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-rw-r--r--GNUmakefile2
-rw-r--r--R/D24_2014.R14
-rw-r--r--data/D24_2014.rdabin20470 -> 5836 bytes
-rw-r--r--inst/dataset_generation/D24_2014.R54
-rw-r--r--man/D24_2014.Rd14
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$ds[[1]], data = TRUE)
-#' m1 = mkinmod(D24 = list(type = "SFO", to = "phenol"),
-#' phenol = list(type = "SFO", to = "anisole"),
-#' anisole = list(type = "SFO"))
+#' m_D24 = mkinmod(D24 = mkinsub("SFO", to = "DCP"),
+#' DCP = mkinsub("SFO", to = "DCA"),
+#' DCA = mkinsub("SFO"))
"D24_2014"
diff --git a/data/D24_2014.rda b/data/D24_2014.rda
index 78a2a4f4..5777ca89 100644
--- a/data/D24_2014.rda
+++ b/data/D24_2014.rda
Binary files differ
diff --git a/inst/dataset_generation/D24_2014.R b/inst/dataset_generation/D24_2014.R
index bea74da5..47f9cfab 100644
--- a/inst/dataset_generation/D24_2014.R
+++ b/inst/dataset_generation/D24_2014.R
@@ -3,65 +3,65 @@
D24_2014 <- mkindsg$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}

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