 162 | Create PELMO runs from psm files and execute them ⠹ | 163 | Create PELMO runs from psm files and execute them ⠸ | 164 | Create PELMO runs from psm files and execute them ⠼ | 165 | Create PELMO runs from psm files and execute them ⠴ | 166 | Create PELMO runs from psm files and execute them ⠦ | 167 | Create PELMO runs from psm files and execute them ⠧ | 168 | Create PELMO runs from psm files and execute them ⠇ | 169 | Create PELMO runs from psm files and execute them ⠏ | 170 | Create PELMO runs from psm files and execute them ⠋ | 171 | Create PELMO runs from psm files and execute them ⠙ | 172 | Create PELMO runs from psm files and execute them ⠹ | 173 | Create PELMO runs from psm files and execute them ⠸ | 174 | Create PELMO runs from psm files and execute them ⠼ | 175 | Create PELMO runs from psm files and execute them ⠴ | 176 | Create PELMO runs from psm files and execute them ⠦ | 177 | Create PELMO runs from psm files and execute them ⠧ | 178 | Create PELMO runs from psm files and execute them ⠇ | 179 | Create PELMO runs from psm files and execute them ⠏ | 180 | Create PELMO runs from psm files and execute them ⠋ | 181 | Create PELMO runs from psm files and execute them ⠙ | 182 | Create PELMO runs from psm files and execute them ⠹ | 183 | Create PELMO runs from psm files and execute them ⠸ | 184 | Create PELMO runs from psm files and execute them ⠼ | 185 | Create PELMO runs from psm files and execute them ⠴ | 186 | Create PELMO runs from psm files and execute them ⠦ | 187 | Create PELMO runs from psm files and execute them ⠧ | 188 | Create PELMO runs from psm files and execute them ⠇ | 189 | Create PELMO runs from psm files and execute them ⠏ | 190 | Create PELMO runs from psm files and execute them ⠋ | 191 | Create PELMO runs from psm files and execute them ⠙ | 192 | Create PELMO runs from psm files and execute them ⠹ | 193 | Create PELMO runs from psm files and execute them ⠸ | 194 | Create PELMO runs from psm files and execute them ⠼ | 195 | Create PELMO runs from psm files and execute them ⠴ | 196 | Create PELMO runs from psm files and execute them ⠦ | 197 | Create PELMO runs from psm files and execute them ⠧ | 198 | Create PELMO runs from psm files and execute them ⠇ | 199 | Create PELMO runs from psm files and execute them ⠏ | 200 | Create PELMO runs from psm files and execute them ⠋ | 201 | Create PELMO runs from psm files and execute them ⠙ | 202 | Create PELMO runs from psm files and execute them ⠹ | 203 | Create PELMO runs from psm files and execute them ⠸ | 204 | Create PELMO runs from psm files and execute them ⠼ | 205 | Create PELMO runs from psm files and execute them ⠴ | 206 | Create PELMO runs from psm files and execute them ⠦ | 207 | Create PELMO runs from psm files and execute them ⠧ | 208 | Create PELMO runs from psm files and execute them ⠇ | 209 | Create PELMO runs from psm files and execute them ⠏ | 210 | Create PELMO runs from psm files and execute them ⠋ | 211 | Create PELMO runs from psm files and execute them ⠙ | 212 | Create PELMO runs from psm files and execute them ⠹ | 213 | Create PELMO runs from psm files and execute them ⠸ | 214 | Create PELMO runs from psm files and execute them ⠼ | 215 | Create PELMO runs from psm files and execute them ⠴ | 216 | Create PELMO runs from psm files and execute them ⠦ | 217 | Create PELMO runs from psm files and execute them ⠧ | 218 | Create PELMO runs from psm files and execute them ⠇ | 219 | Create PELMO runs from psm files and execute them ✔ | 219 | Create PELMO runs from psm files and execute them [73.9 s] + ⠏ | 0 | Actual and time weighted average concentrations for SFO kinetics ⠋ | 1 | Actual and time weighted average concentrations for SFO kinetics ✔ | 1 | Actual and time weighted average concentrations for SFO kinetics + ⠏ | 0 | FOCUS Step 1 calculations ⠋ | 1 | FOCUS Step 1 calculations ⠙ | 2 | FOCUS Step 1 calculations ⠹ | 3 | FOCUS Step 1 calculations ⠸ | 4 | FOCUS Step 1 calculations ⠼ | 5 | FOCUS Step 1 calculations ⠴ | 6 | FOCUS Step 1 calculations ⠦ | 7 | FOCUS Step 1 calculations ⠧ | 8 | FOCUS Step 1 calculations ⠇ | 9 | FOCUS Step 1 calculations ✔ | 9 | FOCUS Step 1 calculations [0.1 s] + ⠏ | 0 | FOCUS Steps 12 input files ⠋ | 1 | FOCUS Steps 12 input files ⠙ | 2 | FOCUS Steps 12 input files ⠹ | 3 | FOCUS Steps 12 input files ⠸ | 4 | FOCUS Steps 12 input files ⠼ | 5 | FOCUS Steps 12 input files ⠴ | 6 | FOCUS Steps 12 input files ⠦ | 7 | FOCUS Steps 12 input files ⠧ | 8 | FOCUS Steps 12 input files ✔ | 8 | FOCUS Steps 12 input files + ⠏ | 0 | Read and analyse TOXSWA cwa files ⠋ | 1 | Read and analyse TOXSWA cwa files ⠙ | 2 | Read and analyse TOXSWA cwa files ⠹ | 3 | Read and analyse TOXSWA cwa files ⠸ | 4 | Read and analyse TOXSWA cwa files ⠼ | 5 | Read and analyse TOXSWA cwa files ⠴ | 6 | Read and analyse TOXSWA cwa files ⠦ | 7 | Read and analyse TOXSWA cwa files ✔ | 7 | Read and analyse TOXSWA cwa files [3.6 s] + ⠏ | 0 | UK drainage PEC calculations ⠋ | 1 | UK drainage PEC calculations ⠙ | 2 | UK drainage PEC calculations ⠹ | 3 | UK drainage PEC calculations ⠸ | 4 | UK drainage PEC calculations ⠼ | 5 | UK drainage PEC calculations ⠴ | 6 | UK drainage PEC calculations ⠦ | 7 | UK drainage PEC calculations ⠧ | 8 | UK drainage PEC calculations ⠇ | 9 | UK drainage PEC calculations ⠏ | 10 | UK drainage PEC calculations ⠋ | 11 | UK drainage PEC calculations ⠙ | 12 | UK drainage PEC calculations ✔ | 12 | UK drainage PEC calculations -DONE =============================================================================================== +══ Results ═════════════════════════════════════════════════════════════════════════════════════════ +Duration: 78.9 s + +OK: 282 +Failed: 0 +Warnings: 0 +Skipped: 0 diff --git a/tests/testthat/test_PEC_soil.R b/tests/testthat/test_PEC_soil.R index 0661a52..34b4749 100644 --- a/tests/testthat/test_PEC_soil.R +++ b/tests/testthat/test_PEC_soil.R @@ -1,4 +1,5 @@ library(pfm) +library(testthat) context("Simple PEC soil calculations") test_that("PEC_soil calculates correctly", { @@ -6,40 +7,73 @@ test_that("PEC_soil calculates correctly", { expect_equal(as.numeric(PEC_soil(100)), 0.1 * 4/3) # or 0.1 mg/kg assuming 25% interception - expect_equal(as.numeric(PEC_soil(100, interception = 0.25)), 0.1) + expect_equal(as.numeric(PEC_soil(100, interception = 0.25)), 0.1) # Mixing depth of 1 cm gives five-fold PEC expect_equal(as.numeric(PEC_soil(100, interception = 0.25, mixing_depth = 1)), 0.5) }) -test_that("Tier 1 PEC soil example for Pesticide A in EFSA guidance can be reproduced", { +test_that("Tier 1 PEC soil example for Pesticide A in EFSA guidance from 2017 can be reproduced", { # Calculate total soil concentrations for tier 1 scenarios - results_pfm <- PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), - scenarios = "EFSA_2015") + # Leaching is calculated from the 5 cm layer to be able to reproduce the + # results from the guidance + results_pfm_2017 <- PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), + scenarios = "EFSA_2017", Kom = 1000, + leaching_depth = 5) + + # From Table G.2, p. 92 + results_guidance_2017 <- matrix(c(18.6, 13.0, 9.9, 18.2, 12.7, 9.6), + ncol = 3, byrow = TRUE) + dimnames(results_guidance_2017) <- list(t_avg = c(0, 21), + scenario = c("CTN", "CTC", "CTS")) + + + expect_equal(round(results_pfm_2017, 1)[1, ], results_guidance_2017[1, ]) + # I do not get the same TWA concentrations as in the 2017 guidance on p. 92 + + # Calculate porewater soil concentrations for tier 1 scenarios + results_pfm_pw_2017 <- PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), + Kom = 1000, scenarios = "EFSA_2017", porewater = TRUE, + leaching_depth = 5) # From Table I.5, p. 80 - results_guidance <- matrix(c(22.0, 11.5, 9.1, 21.8, 11.4, 9.0), - ncol = 3, byrow = TRUE) - dimnames(results_guidance) <- list(t_avg = c(0, 21), - scenario = c("CTN", "CTC", "CTS")) + results_guidance_pw_2017 <- matrix(c(0.48, 0.60, 0.91, 0.47, 0.58, 0.86), + ncol = 3, byrow = TRUE) + dimnames(results_guidance_pw_2017) <- list(t_avg = c(0, 21), + scenario = c("CLN", "CLC", "CLS")) + expect_equal(round(results_pfm_pw_2017, 2)[1, ], results_guidance_pw_2017[1, ]) + # Here I also do not get the same TWA concentrations as in the guidance p. 92 +}) + +test_that("Tier 1 PEC soil example for Pesticide A in EFSA guidance from 2015 can be reproduced", { + # Calculate total soil concentrations for tier 1 scenarios + results_pfm_2015 <- PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), + scenarios = "EFSA_2015") + + # From Table I.5, p. 80 + results_guidance_2015 <- matrix(c(22.0, 11.5, 9.1, 21.8, 11.4, 9.0), + ncol = 3, byrow = TRUE) + dimnames(results_guidance_2015) <- list(t_avg = c(0, 21), + scenario = c("CTN", "CTC", "CTS")) - expect_equal(round(results_pfm, 1), results_guidance) + + expect_equal(round(results_pfm_2015, 1), results_guidance_2015) # Calculate porewater soil concentrations for tier 1 scenarios - results_pfm_pw <- PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), - Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) + results_pfm_pw_2015 <- PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), + Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) # From Table I.5, p. 80 - results_guidance_pw <- matrix(c(0.76, 0.67, 0.91, 0.75, 0.66, 0.90), - ncol = 3, byrow = TRUE) - dimnames(results_guidance_pw) <- list(t_avg = c(0, 21), - scenario = c("CLN", "CLC", "CLS")) + results_guidance_pw_2015 <- matrix(c(0.76, 0.67, 0.91, 0.75, 0.66, 0.90), + ncol = 3, byrow = TRUE) + dimnames(results_guidance_pw_2015) <- list(t_avg = c(0, 21), + scenario = c("CLN", "CLC", "CLS")) - expect_equal(round(results_pfm_pw, 2), results_guidance_pw) + expect_equal(round(results_pfm_pw_2015, 2), results_guidance_pw_2015) }) -test_that("Tier 1 PEC soil example for Pesticide F in EFSA guidance can be reproduced", { +test_that("Tier 1 PEC soil example for Pesticide F in EFSA guidance from 2015 can be reproduced", { # Parent F # Calculate total and porewater soil concentrations for tier 1 scenarios results_pfm <- PEC_soil(1000, interval = 365, DT50 = 25, t_avg = c(0, 21), diff --git a/tests/testthat/test_PELMO.R b/tests/testthat/test_PELMO.R index be0b410..49c03d3 100644 --- a/tests/testthat/test_PELMO.R +++ b/tests/testthat/test_PELMO.R @@ -45,6 +45,7 @@ test_that("PELMO runs are correctly set up", { } # Prepare runs in analogy to the test archive + skip_on_cran() PELMO_runs(runs, psm_dir = PELMO_base, execute = FALSE, evaluate = FALSE, overwrite = TRUE) # Check that input files are correctly generated in the right location @@ -70,6 +71,7 @@ test_that("PELMO runs can be run and give the expected result files", { skip("A wine installation is needed for this test") } + skip_on_cran() run_PELMO(runs, cores = 7) plm_files <- c("CHEM.PLM", "ECHO.PLM", @@ -89,8 +91,12 @@ test_that("PELMO runs can be run and give the expected result files", { new <- readLines(file.path(PELMO_base, "FOCUS", pp, plm)) test <- readLines(file.path(test_dir, pp, plm)) + # Don't check for differences in the PESTICIDE BALANCE ERROR + pest_balance_error <- suppressWarnings(grep("PESTICIDE BALANCE ERROR", new)) + # Suppress warnings about invalid strings in this locale caused by the files + # Check if the ouput files are correctly reproduced - expect_identical(new, test) + expect_identical(new[!pest_balance_error], test[!pest_balance_error]) } } } @@ -105,6 +111,7 @@ test_that("PELMO runs are correctly evaluated", { skip("A wine installation is needed for this test") } + skip_on_cran() # Check that if output is the same as in the test archive for (run in runs) { psm <- run$psm @@ -164,6 +171,7 @@ test_that("PECgw from FOCUS summary files can be reproduced", { if (!wine_installed) { skip("A wine installation is needed for this test") } + skip_on_cran() focus_summary <- list() for (run in runs) { diff --git a/tests/testthat/test_TOXSWA.R b/tests/testthat/test_TOXSWA.R index 7c9a73c..de60d48 100644 --- a/tests/testthat/test_TOXSWA.R +++ b/tests/testthat/test_TOXSWA.R @@ -1,26 +1,23 @@ library(pfm) context("Read and analyse TOXSWA cwa files") -zipfile_test = system.file("testdata/SwashProjects.zip", package = "pfm") -basedir_test = "SwashProjects/project_H_sw/TOXSWA" - -H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", - basedir = basedir_test, - zipfile = zipfile_test) - -H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", - basedir = basedir_test, - zipfile = zipfile_test) +# zipfile_test = tempfile() +# download.file("https://cgit.jrwb.de/pfm/plain/inst/testdata/SwashProjects.zip", zipfile_test) +zipfile_test <- system.file("testdata/SwashProjects.zip", package = "pfm") +basedir_test = "SwashProjects/project_H_sw/TOXSWA" # cwa files from TOXSWA 3.x +# .out file produced with TOXSWA 4.4.2 basedir_test_2 = "SwashProjects/Project_1/TOXSWA" -EXSW2_R1_stream <- read.TOXSWA_cwa("3.out", - basedir = basedir_test_2, - zipfile = zipfile_test) - +H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", + basedir = basedir_test, + zipfile = zipfile_test) +H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", + basedir = basedir_test, + zipfile = zipfile_test) -test_that("TOXSWA cwa file is correctly read and printed", { +test_that("Old TOXSWA cwa and out files are correctly read and printed", { # This was the setting when printing the output into text files options(width = 100) @@ -37,15 +34,31 @@ test_that("TOXSWA cwa file is correctly read and printed", { # The basedir is not printed, therefore tested separately expect_equal(H_sw_D4_pond$basedir, basedir_test) + + EXSW2_R1_stream <- read.TOXSWA_cwa("3.out", + basedir = basedir_test_2, + zipfile = zipfile_test) EXSW2_R1_stream_printed <- capture.output(print(EXSW2_R1_stream)) expect_equal(EXSW2_R1_stream_printed, readLines("EXSW2_R1_stream_printed.txt")) +}) - # The basedir is not printed, therefore tested separately - expect_equal(H_sw_D4_pond$basedir, basedir_test) +test_that("A TOXSWA 5.5.3 out file is correctly read and printed", { + # zipfile_test_3 = tempfile() + # download.file("https://cgit.jrwb.de/pfm/plain/inst/testdata/SwashProjects_TOXSWA_553.zip", + # zipfile_test_3) + zipfile_test_3 <- system.file("testdata/SwashProjects_TOXSWA_553.zip", package = "pfm") + basedir_test_3 = "SwashProjects/Project_1/TOXSWA" + + EXSW2_R1_stream_TOXSWA_553 <- read.TOXSWA_cwa("3.out", + basedir = basedir_test_3, + zipfile = zipfile_test_3) + EXSW2_R1_stream_printed_TOXSWA_553 <- capture.output(print(EXSW2_R1_stream_TOXSWA_553)) + + # We actually get the same results, at least judged by the printed object + expect_equal(EXSW2_R1_stream_printed_TOXSWA_553, readLines("EXSW2_R1_stream_printed.txt")) }) test_that("Getting events and moving window analysis works", { - # Event analysis with two different thresholds H_sw_R1_stream$get_events(c(2, 10)) expect_equal_to_reference(H_sw_R1_stream$events, file = "H_sw_R1_stream_events.rds") -- cgit v1.2.1 From 22b36c824fe5e1561868a649216fe079c6fbfb85 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 10 Jul 2018 18:06:29 +0200 Subject: Update static docs --- _pkgdown.yml | 2 + docs/authors.html | 2 +- docs/index.html | 4 +- docs/reference/FOCUS_GW_scenarios_2012.html | 2 +- docs/reference/FOCUS_PELMO_crop_sze_names.html | 2 +- docs/reference/FOCUS_PELMO_crops.html | 2 +- docs/reference/FOCUS_PELMO_location_codes.html | 2 +- docs/reference/FOCUS_Step_12_scenarios.html | 2 +- docs/reference/FOMC_actual_twa.html | 2 +- docs/reference/GUS.html | 2 +- docs/reference/PEC_soil.html | 77 ++++++++-- docs/reference/PEC_sw_drainage_UK.html | 2 +- docs/reference/PEC_sw_drift.html | 2 +- docs/reference/PEC_sw_exposit_runoff.html | 2 +- docs/reference/PEC_sw_focus.html | 2 +- docs/reference/PEC_sw_sed.html | 2 +- docs/reference/PELMO_path.html | 2 +- docs/reference/PELMO_runs.html | 4 +- docs/reference/SFO_actual_twa.html | 2 +- docs/reference/SSLRC_mobility_classification.html | 2 +- docs/reference/TOXSWA_cwa.html | 2 +- docs/reference/chent_focus_sw.html | 2 +- docs/reference/create_run_list.html | 2 +- docs/reference/drift_data_JKI.html | 2 +- docs/reference/endpoint.html | 2 +- docs/reference/focus_80th.html | 2 +- docs/reference/geomean.html | 2 +- docs/reference/get_flux.html | 2 +- docs/reference/get_interval.html | 2 +- docs/reference/index.html | 14 +- docs/reference/max_twa.html | 2 +- docs/reference/one_box.html | 2 +- docs/reference/perc_runoff_exposit.html | 3 +- docs/reference/perc_runoff_reduction_exposit.html | 2 +- docs/reference/pesticide.txt | 4 + docs/reference/pfm_degradation.html | 2 +- docs/reference/plot.TOXSWA_cwa.html | 2 +- docs/reference/plot.one_box.html | 2 +- docs/reference/read.TOXSWA_cwa.html | 2 +- docs/reference/sawtooth.html | 2 +- docs/reference/soil_scenario_data_EFSA_2015.html | 10 +- docs/reference/soil_scenario_data_EFSA_2017.html | 177 ++++++++++++++++++++++ docs/reference/sum_periods.html | 2 +- docs/reference/twa.html | 2 +- 44 files changed, 308 insertions(+), 57 deletions(-) create mode 100644 docs/reference/soil_scenario_data_EFSA_2017.html diff --git a/_pkgdown.yml b/_pkgdown.yml index 4f16d24..7252624 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -15,10 +15,12 @@ reference: - max_twa - pfm_degradation - SFO_actual_twa + - FOMC_actual_twa - title: Predicted environmental concentrations in soil contents: - PEC_soil - soil_scenario_data_EFSA_2015 + - soil_scenario_data_EFSA_2017 - title: Predicted environmental concentrations in groundwater contents: - FOCUS_GW_scenarios_2012 diff --git a/docs/authors.html b/docs/authors.html index 27e5e7c..e128b4d 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -58,7 +58,7 @@ pfm - 0.4.6 + 0.5.1
diff --git a/docs/index.html b/docs/index.html index b7f32cc..70a1fed 100644 --- a/docs/index.html +++ b/docs/index.html @@ -31,7 +31,7 @@ pfm - 0.4.6 + 0.5.1
@@ -84,7 +84,7 @@ this program. If not, see <http:

Installation

-

The easiest way to install the package is probably to use drat:

+

The easiest way to install the package is probably to use drat:

install.packages("drat")
 drat::addRepo("jranke")
 install.packages("pfm")
diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 1a9d513..af6d243 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -62,7 +62,7 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> pfm - 0.4.6 + 0.5.1
diff --git a/docs/reference/FOCUS_PELMO_crop_sze_names.html b/docs/reference/FOCUS_PELMO_crop_sze_names.html index 89348f6..4eed679 100644 --- a/docs/reference/FOCUS_PELMO_crop_sze_names.html +++ b/docs/reference/FOCUS_PELMO_crop_sze_names.html @@ -64,7 +64,7 @@ files used for Beans (field) and Beans (vegetable) are the same." /> pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/FOCUS_PELMO_crops.html b/docs/reference/FOCUS_PELMO_crops.html index 16653d9..e4928cd 100644 --- a/docs/reference/FOCUS_PELMO_crops.html +++ b/docs/reference/FOCUS_PELMO_crops.html @@ -65,7 +65,7 @@ in the three letter code, i.e. 'Peas (animals)' has the code ape." /> pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/FOCUS_PELMO_location_codes.html b/docs/reference/FOCUS_PELMO_location_codes.html index 817d888..8177747 100644 --- a/docs/reference/FOCUS_PELMO_location_codes.html +++ b/docs/reference/FOCUS_PELMO_location_codes.html @@ -62,7 +62,7 @@ indexed by three letter acronyms." /> pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index 9ceb79d..b9f2e0d 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -62,7 +62,7 @@ The text file is not included in the package as its licence is not clear." /> pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/FOMC_actual_twa.html b/docs/reference/FOMC_actual_twa.html index 7a62183..685edc3 100644 --- a/docs/reference/FOMC_actual_twa.html +++ b/docs/reference/FOMC_actual_twa.html @@ -61,7 +61,7 @@ pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html index 87714e0..65763bc 100644 --- a/docs/reference/GUS.html +++ b/docs/reference/GUS.html @@ -63,7 +63,7 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index 5073067..8903470 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -33,9 +33,10 @@ +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)." /> @@ -64,7 +65,7 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012)." /> pfm - 0.4.6 + 0.5.1 @@ -108,17 +109,20 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012)." />

This is a basic calculation of a contaminant concentration in bulk soil -based on complete, instantaneous mixing. If an interval is given, an +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 for example in the PPR panel opinion (EFSA 2012).

+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).

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, chent = NA, DT50 = NA,
+  n_periods = Inf, tillage_depth = 20, leaching_depth = tillage_depth,
+  crop = "annual", cultivation = FALSE, chent = NA, DT50 = NA,
   Koc = NA, Kom = Koc/1.724, t_avg = 0, scenarios = c("default",
-  "EFSA_2015"), porewater = FALSE)
+ "EFSA_2017", "EFSA_2015"), leaching = scenarios == "EFSA_2017", + porewater = FALSE)

Arguments

@@ -160,9 +164,28 @@ degradation rate units are in days

+ + + + + + + + + + + + - @@ -193,6 +216,11 @@ the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when 'chents' 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.

+ + + + @@ -212,14 +240,24 @@ p. 13).

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 (PPR panel 2012), only temperature correction using the +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 (2015, p. 13) can easily be calculated.

+guidance (2017, p. 14/15) can easily be calculated.

Note

-

If temperature information is available in the selected scenarios, as +

While time weighted average (TWA) concentrations given in the examples +from the EFSA guidance from 2015 (p. 80) are 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'.

@@ -231,6 +269,11 @@ guidance (2015, p. 13) can easily be calculated.

selection and scenario parameterisation for predicting environmental concentrations of plant protection products in soil. EFSA Journal10(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 @@ -242,6 +285,18 @@ guidance (2015, p. 13) can easily be calculated.

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
diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html
index 91eeccb..e183ae2 100644
--- a/docs/reference/PEC_sw_drainage_UK.html
+++ b/docs/reference/PEC_sw_drainage_UK.html
@@ -62,7 +62,7 @@ published on the CRC website" />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     

 
diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html
index 02b641f..b5608db 100644
--- a/docs/reference/PEC_sw_drift.html
+++ b/docs/reference/PEC_sw_drift.html
@@ -63,7 +63,7 @@ with input via spray drift." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html
index 2942ebb..9fab616 100644
--- a/docs/reference/PEC_sw_exposit_runoff.html
+++ b/docs/reference/PEC_sw_exposit_runoff.html
@@ -62,7 +62,7 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html
index 535e82e..88f5b43 100644
--- a/docs/reference/PEC_sw_focus.html
+++ b/docs/reference/PEC_sw_focus.html
@@ -67,7 +67,7 @@ to be used with the FOCUS calculator." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html
index 532031b..01ccf29 100644
--- a/docs/reference/PEC_sw_sed.html
+++ b/docs/reference/PEC_sw_sed.html
@@ -64,7 +64,7 @@ PEC calculator" />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/PELMO_path.html b/docs/reference/PELMO_path.html
index a678cb6..b390917 100644
--- a/docs/reference/PELMO_path.html
+++ b/docs/reference/PELMO_path.html
@@ -61,7 +61,7 @@
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html
index 5d53104..12a4244 100644
--- a/docs/reference/PELMO_runs.html
+++ b/docs/reference/PELMO_runs.html
@@ -67,7 +67,7 @@ and run using wine." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
@@ -229,7 +229,7 @@ the period.plm file generated by the FOCUS PELMO GUI.

 #> 
 #> 
# We get exactly the same PECgw values (on Linux, calling PELMO using Wine).
 print(time_1)
#>        User      System verstrichen 
-#>       0.384       0.095      30.954 
if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) {
+#>       0.383       0.129      30.547 
if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) {
   cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]]))
 }
#> CPU model: AMD Ryzen 7 1700 Eight-Core Processor

 # Demonstrate some results with metabolites.
diff --git a/docs/reference/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html
index e5b1e8a..b7b65f5 100644
--- a/docs/reference/SFO_actual_twa.html
+++ b/docs/reference/SFO_actual_twa.html
@@ -61,7 +61,7 @@
       
       
         pfm
-        0.4.6
+        0.5.1
       
     

 
diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html
index 49b80e7..06be24e 100644
--- a/docs/reference/SSLRC_mobility_classification.html
+++ b/docs/reference/SSLRC_mobility_classification.html
@@ -62,7 +62,7 @@ checked against the spreadsheet published on the CRC website" />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html
index 932e6ef..a1b6bfe 100644
--- a/docs/reference/TOXSWA_cwa.html
+++ b/docs/reference/TOXSWA_cwa.html
@@ -62,7 +62,7 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html
index 1683067..39b3c9e 100644
--- a/docs/reference/chent_focus_sw.html
+++ b/docs/reference/chent_focus_sw.html
@@ -61,7 +61,7 @@
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/create_run_list.html b/docs/reference/create_run_list.html
index 255aa1d..c52719d 100644
--- a/docs/reference/create_run_list.html
+++ b/docs/reference/create_run_list.html
@@ -61,7 +61,7 @@
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html
index ada93e7..c3f1f4d 100644
--- a/docs/reference/drift_data_JKI.html
+++ b/docs/reference/drift_data_JKI.html
@@ -64,7 +64,7 @@ published by the German Julius-Kühn Institute (JKI)." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html
index a078bd8..819d8bc 100644
--- a/docs/reference/endpoint.html
+++ b/docs/reference/endpoint.html
@@ -64,7 +64,7 @@ this function." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/focus_80th.html b/docs/reference/focus_80th.html
index 375e15a..0604fa7 100644
--- a/docs/reference/focus_80th.html
+++ b/docs/reference/focus_80th.html
@@ -64,7 +64,7 @@ values obtained by PELMO." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html
index 5673322..dfcd15e 100644
--- a/docs/reference/geomean.html
+++ b/docs/reference/geomean.html
@@ -64,7 +64,7 @@ returns 0 if at least one element of the vector is 0." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/get_flux.html b/docs/reference/get_flux.html
index 025b4ad..518b09c 100644
--- a/docs/reference/get_flux.html
+++ b/docs/reference/get_flux.html
@@ -61,7 +61,7 @@
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/get_interval.html b/docs/reference/get_interval.html
index 0cd69f3..4b73ca2 100644
--- a/docs/reference/get_interval.html
+++ b/docs/reference/get_interval.html
@@ -61,7 +61,7 @@
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 162298b..12abbd4 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -58,7 +58,7 @@
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
@@ -160,6 +160,12 @@
           
SFO_actual_twa()
+ + + + @@ -180,6 +186,12 @@

soil_scenario_data_EFSA_2015

+ + + + diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html index 6e5ee67..c603fb4 100644 --- a/docs/reference/max_twa.html +++ b/docs/reference/max_twa.html @@ -65,7 +65,7 @@ max_twa." /> pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html index 9cd4d61..f3a6324 100644 --- a/docs/reference/one_box.html +++ b/docs/reference/one_box.html @@ -61,7 +61,7 @@ pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html index e243efb..2c7dd2a 100644 --- a/docs/reference/perc_runoff_exposit.html +++ b/docs/reference/perc_runoff_exposit.html @@ -61,7 +61,7 @@ pfm - 0.4.6 + 0.5.1 @@ -113,6 +113,7 @@

A data frame with percentage values for the dissolved fraction and the fraction bound to eroding particles, with Koc classes used as row names

+
Koc_lower_bound

The lower bound of the Koc class

dissolved

The percentage of the applied substance transferred to an adjacent water body in the dissolved phase

bound

The percentage of the applied substance transferred to an diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html index 4e10a64..9a8f10a 100644 --- a/docs/reference/perc_runoff_reduction_exposit.html +++ b/docs/reference/perc_runoff_reduction_exposit.html @@ -61,7 +61,7 @@ pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt index d4fd84e..1f9181a 100644 --- a/docs/reference/pesticide.txt +++ b/docs/reference/pesticide.txt @@ -37,3 +37,7 @@ Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Du M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html index e547ed1..16df913 100644 --- a/docs/reference/pfm_degradation.html +++ b/docs/reference/pfm_degradation.html @@ -61,7 +61,7 @@ pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html index 8612bac..65703e8 100644 --- a/docs/reference/plot.TOXSWA_cwa.html +++ b/docs/reference/plot.TOXSWA_cwa.html @@ -62,7 +62,7 @@ segment of a TOXSWA surface water body." /> pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html index a8f62d4..473243a 100644 --- a/docs/reference/plot.one_box.html +++ b/docs/reference/plot.one_box.html @@ -61,7 +61,7 @@ pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index aa18ec4..5f6aba2 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -66,7 +66,7 @@ renamed to ConLiqWatLay in the out file." /> pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html index 175e045..87dcab2 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.html @@ -63,7 +63,7 @@ times, with an interval i." /> pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html index 64c9c28..23fe106 100644 --- a/docs/reference/soil_scenario_data_EFSA_2015.html +++ b/docs/reference/soil_scenario_data_EFSA_2015.html @@ -63,7 +63,7 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> pfm - 0.4.6 + 0.5.1 @@ -122,10 +122,10 @@ scenario and model adjustment factors from p. 15 and p. 17 are included.

Source

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

+ 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

Examples

diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html new file mode 100644 index 0000000..be49263 --- /dev/null +++ b/docs/reference/soil_scenario_data_EFSA_2017.html @@ -0,0 +1,177 @@ + + + + + + + + +Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • pfm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Properties of the predefined scenarios from the EFSA guidance from 2017

+ Source: R/soil_scenario_data_EFSA_2017.R + +
+ +
+ +

Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the +concentration in soil as given in the EFSA guidance (2017, p. 14/15). Also, the +scenario and model adjustment factors from p. 16 and p. 18 are included.

+ +
+ + +

Format

+ +

A data frame with one row for each scenario. Row names are the scenario codes, + e.g. CTN for the Northern scenario for the total concentration in soil. Columns are + mostly self-explanatory. rho is the dry bulk density of the top soil.

+ +

Source

+ +

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

+ + +

Examples

+ 
soil_scenario_data_EFSA_2017
#>        Zone Country T_arit T_arr Texture  f_om theta_fc   rho f_sce f_mod
+#> CTN   North Estonia    5.7   7.6  Coarse 0.220    0.244 0.707   1.4     3
+#> CTC Central  Poland    7.4   9.3  Coarse 0.122    0.244 0.934   1.4     3
+#> CTS   South  France   10.2  11.7  Medium 0.070    0.349 1.117   1.4     3
+#> CLN   North Denmark    8.0   9.2  Medium 0.025    0.349 1.371   1.6     4
+#> CLC Central Austria    9.3  11.3  Medium 0.018    0.349 1.432   1.6     4
+#> CLS   South   Spain   15.4  16.7  Medium 0.010    0.349 1.521   1.6     4
+#>     FOCUS_zone prec
+#> CTN    Hamburg  639
+#> CTC    Hamburg  617
+#> CTS    Hamburg  667
+#> CLN    Hamburg  602
+#> CLC Châteaudun  589
+#> CLS    Sevilla  526
+
+ +
+ +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + + + + diff --git a/docs/reference/sum_periods.html b/docs/reference/sum_periods.html index ec0c34b..109d9e7 100644 --- a/docs/reference/sum_periods.html +++ b/docs/reference/sum_periods.html @@ -61,7 +61,7 @@ pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/twa.html b/docs/reference/twa.html index da44f92..f74399c 100644 --- a/docs/reference/twa.html +++ b/docs/reference/twa.html @@ -63,7 +63,7 @@ is after one window has passed." /> pfm - 0.4.6 + 0.5.1 -- cgit v1.2.1
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 +

An optional chent object holding substance specific information. Can also be a name for the substance as a character string
leaching

Should leaching be taken into account? The default is FALSE, +except when the EFSA_2017 scenarios are used.
porewater

Actual and maximum moving window time average concentrations for SFO kinetics

+

FOMC_actual_twa()

+

Actual and maximum moving window time average concentrations for FOMC kinetics

Properties of the predefined scenarios from the EFSA guidance from 2015

+

soil_scenario_data_EFSA_2017

+

Properties of the predefined scenarios from the EFSA guidance from 2017