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

10 files changed, 33 insertions, 135 deletions

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}