From 95178837d3f91e84837628446b5fd468179af2b9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 4 Jun 2019 15:09:28 +0200 Subject: Additional algorithm "d_c", more tests, docs The new algorithm tries direct optimization of the likelihood, as well as a three step procedure. In this way, we consistently get the model with the highest likelihood for SFO, DFOP and HS for all 12 new test datasets. --- docs/reference/experimental_data_for_UBA.html | 223 ++++++++++++++++++++++++++ 1 file changed, 223 insertions(+) create mode 100644 docs/reference/experimental_data_for_UBA.html (limited to 'docs/reference/experimental_data_for_UBA.html') diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html new file mode 100644 index 00000000..3e8d20ef --- /dev/null +++ b/docs/reference/experimental_data_for_UBA.html @@ -0,0 +1,223 @@ + + + + + + + + +Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019 • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Experimental datasets used for development and testing of error models

+ + +
+ +
+ +

The 12 datasets were extracted from active substance evaluation dossiers published + by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate + and advance error model specifications. The fact that these data and some + results are shown here do not imply a license to use them in the context of + pesticide registrations, as the use of the data may be constrained by + data protection regulations.

+ +
+ + 
experimental_data_for_UBA_2019
+ +

Format

+ +

A list containing twelve datasets as an R6 class defined by mkinds, + each containing, among others, the following components

+
title

The name of the dataset, e.g. Soil 1

+
data

A data frame with the data in the form expected by mkinfit

+
+ +

Source

+ +

Ranke (2019) Documentation of results obtained for the error model expertise + written for the German Umweltbundesamt.

+ + +

Examples

+ 

+# Model definitions
+sfo_sfo <- mkinmod(
+  parent = mkinsub("SFO", to = "A1"),
+  A1 = mkinsub("SFO"),
+  use_of_ff = "max"
+)
#> Successfully compiled differential equation model from auto-generated C code.

+dfop_sfo <- mkinmod(
+  parent = mkinsub("DFOP", to = "A1"),
+  A1 = mkinsub("SFO"),
+  use_of_ff = "max"
+)
#> Successfully compiled differential equation model from auto-generated C code.

+sfo_sfo_sfo <- mkinmod(
+  parent = mkinsub("SFO", to = "A1"),
+  A1 = mkinsub("SFO", to = "A2"),
+  A2 = mkinsub("SFO"),
+  use_of_ff = "max"
+)
#> Successfully compiled differential equation model from auto-generated C code.

+dfop_sfo_sfo <- mkinmod(
+  parent = mkinsub("DFOP", to = "A1"),
+  A1 = mkinsub("SFO", to = "A2"),
+  A2 = mkinsub("SFO"),
+  use_of_ff = "max"
+)
#> Successfully compiled differential equation model from auto-generated C code.
d_1_2 <- lapply(experimental_data_for_UBA_2019[1:2], function(x) x$data)
+names(d_1_2) <- paste("Soil", 1:2)
+
+
+f_1_2_tc <- mmkin(list("DFOP-SFO-SFO" = dfop_sfo_sfo), d_1_2, error_model = "tc")
+
+plot(f_1_2_tc, resplot = "errmod")

+
+
+ +
+ +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown 1.3.0.

+
+
+
+ + + + + + -- cgit v1.2.1 From b6027bbd157734e1c7f8c3ba6373451f5c85fc38 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 5 Jun 2019 15:16:59 +0200 Subject: Add error model algorithm to output --- docs/reference/experimental_data_for_UBA.html | 66 ++++++++++++++++++++++++++- 1 file changed, 64 insertions(+), 2 deletions(-) (limited to 'docs/reference/experimental_data_for_UBA.html') diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index 3e8d20ef..bb94fd11 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -37,7 +37,30 @@ and advance error model specifications. The fact that these data and some results are shown here do not imply a license to use them in the context of pesticide registrations, as the use of the data may be constrained by - data protection regulations." /> + data protection regulations. +Preprocessing of data was performed based on the recommendations of the FOCUS + kinetics workgroup (FOCUS, 2014) as described below. +Datasets 1 and 2 are from the Renewal Assessment Report (RAR) for imazamox + (France, 2015, p. 15). For setting values reported as zero, an LOQ of 0.1 + was assumed. Metabolite residues reported for day zero were added to the + parent compound residues. +Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid + (Belgium, 2014, p. 8) and show the data for two different radiolabels. For + dataset 4, the value given for the metabolite in the day zero sampling + in replicate B was added to the parent compound, following the respective + FOCUS recommendation. +Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate + (Austria, 2015, p. 16). +Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate + (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling, + the residues given for the metabolite were added to the parent + value, following the recommendation of the FOCUS kinetics workgroup. +Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D + (Germany, 2013b, p. 644). Values reported as zero were set to NA, with + the exception of the day three sampling of metabolite A2, which was set + to one half of the LOD reported to be 1% AR. +Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl + (United Kingdom, 2014, p. 81)." /> @@ -139,6 +162,29 @@ results are shown here do not imply a license to use them in the context of pesticide registrations, as the use of the data may be constrained by data protection regulations.

+

Preprocessing of data was performed based on the recommendations of the FOCUS + kinetics workgroup (FOCUS, 2014) as described below.

+

Datasets 1 and 2 are from the Renewal Assessment Report (RAR) for imazamox + (France, 2015, p. 15). For setting values reported as zero, an LOQ of 0.1 + was assumed. Metabolite residues reported for day zero were added to the + parent compound residues.

+

Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid + (Belgium, 2014, p. 8) and show the data for two different radiolabels. For + dataset 4, the value given for the metabolite in the day zero sampling + in replicate B was added to the parent compound, following the respective + FOCUS recommendation.

+

Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate + (Austria, 2015, p. 16).

+

Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate + (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling, + the residues given for the metabolite were added to the parent + value, following the recommendation of the FOCUS kinetics workgroup.

+

Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D + (Germany, 2013b, p. 644). Values reported as zero were set to NA, with + the exception of the day three sampling of metabolite A2, which was set + to one half of the LOD reported to be 1% AR.

+

Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl + (United Kingdom, 2014, p. 81).

@@ -154,8 +200,24 @@

Source

-

Ranke (2019) Documentation of results obtained for the error model expertise + +

Austria (2015). Ethofumesate Renewal Assessment Report Volume 3 Annex B.8 (AS)

+

Belgium (2014). Isofetamid (IKF-5411) Draft Assessment Report Volume 3 Annex B.8 (AS)

+

France (2015). Imazamox Draft Renewal Assessment Report Volume 3 Annex B.8 (AS)

+

FOCUS (2014) “Generic guidance for Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Version 1.1, 18 December 2014 + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

+

Germany (2013a). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate + and Behaviour

+

Germany (2013b). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate and behaviour in the + environment

+

Ranke (2019) Documentation of results obtained for the error model expertise written for the German Umweltbundesamt.

+

United Kingdom (2014). Thifensulfuron-methyl - Annex B.8 (Volume 3) to the Report and Proposed + Decision of the United Kingdom made to the European Commission under Regulation (EC) No. + 1141/2010 for renewal of an active substance

Examples

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