From aed160d7f0eaf5865e2bd9bf6c4b1c9d7b13d911 Mon Sep 17 00:00:00 2001 From: Ranke Johannes Date: Wed, 31 Jan 2024 13:16:17 +0100 Subject: Reorganise data generation - Use inst/data_generation for R code generating data as in some of my other packages - data/*.RData files were checked using https://github.com/jranke/dotfiles/blob/main/bin/rda_diff contents were not changed - Remove ChangeLog, the history is in the git logs - Update docs and some links contained therein - use \doi{} markup - Move logs to log directory --- man/EFSA_GW_interception_2014.Rd | 32 +++-------------------- man/EFSA_washoff_2017.Rd | 32 +++-------------------- man/PEC_sw_exposit_drainage.Rd | 2 +- man/PEC_sw_exposit_runoff.Rd | 2 +- man/PEC_sw_focus.Rd | 10 ++++---- man/drift_data_JKI.Rd | 49 +----------------------------------- man/perc_runoff_exposit.Rd | 7 +++++- man/perc_runoff_reduction_exposit.Rd | 2 +- man/soil_scenario_data_EFSA_2015.Rd | 25 +++--------------- man/soil_scenario_data_EFSA_2017.Rd | 7 +++++- 10 files changed, 33 insertions(+), 135 deletions(-) (limited to 'man') diff --git a/man/EFSA_GW_interception_2014.Rd b/man/EFSA_GW_interception_2014.Rd index 2334d7f..ed29454 100644 --- a/man/EFSA_GW_interception_2014.Rd +++ b/man/EFSA_GW_interception_2014.Rd @@ -14,37 +14,13 @@ of active substances of plant protection products and transformation products of these active substances in soil. \emph{EFSA Journal} \bold{12}(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662 } +\usage{ +EFSA_GW_interception_2014 +} \description{ Subset of EFSA crop interception default values for groundwater modelling } \examples{ -\dontrun{ - # This is the code that was used to define the data - bbch <- paste0(0:9, "x") - crops <- c( - "Beans (field + vegetable)", - "Peas", - "Summer oilseed rape", "Winter oilseed rape", - "Tomatoes", - "Spring cereals", "Winter cereals") - EFSA_GW_interception_2014 <- matrix(NA, length(crops), length(bbch), - dimnames = list(Crop = crops, BBCH = bbch)) - EFSA_GW_interception_2014["Beans (field + vegetable)", ] <- - c(0, 0.25, rep(0.4, 2), rep(0.7, 5), 0.8) - EFSA_GW_interception_2014["Peas", ] <- - c(0, 0.35, rep(0.55, 2), rep(0.85, 5), 0.85) - EFSA_GW_interception_2014["Summer oilseed rape", ] <- - c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) - EFSA_GW_interception_2014["Winter oilseed rape", ] <- - c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) - EFSA_GW_interception_2014["Tomatoes", ] <- - c(0, 0.5, rep(0.7, 2), rep(0.8, 5), 0.5) - EFSA_GW_interception_2014["Spring cereals", ] <- - c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) - EFSA_GW_interception_2014["Winter cereals", ] <- - c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) - save(EFSA_GW_interception_2014, - file = "../data/EFSA_GW_interception_2014.RData") -} EFSA_GW_interception_2014 } +\keyword{datasets} diff --git a/man/EFSA_washoff_2017.Rd b/man/EFSA_washoff_2017.Rd index e153fbe..28c50df 100644 --- a/man/EFSA_washoff_2017.Rd +++ b/man/EFSA_washoff_2017.Rd @@ -14,37 +14,13 @@ European Food Safety Authority (2017) EFSA guidance document for in soil. \emph{EFSA Journal} \bold{15}(10) 4982 doi:10.2903/j.efsa.2017.4982 } +\usage{ +EFSA_washoff_2017 +} \description{ Subset of EFSA crop washoff default values } \examples{ -\dontrun{ - # This is the code that was used to define the data - bbch <- paste0(0:9, "x") - crops <- c( - "Beans (field + vegetable)", - "Peas", - "Summer oilseed rape", "Winter oilseed rape", - "Tomatoes", - "Spring cereals", "Winter cereals") - EFSA_washoff_2017 <- matrix(NA, length(crops), length(bbch), - dimnames = list(Crop = crops, BBCH = bbch)) - EFSA_washoff_2017["Beans (field + vegetable)", ] <- - c(NA, 0.6, rep(0.75, 2), rep(0.8, 5), 0.35) - EFSA_washoff_2017["Peas", ] <- - c(NA, 0.4, rep(0.6, 2), rep(0.65, 5), 0.35) - EFSA_washoff_2017["Summer oilseed rape", ] <- - c(NA, 0.4, rep(0.5, 2), rep(0.6, 5), 0.5) - EFSA_washoff_2017["Winter oilseed rape", ] <- - c(NA, 0.1, rep(0.4, 2), rep(0.55, 5), 0.3) - EFSA_washoff_2017["Tomatoes", ] <- - c(NA, 0.55, rep(0.75, 2), rep(0.7, 5), 0.35) - EFSA_washoff_2017["Spring cereals", ] <- - c(NA, 0.4, 0.5, 0.5, rep(0.65, 3), rep(0.65, 2), 0.55) - EFSA_washoff_2017["Winter cereals", ] <- - c(NA, 0.1, 0.4, 0.6, rep(0.55, 3), rep(0.6, 2), 0.4) - save(EFSA_washoff_2017, - file = "../data/EFSA_washoff_2017.RData") -} EFSA_washoff_2017 } +\keyword{datasets} diff --git a/man/PEC_sw_exposit_drainage.Rd b/man/PEC_sw_exposit_drainage.Rd index 5a543c8..6f7f41a 100644 --- a/man/PEC_sw_exposit_drainage.Rd +++ b/man/PEC_sw_exposit_drainage.Rd @@ -5,7 +5,7 @@ \title{Calculate PEC surface water due to drainage as in Exposit 3} \source{ Excel 3.02 spreadsheet available from - \url{https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3} + \url{https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html} } \usage{ PEC_sw_exposit_drainage( diff --git a/man/PEC_sw_exposit_runoff.Rd b/man/PEC_sw_exposit_runoff.Rd index a415a63..4b6efba 100644 --- a/man/PEC_sw_exposit_runoff.Rd +++ b/man/PEC_sw_exposit_runoff.Rd @@ -5,7 +5,7 @@ \title{Calculate PEC surface water due to runoff and erosion as in Exposit 3} \source{ Excel 3.02 spreadsheet available from - \url{https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3} + \url{https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html} } \usage{ PEC_sw_exposit_runoff( diff --git a/man/PEC_sw_focus.Rd b/man/PEC_sw_focus.Rd index f23423b..362c432 100644 --- a/man/PEC_sw_focus.Rd +++ b/man/PEC_sw_focus.Rd @@ -21,7 +21,7 @@ PEC_sw_focus( met_form_water = TRUE, txt_file = "pesticide.txt", overwrite = FALSE, - append = TRUE + append = FALSE ) } \arguments{ @@ -73,7 +73,7 @@ should be written} \item{overwrite}{Should an existing file a the location specified in \code{txt_file} be overwritten? Only takes effect if append is FALSE.} -\item{append}{Should the input text file be appended?} +\item{append}{Should the input text file be appended, if it exists?} } \description{ This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2, @@ -81,8 +81,8 @@ authored by Michael Klein, in R. Note that results for multiple applications should be compared to the corresponding results for a single application. At current, this is not done automatically in this implementation. Only Step 1 PECs are calculated. However, -input files are generated that are suitable as input also for Step 2 -to be used with the FOCUS calculator. +input files can be generated that are suitable as input for +the FOCUS calculator. } \note{ The formulas for input to the waterbody via runoff/drainage of the @@ -97,7 +97,7 @@ Step 2 is not implemented. \examples{ # Parent only dummy_1 <- chent_focus_sw("Dummy 1", cwsat = 6000, DT50_ws = 6, Koc = 344.8) -PEC_sw_focus(dummy_1, 3000, f_drift = 0, overwrite = TRUE, append = FALSE) +PEC_sw_focus(dummy_1, 3000, f_drift = 0) # Metabolite new_dummy <- chent_focus_sw("New Dummy", mw = 250, Koc = 100) diff --git a/man/drift_data_JKI.Rd b/man/drift_data_JKI.Rd index bde9aad..49b7552 100644 --- a/man/drift_data_JKI.Rd +++ b/man/drift_data_JKI.Rd @@ -14,7 +14,7 @@ data for field crops (Ackerbau), and Pome/stone fruit, early and late JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved from http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html -on 2015-06-11 +on 2015-06-11, not present any more 2024-01-31 Rautmann, D., Streloke, M and Winkler, R (2001) New basic drift values in the authorization procedure for plant protection products Mitt. Biol. @@ -43,53 +43,6 @@ Values for non-professional use listed in the JKI spreadsheet were not included. } \examples{ - -\dontrun{ - # This is the code that was used to extract the data - library(readxl) - abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls" - JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet", "Weinbau frueh", "Weinbau spaet", - "Hopfenbau", "Flaechenkulturen > 900 l/ha", "Gleisanlagen") - names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late", - "Vines early", "Vines late", "Hops", "Areic cultures > 900 L/ha", "Railroad tracks") - drift_data_JKI <- list() - - for (n in 1:8) { - drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2) - drift_data <- matrix(NA, nrow = 9, ncol = length(JKI_crops)) - dimnames(drift_data) <- list(distance = drift_data_raw[[1]][1:9], - crop = JKI_crops) - if (n == 1) { # Values for railroad tracks only present for one application - drift_data[, c(1:3, 5:8)] <- as.matrix(drift_data_raw[c(2:7, 11)][1:9, ]) - } else { - drift_data[, c(1:3, 5:7)] <- as.matrix(drift_data_raw[c(2:7)][1:9, ]) - } - drift_data_JKI[[n]] <- drift_data - } - - # Manual data entry from the Rautmann paper - drift_data_JKI[[1]]["3", "Ackerbau"] <- 0.95 - drift_data_JKI[[1]][, "Weinbau frueh"] <- c(NA, 2.7, 1.18, 0.39, 0.2, 0.13, 0.07, 0.04, 0.03) - drift_data_JKI[[2]]["3", "Ackerbau"] <- 0.79 - drift_data_JKI[[2]][, "Weinbau frueh"] <- c(NA, 2.53, 1.09, 0.35, 0.18, 0.11, 0.06, 0.03, 0.02) - drift_data_JKI[[3]]["3", "Ackerbau"] <- 0.68 - drift_data_JKI[[3]][, "Weinbau frueh"] <- c(NA, 2.49, 1.04, 0.32, 0.16, 0.10, 0.05, 0.03, 0.02) - drift_data_JKI[[4]]["3", "Ackerbau"] <- 0.62 - drift_data_JKI[[4]][, "Weinbau frueh"] <- c(NA, 2.44, 1.02, 0.31, 0.16, 0.10, 0.05, 0.03, 0.02) - drift_data_JKI[[5]]["3", "Ackerbau"] <- 0.59 - drift_data_JKI[[5]][, "Weinbau frueh"] <- c(NA, 2.37, 1.00, 0.31, 0.15, 0.09, 0.05, 0.03, 0.02) - drift_data_JKI[[6]]["3", "Ackerbau"] <- 0.56 - drift_data_JKI[[6]][, "Weinbau frueh"] <- c(NA, 2.29, 0.97, 0.30, 0.15, 0.09, 0.05, 0.03, 0.02) - drift_data_JKI[[7]]["3", "Ackerbau"] <- 0.55 - drift_data_JKI[[7]][, "Weinbau frueh"] <- c(NA, 2.24, 0.94, 0.29, 0.15, 0.09, 0.05, 0.03, 0.02) - drift_data_JKI[[8]]["3", "Ackerbau"] <- 0.52 - drift_data_JKI[[8]][, "Weinbau frueh"] <- c(NA, 2.16, 0.91, 0.28, 0.14, 0.09, 0.04, 0.03, 0.02) - - # Save the data - save(drift_data_JKI, file = "data/drift_data_JKI.RData") -} - -# And these are the resulting data drift_data_JKI } \keyword{datasets} diff --git a/man/perc_runoff_exposit.Rd b/man/perc_runoff_exposit.Rd index 0bd2827..5b92ab3 100644 --- a/man/perc_runoff_exposit.Rd +++ b/man/perc_runoff_exposit.Rd @@ -1,5 +1,6 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/PEC_sw_exposit_runoff.R +\docType{data} \name{perc_runoff_exposit} \alias{perc_runoff_exposit} \title{Runoff loss percentages as used in Exposit 3} @@ -16,7 +17,10 @@ A data frame with percentage values for the dissolved fraction and the fraction } \source{ Excel 3.02 spreadsheet available from - \url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html} + \url{https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html} +} +\usage{ +perc_runoff_exposit } \description{ A table of the loss percentages used in Exposit 3 for the twelve different Koc classes @@ -24,3 +28,4 @@ A table of the loss percentages used in Exposit 3 for the twelve different Koc c \examples{ print(perc_runoff_exposit) } +\keyword{datasets} diff --git a/man/perc_runoff_reduction_exposit.Rd b/man/perc_runoff_reduction_exposit.Rd index 93016b7..0157e48 100644 --- a/man/perc_runoff_reduction_exposit.Rd +++ b/man/perc_runoff_reduction_exposit.Rd @@ -16,7 +16,7 @@ from which the values were taken. } \source{ Excel 3.02 spreadsheet available from - \url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html} + \url{https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html} Agroscope version 3.01a with additional runoff factors for 3 m and 6 m buffer zones received from Muris Korkaric (not published). The variant 3.01a2 was introduced for consistency with previous calculations performed by Agroscope for a 3 m buffer zone. diff --git a/man/soil_scenario_data_EFSA_2015.Rd b/man/soil_scenario_data_EFSA_2015.Rd index dfad4aa..4d625f8 100644 --- a/man/soil_scenario_data_EFSA_2015.Rd +++ b/man/soil_scenario_data_EFSA_2015.Rd @@ -14,7 +14,10 @@ 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 + \doi{10.2903/j.efsa.2015.4093} +} +\usage{ +soil_scenario_data_EFSA_2015 } \description{ Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the @@ -22,26 +25,6 @@ concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the scenario and model adjustment factors from p. 15 and p. 17 are included. } \examples{ -\dontrun{ - # This is the code that was used to define the data - soil_scenario_data_EFSA_2015 <- data.frame( - Zone = rep(c("North", "Central", "South"), 2), - Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"), - T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8), - T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7), - Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"), - f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011), - theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347), - rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51), - f_sce = c(3, 2, 2, 2, 1.5, 1.5), - f_mod = c(2, 2, 2, 4, 4, 4), - stringsAsFactors = FALSE, - row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS") - ) - save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData') -} - -# And this is the resulting dataframe soil_scenario_data_EFSA_2015 } \keyword{datasets} diff --git a/man/soil_scenario_data_EFSA_2017.Rd b/man/soil_scenario_data_EFSA_2017.Rd index f6de290..c43a5b7 100644 --- a/man/soil_scenario_data_EFSA_2017.Rd +++ b/man/soil_scenario_data_EFSA_2017.Rd @@ -14,7 +14,10 @@ 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 + \doi{10.2903/j.efsa.2017.4982} +} +\usage{ +soil_scenario_data_EFSA_2017 } \description{ Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the @@ -23,5 +26,7 @@ scenario and model adjustment factors from p. 16 and p. 18 are included. } \examples{ soil_scenario_data_EFSA_2017 + +waldo::compare(soil_scenario_data_EFSA_2017, soil_scenario_data_EFSA_2015) } \keyword{datasets} -- cgit v1.2.1