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

6 files changed, 23 insertions, 168 deletions

diff --git a/R/EFSA_GW_interception_2014.R b/R/EFSA_GW_interception_2014.R
index 15d7835..386fddf 100644
--- a/R/EFSA_GW_interception_2014.R
+++ b/R/EFSA_GW_interception_2014.R
@@ -9,33 +9,5 @@
 #' \bold{12}(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662
 #' @format A matrix containing interception values, currently only for some selected crops
 #' @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
-NULL
+"EFSA_GW_interception_2014"
diff --git a/R/EFSA_washoff_2017.R b/R/EFSA_washoff_2017.R
index 450c12e..59e299c 100644
--- a/R/EFSA_washoff_2017.R
+++ b/R/EFSA_washoff_2017.R
@@ -10,33 +10,5 @@
 #'   doi:10.2903/j.efsa.2017.4982
 #' @format A matrix containing wash-off factors, currently only for some selected crops
 #' @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
-NULL
+"EFSA_washoff_2017"
diff --git a/R/PEC_sw_exposit_runoff.R b/R/PEC_sw_exposit_runoff.R
index d68a521..8b89cd9 100644
--- a/R/PEC_sw_exposit_runoff.R
+++ b/R/PEC_sw_exposit_runoff.R
@@ -13,18 +13,11 @@
 #'       adjacent water body bound to eroding particles}
 #'   }
 #' @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}
-#' @export perc_runoff_exposit
+#'   \url{https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html}
+#' @docType data
 #' @examples
 #' print(perc_runoff_exposit)
-{Koc_breaks <- c(0, 20, 50, 100, 200, 500, 1000, 2000, 5000, 10000, 20000, 50000, Inf)
-tmp <- paste(Koc_breaks[1:11], Koc_breaks[2:12], sep = "-")
-Koc_classes <- c(tmp[1], paste0(">", tmp[2:11]), ">50000")}
-perc_runoff_exposit <- data.frame(
-  Koc_lower_bound = Koc_breaks[1:12],
-  dissolved = c(0.11, 0.151, 0.197, 0.248, 0.224, 0.184, 0.133, 0.084, 0.037, 0.031, 0.014, 0.001),
-  bound = c(0, 0, 0, 0.001, 0.004, 0.020, 0.042, 0.091, 0.159, 0.192, 0.291, 0.451))
-rownames(perc_runoff_exposit) <- Koc_classes
+"perc_runoff_exposit"
 
 #' Runoff reduction percentages as used in Exposit
 #'
@@ -40,31 +33,14 @@ rownames(perc_runoff_exposit) <- Koc_classes
 #'     \item{bound}{The reduction percentage for the particulate phase}
 #'   }
 #' @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.
-#' @export
+#' @docType data
 #' @examples
 #' print(perc_runoff_reduction_exposit)
-perc_runoff_reduction_exposit <- list(
-   "3.02" = data.frame(
-    dissolved = c(0, 40, 60, 80),
-    bound = c(0, 40, 85, 95),
-    row.names = c("No buffer", paste(c(5, 10, 20), "m"))),
-   "3.01a" = data.frame(
-    dissolved = c(0, 25, 40, 45, 60, 80),
-    bound = c(0, 30, 40, 55, 85, 95),
-    row.names = c("No buffer", paste(c(3, 5, 6, 10, 20), "m"))),
-   "3.01a2" = data.frame(
-    dissolved = c(0, 25),
-    bound = c(0, 25),
-    row.names = c("No buffer", paste(c(3), "m"))),
-  "2.0" = data.frame(
-    dissolved = c(0, 97.5),
-    bound = c(0, 97.5),
-    row.names = c("No buffer", "20 m"))
-)
+"perc_runoff_reduction_exposit"
 
 #' Calculate PEC surface water due to runoff and erosion as in Exposit 3
 #'
@@ -93,7 +69,7 @@ perc_runoff_reduction_exposit <- list(
 #'   }
 #' @export
 #' @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}
 #' @seealso \code{\link{perc_runoff_exposit}} for runoff loss percentages and \code{\link{perc_runoff_reduction_exposit}} for runoff reduction percentages used
 #' @examples
 #'   PEC_sw_exposit_runoff(500, Koc = 150)
@@ -108,18 +84,18 @@ PEC_sw_exposit_runoff <- function(rate, interception = 0, Koc, DT50 = Inf, t_run
   if (length(Koc) > 1) stop("Only one compound at a time supported")
 
   exposit_reduction_version <- match.arg(exposit_reduction_version)
-  red_water <- perc_runoff_reduction_exposit[[exposit_reduction_version]]["dissolved"] / 100
-  red_bound <- perc_runoff_reduction_exposit[[exposit_reduction_version]]["bound"] / 100
-  reduction_runoff <- perc_runoff_reduction_exposit[[exposit_reduction_version]] / 100
+  red_water <- pfm::perc_runoff_reduction_exposit[[exposit_reduction_version]]["dissolved"] / 100
+  red_bound <- pfm::perc_runoff_reduction_exposit[[exposit_reduction_version]]["bound"] / 100
+  reduction_runoff <- pfm::perc_runoff_reduction_exposit[[exposit_reduction_version]] / 100
   transfer_runoff <- 1 - reduction_runoff
 
   V_runoff <- V_event * (1 - reduction_runoff[["dissolved"]]) # m3
   V_flowing_ditch_runoff <- dilution * (V_ditch + V_runoff)
 
   f_runoff_exposit <- function(Koc) {
-    Koc_breaks <- c(perc_runoff_exposit$Koc_lower_bound, Inf)
-    Koc_classes <- as.character(cut(Koc, Koc_breaks, labels = rownames(perc_runoff_exposit)))
-    perc_runoff <- perc_runoff_exposit[Koc_classes, c("dissolved", "bound")]
+    Koc_breaks <- c(pfm::perc_runoff_exposit$Koc_lower_bound, Inf)
+    Koc_classes <- as.character(cut(Koc, Koc_breaks, labels = rownames(pfm::perc_runoff_exposit)))
+    perc_runoff <- pfm::perc_runoff_exposit[Koc_classes, c("dissolved", "bound")]
     if (identical(Koc, 0)) perc_runoff <- c(dissolved = 0, bound = 0)
     return(unlist(perc_runoff) / 100)
   }
@@ -168,7 +144,7 @@ PEC_sw_exposit_runoff <- function(rate, interception = 0, Koc, DT50 = Inf, t_run
 #'   }
 #' @export
 #' @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}
 #' @seealso \code{\link{perc_runoff_exposit}} for runoff loss percentages and \code{\link{perc_runoff_reduction_exposit}} for runoff reduction percentages used
 #' @examples
 #'   PEC_sw_exposit_drainage(500, Koc = 150)
diff --git a/R/drift_data_JKI.R b/R/drift_data_JKI.R
index 3b02f43..8f78e4d 100644
--- a/R/drift_data_JKI.R
+++ b/R/drift_data_JKI.R
@@ -29,59 +29,12 @@
 #' @source 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.
 #' Bundesanst. Land- Forstwirtsch. 383, 133-141
 #' @keywords datasets
 #' @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
 NULL
diff --git a/R/soil_scenario_data_EFSA_2015.R b/R/soil_scenario_data_EFSA_2015.R
index 660cafe..0660d40 100644
--- a/R/soil_scenario_data_EFSA_2015.R
+++ b/R/soil_scenario_data_EFSA_2015.R
@@ -13,28 +13,8 @@
 #'   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}
 #' @keywords datasets
 #' @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
-NULL
+"soil_scenario_data_EFSA_2015"
diff --git a/R/soil_scenario_data_EFSA_2017.R b/R/soil_scenario_data_EFSA_2017.R
index 79ee15f..f7cbea0 100644
--- a/R/soil_scenario_data_EFSA_2017.R
+++ b/R/soil_scenario_data_EFSA_2017.R
@@ -13,8 +13,10 @@
 #'   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}
 #' @keywords datasets
 #' @examples
 #' soil_scenario_data_EFSA_2017
-NULL
+#'
+#' waldo::compare(soil_scenario_data_EFSA_2017, soil_scenario_data_EFSA_2015)
+"soil_scenario_data_EFSA_2017"