From d1a94f2bb3742f50f3dd98a03d5fec338dd0cf65 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 12 Nov 2020 11:57:37 +0100 Subject: Use preprocessed data for 2,4-D, update docs --- GNUmakefile | 2 +- R/D24_2014.R | 14 +++++----- data/D24_2014.rda | Bin 20470 -> 5836 bytes inst/dataset_generation/D24_2014.R | 54 ++++++++++++++++++------------------- man/D24_2014.Rd | 14 +++++----- 5 files changed, 44 insertions(+), 40 deletions(-) diff --git a/GNUmakefile b/GNUmakefile index 49f64c45..f27d02a3 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -23,7 +23,7 @@ pkgfiles = \ data/* \ DESCRIPTION \ inst/WORDLIST \ - inst/extdata/* \ + inst/dataset_generation/* \ inst/testdata/fit_old_FOCUS_D.rda \ man/* \ NAMESPACE \ diff --git a/R/D24_2014.R b/R/D24_2014.R index 81316833..bca56dc2 100644 --- a/R/D24_2014.R +++ b/R/D24_2014.R @@ -7,7 +7,10 @@ #' context of pesticide registrations, as the use of the data may be #' constrained by data protection regulations. #' -#' Metabolite residues at early sampling times reported as 0.0 were set to NA. +#' Data for the first dataset are from p. 685. Data for the other four +#' datasets were used in the preprocessed versions given in the kinetics +#' section (p. 761ff.), with the exception of residues smaller than 1 for DCP +#' in the soil from Site I2, where the values given on p. 694 were used. #' #' The R code used to create this data object is installed with this package #' in the 'dataset_generation' directory. In the code, page numbers are given for @@ -16,13 +19,12 @@ #' @format An [mkindsg] object grouping five datasets #' @source Hellenic Ministry of Rural Development and Agriculture (2014) #' Final addendum to the Renewal Assessment Report - public version - 2,4-D -#' Volume 3 Annex B.8 Fate and behaviour in the environment p. 638, 640, -#' 644-646. +#' Volume 3 Annex B.8 Fate and behaviour in the environment #' \url{http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-3812} #' @examples #' print(D24_2014) #' print(D24_2014$ds[[1]], data = TRUE) -#' m1 = mkinmod(D24 = list(type = "SFO", to = "phenol"), -#' phenol = list(type = "SFO", to = "anisole"), -#' anisole = list(type = "SFO")) +#' m_D24 = mkinmod(D24 = mkinsub("SFO", to = "DCP"), +#' DCP = mkinsub("SFO", to = "DCA"), +#' DCA = mkinsub("SFO")) "D24_2014" diff --git a/data/D24_2014.rda b/data/D24_2014.rda index 78a2a4f4..5777ca89 100644 Binary files a/data/D24_2014.rda and b/data/D24_2014.rda differ diff --git a/inst/dataset_generation/D24_2014.R b/inst/dataset_generation/D24_2014.R index bea74da5..47f9cfab 100644 --- a/inst/dataset_generation/D24_2014.R +++ b/inst/dataset_generation/D24_2014.R @@ -3,65 +3,65 @@ D24_2014 <- mkindsg$new( title = "Aerobic soil degradation data on 2,4-D from the EU assessment in 2014", ds = list( - mkinds$new("Mississippi", + mkinds$new("Mississippi", # p. 685 data.frame( name = "D24", time = c(0, 2, 4, 7, 15, 24, 35, 56, 71, 114, 183, 273, 365), value = c(96.8, 81.0, 81.7, 88.2, 66.3, 72.9, 62.6, 54.6, 35.2, 18.0, 11.3, 9.9, 6.3)) ), - mkinds$new("Fayette", + mkinds$new("Fayette", # Processed data p. 761 mkin_wide_to_long( data.frame( - t = rep(c(0, 0.1, 0.3, 1, 3, 5, 10, 17, 26), each = 2), - D24 = c(96.9, 96.6, 93.2, 93.2, 90.5, 91.5, 86.3, 87.1, 79.0, 80.8, - 74.0, 65.6, 35.0, 36.7, 6.6, 4.5, 1.6, 1.7), - DCP = c(NA, NA, 1.4, 1.6, 2.5, 2.4, 2.9, 3.1, 4.4, 4.2, 5.8, 5.4, - 8.2, 8.7, 5.8, 3.8, 1.8, 2.0), - DCA = c(rep(NA, 10), 3.2, 3.5, 9.5, 9.1, 15.0, 13.0, 11.8, 11.7)) + t = rep(c(0, 0.1, 0.3, 1, 3, 5, 10, 17), each = 2), + D24 = c(100.8, 101.0, 93.2, 93.2, 90.5, 91.5, 86.3, 87.1, 79.0, 80.8, + 74.0, 65.6, 35.0, 36.7, 6.6, NA), + DCP = c(0, 0, 1.4, 1.6, 2.5, 2.4, 2.9, 3.1, 4.4, 4.2, 5.8, 5.4, + 8.2, 8.7, 5.8, NA), + DCA = c(0, 0, rep(NA, 6), 0.5, 0.5, 3.2, 3.5, 9.5, 9.1, 15.0, NA)) ) ), - mkinds$new("RefSol 03-G", + mkinds$new("RefSol 03-G", # Processed data p. 761 mkin_wide_to_long( data.frame( t = rep(c(0, 0.1, 0.3, 1, 3, 5, 10, 17, 26), each = 2), - D24 = c(92.9, 93.1, 87.4, 87.9, 78.1, 78.8, 57.1, 56.1, 25.0, 32.3, + D24 = c(98.8, 98.8, 87.4, 87.9, 78.1, 78.8, 57.1, 56.1, 25.0, 32.3, 14.7, NA, 3.1, 3.1, 2.7, 2.1, 2.0, 2.2), - DCP = c(NA, NA, 2.8, 2.5, 5.5, 5.4, 8.5, 8.6, 6.7, 5.3, 5.7, NA, + DCP = c(0, 0, 2.8, 2.5, 5.5, 5.4, 8.5, 8.6, 6.7, 5.3, 5.7, NA, 3.2, 2.7, 2.3, 1.7, 1.3, 1.7), - DCA = c(rep(NA, 6), 3.3, 3.7, 8.0, 7.0, 10.6, NA, 7.7, 7.9, 5.2, - 6.7, 4.6, 4.2)) + DCA = c(0, 0, NA, NA, 0.5, 0.5, 3.3, 3.7, 8.0, 7.0, 10.6, NA, 7.7, + 7.9, 5.2, 6.7, 4.6, 4.2)) ) ), - mkinds$new("Site E1", + mkinds$new("Site E1", # Processed data p. 762 mkin_wide_to_long( data.frame( t = rep(c(0, 0.1, 0.3, 1, 3, 7, 10, 17, 26), each = 2), - D24 = c(97.5, 97.9, 97.9, 98.3, 92.4, 91.9, 65.8, 69.5, 37.5, - 40, 18.8, 14.4, 3.3, 5.7, 2.6, 2.3, 2.4, 2), - DCP = c(rep(NA, 4), 1.8, 2.3, 4.4, 3.6, 4.8, 4.3, 3.3, 3.7, - 1.7, 2.3, NA, 0.8, 0.8, 0.8), - DCA = c(rep(NA, 6), 3.9, 2.9, 6.3, 5.4, 5.7, 5.5, 4.5, 4.2, - 3.0, 2.5, 1.5, 1.7)) + D24 = c(100.2, 100.9, 97.9, 98.3, 92.4, 91.9, 65.8, 69.5, 37.5, + 40, 18.8, 14.4, 3.3, 5.7, 2.6, NA, 2.4, NA), + DCP = c(0, 0, 0.5, 0.5, 1.8, 2.3, 4.4, 3.6, 4.8, 4.3, 3.3, 3.7, + 1.7, 2.3, 0.5, rep(NA, 3)), + DCA = c(0, 0, NA, NA, 0.5, 0.5, 3.9, 2.9, 6.3, 5.4, 5.7, 5.5, + 4.5, 4.2, 3.0, NA, 1.5, NA)) ) ), - mkinds$new("Site I2", + mkinds$new("Site I2", # Processed data p. 763 "uncorr" except values <1 mkin_wide_to_long( data.frame( t = rep(c(0, 0.1, 0.3, 1, 3, 5, 10, 17, 26), each = 2), - D24 = c(94.1, 91.6, 90.1, 89.2, 86.3, 86.5, 76.7, 74.7, + D24 = c(99.0, 98.8, 90.1, 89.2, 86.3, 86.5, 76.7, 74.7, 33.1, NA, 8.8, 6.7, 3.1, 3.2, 1.6, 1.7, 1.5, 1.9), - DCP = c(NA, NA, 0.9, 1.2, 1.7, 1.3, 2.5, 5.1, 2.5, NA, + DCP = c(0, 0, 0.9, 1.2, 1.7, 1.3, 2.5, 5.1, 2.5, NA, # < 1 p. 694 1.9, 1.7, 0.5, 0.9, 0.9, 1.2, 0.7, NA), - DCA = c(rep(NA, 8), 4.5, NA, 6.6, 5.7, 5.1, 4.3, 2.3, 2.2, - 2.1, 2.1)) + DCA = c(0, 0, rep(NA, 4), 0.5, 0.5, 4.5, NA, 6.6, 5.7, 5.1, + 4.3, 2.3, 2.2, 2.1, 2.1)) ) ) ), meta = data.frame( study = c("Cohen 1991", rep("Liu and Adelfinskaya 2011", 4)), - usda_soil_type = c("Silt loam", # p. 683 - "Clay loam", "Clay loam", "Sandy loam", "Sandy loam"), # EFSA 204 p. 41/42 + usda_soil_type = c("Silt loam", # p. 683, EFSA conclusion p. 41/42 + "Clay loam", "Clay loam", "Sandy loam", "Sandy loam"), moisture_ref_type = c(NA, rep("% MWHC", 4)), # p. 687 rel_moisture = c(NA, 0.5, 0.5, 0.5, 0.5), # p. 687 moisture_ref = c(NA, 65.7, 59.9, 75.3, 48.5), # p. 687 diff --git a/man/D24_2014.Rd b/man/D24_2014.Rd index 90b0605e..d0ab516a 100644 --- a/man/D24_2014.Rd +++ b/man/D24_2014.Rd @@ -10,8 +10,7 @@ An \link{mkindsg} object grouping five datasets \source{ Hellenic Ministry of Rural Development and Agriculture (2014) Final addendum to the Renewal Assessment Report - public version - 2,4-D -Volume 3 Annex B.8 Fate and behaviour in the environment p. 638, 640, -644-646. +Volume 3 Annex B.8 Fate and behaviour in the environment \url{http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-3812} } \usage{ @@ -26,7 +25,10 @@ context of pesticide registrations, as the use of the data may be constrained by data protection regulations. } \details{ -Metabolite residues at early sampling times reported as 0.0 were set to NA. +Data for the first dataset are from p. 685. Data for the other four +datasets were used in the preprocessed versions given in the kinetics +section (p. 761ff.), with the exception of residues smaller than 1 for DCP +in the soil from Site I2, where the values given on p. 694 were used. The R code used to create this data object is installed with this package in the 'dataset_generation' directory. In the code, page numbers are given for @@ -35,8 +37,8 @@ specific pieces of information in the comments. \examples{ print(D24_2014) print(D24_2014$ds[[1]], data = TRUE) -m1 = mkinmod(D24 = list(type = "SFO", to = "phenol"), - phenol = list(type = "SFO", to = "anisole"), - anisole = list(type = "SFO")) +m_D24 = mkinmod(D24 = mkinsub("SFO", to = "DCP"), + DCP = mkinsub("SFO", to = "DCA"), + DCA = mkinsub("SFO")) } \keyword{datasets} -- cgit v1.2.1