From 35eaf4f7bac89b249ff488e4e3021d4226ed9e23 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 15 Sep 2021 11:22:36 +0200
Subject: Correction of the dimethenamid dataset

The data given in previous mkin versions for "Borstel 2" (Staudenmaier
2013) are in fact a subset of the "Borstel 1" data, with the "Borstel 2"
data simply being further analysed for isomer composition by
Staudenmaier (2013).

While correcting this, the URL of the RAR published by EFSA was
updated, as the EFSA Register of Questions was replaced by the
Open EFSA portal.

This also affects the recent publication in "Environments" [1], where
these two datasets were pooled. However, the influence on the final
results can be expected to be minimal. Out of the 16 observations for
the Borstel soil, five were erroneously duplicated which just changes
the weight of the different sampling points and modifies the variance.
The conclusions of the publication are qualitative and are not
considered to be affected.

[1] https://doi.org/10.3390/environments8080071
---
 R/dimethenamid_2018.R                       |   4 ++--
 data/dimethenamid_2018.rda                  | Bin 8231 -> 7945 bytes
 inst/dataset_generation/dimethenamid_2018.R |  24 ++++++++----------------
 3 files changed, 10 insertions(+), 18 deletions(-)

diff --git a/R/dimethenamid_2018.R b/R/dimethenamid_2018.R
index 189da618..1a7e14a2 100644
--- a/R/dimethenamid_2018.R
+++ b/R/dimethenamid_2018.R
@@ -11,11 +11,11 @@
 #' in the 'dataset_generation' directory. In the code, page numbers are given for
 #' specific pieces of information in the comments.
 #'
-#' @format An [mkindsg] object grouping eight datasets with some meta information
+#' @format An [mkindsg] object grouping seven datasets with some meta information
 #' @source Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria (2018)
 #'   Renewal Assessment Report Dimethenamid-P Volume 3 - B.8 Environmental fate and behaviour
 #'   Rev. 2 - November 2017
-#'   \url{http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-5211}
+#'   \url{https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716}
 #' @examples
 #' print(dimethenamid_2018)
 "dimethenamid_2018"
diff --git a/data/dimethenamid_2018.rda b/data/dimethenamid_2018.rda
index dd3d934b..39168e9c 100644
Binary files a/data/dimethenamid_2018.rda and b/data/dimethenamid_2018.rda differ
diff --git a/inst/dataset_generation/dimethenamid_2018.R b/inst/dataset_generation/dimethenamid_2018.R
index 34a9dad1..52eef995 100644
--- a/inst/dataset_generation/dimethenamid_2018.R
+++ b/inst/dataset_generation/dimethenamid_2018.R
@@ -15,15 +15,7 @@ dimethenamid_2018 <- mkindsg$new(
         )
       )
     ),
-    mkinds$new("Borstel 1", # p. 22
-      mkin_wide_to_long(
-        data.frame(
-          t = c(0, 28, 58, 89, 119),
-          DMTAP = c(100.5, 51.4, 26.8, 15.7, 7.9)
-        )
-      )
-    ),
-    mkinds$new("Borstel 2", # p. 19/20
+    mkinds$new("Borstel", # p. 19/20
       mkin_wide_to_long(
         data.frame(
           t = rep(c(0, 2, 7, 14, 28, 58, 89, 119), each = 2),
@@ -134,20 +126,20 @@ dimethenamid_2018 <- mkindsg$new(
   # but the FOCUS generic guidance suggests them to be equivalent to the USDA
   # classes with the same name
   meta = data.frame(
-    study = c("Unsworth 2014", "Staudenmaier 2013", "Staudenmaier 2009",
+    study = c("Unsworth 2014", "Staudenmaier 2009",
       rep("Wendt 1997", 2), "König 1996", rep("König 1995", 2)),
-    usda_soil_type = c("Sandy loam", rep("Sand", 2),
+    usda_soil_type = c("Sandy loam", "Sand",
       rep("Clay loam", 2), "Sandy clay loam", "Loamy sand",
       "Sandy loam"),
-    study_moisture_ref_type = c("pF2", rep("pF1", 2),
+    study_moisture_ref_type = c("pF2", "pF1",
       rep("pF2.5", 2), rep("pF1", 3)),
-    rel_moisture = c(1, rep(0.5, 2),
+    rel_moisture = c(1, 0.5,
       rep(0.75, 2), rep(0.4, 3)),
-    study_ref_moisture = c(NA, rep(23, 2), rep(33.37, 2), rep(NA, 3)),
-    temperature = c(20, rep(20, 2),
+    study_ref_moisture = c(NA, 23, rep(33.37, 2), rep(NA, 3)),
+    temperature = c(20, 20,
       rep(23, 2), rep(20, 3))
   )
 )
-f_time_norm_focus(dimethenamid_2018)
+f_time_norm_focus(dimethenamid_2018) # This modifies the R6 object in place
 
 save(dimethenamid_2018, file = "data/dimethenamid_2018.rda", version = 2)
-- 
cgit v1.2.1