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/Extract.mmkin.html | 8 ++-- docs/reference/experimental_data_for_UBA.html | 66 ++++++++++++++++++++++++++- docs/reference/mkinfit.html | 50 +++++++++++--------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 6 +-- docs/reference/mmkin.html | 4 +- docs/reference/summary.mkinfit.html | 11 +++-- 7 files changed, 108 insertions(+), 39 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 1d1da50e..37c0b361 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -172,16 +172,16 @@ cores = 1, quiet = TRUE) fits["FOMC", ]
#> dataset #> model B C -#> FOMC List,36 List,36 +#> FOMC List,37 List,37 #> attr(,"class") #> [1] "mmkin"
fits[, "B"]
#> dataset #> model B -#> SFO List,36 -#> FOMC List,36 +#> SFO List,37 +#> FOMC List,37 #> attr(,"class") #> [1] "mmkin"
fits["SFO", "B"]
#> dataset #> model B -#> SFO List,36 +#> SFO List,37 #> attr(,"class") #> [1] "mmkin"
head( 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

diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 8cabcb21..700b6805 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -399,18 +399,19 @@ Per default, parameters in the kinetic models are internally transformed in fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue Jun 4 15:01:15 2019 -#> Date of summary: Tue Jun 4 15:01:15 2019 +#> Date of fit: Wed Jun 5 15:08:20 2019 +#> Date of summary: Wed Jun 5 15:08:20 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.461 s +#> Fitted using 222 model solutions performed in 0.469 s #> -#> Error model: -#> Constant variance +#> Error model: Constant variance +#> +#> Error model algorithm: d_3 #> #> Starting values for parameters to be optimised: #> value type @@ -480,7 +481,7 @@ Per default, parameters in the kinetic models are internally transformed in m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE)))
#> Warning: Observations with value of zero were removed from the data
#> User System verstrichen -#> 1.521 0.000 1.526
coef(fit)
#> NULL
endpoints(fit)
#> $ff +#> 1.579 0.000 1.581
coef(fit)
#> NULL
endpoints(fit)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -552,7 +553,7 @@ Per default, parameters in the kinetic models are internally transformed in #> Sum of squared residuals at call 126: 371.2134 #> Sum of squared residuals at call 135: 371.2134 #> Negative log-likelihood at call 145: 97.22429
#> Optimisation successfully terminated.
#> User System verstrichen -#> 1.093 0.000 1.093
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff +#> 1.159 0.000 1.160
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -584,8 +585,8 @@ Per default, parameters in the kinetic models are internally transformed in SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue Jun 4 15:01:31 2019 -#> Date of summary: Tue Jun 4 15:01:31 2019 +#> Date of fit: Wed Jun 5 15:08:36 2019 +#> Date of summary: Wed Jun 5 15:08:36 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -593,10 +594,11 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.096 s +#> Fitted using 421 model solutions performed in 1.181 s +#> +#> Error model: Constant variance #> -#> Error model: -#> Constant variance +#> Error model algorithm: d_3 #> #> Starting values for parameters to be optimised: #> value type @@ -702,8 +704,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 120 m1 25.15 28.78984 -3.640e+00 #> 120 m1 33.31 28.78984 4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue Jun 4 15:01:34 2019 -#> Date of summary: Tue Jun 4 15:01:34 2019 +#> Date of fit: Wed Jun 5 15:08:39 2019 +#> Date of summary: Wed Jun 5 15:08:39 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -711,10 +713,12 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 979 model solutions performed in 2.603 s +#> Fitted using 979 model solutions performed in 2.672 s #> -#> Error model: -#> Variance unique to each observed variable +#> Error model: Variance unique to each observed variable +#> +#> Error model algorithm: d_3 +#> Direct fitting and three-step fitting yield approximately the same likelihood #> #> Starting values for parameters to be optimised: #> value type @@ -832,8 +836,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 120 m1 25.15 28.80429 -3.654e+00 #> 120 m1 33.31 28.80429 4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue Jun 4 15:01:43 2019 -#> Date of summary: Tue Jun 4 15:01:43 2019 +#> Date of fit: Wed Jun 5 15:08:50 2019 +#> Date of summary: Wed Jun 5 15:08:50 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -841,10 +845,12 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 2289 model solutions performed in 9.499 s +#> Fitted using 2289 model solutions performed in 10.959 s +#> +#> Error model: Two-component variance function #> -#> Error model: -#> Two-component variance function +#> Error model algorithm: d_3 +#> Direct fitting and three-step fitting yield approximately the same likelihood #> #> Starting values for parameters to be optimised: #> value type diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 2c5f056e..ddab656c 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -234,7 +234,7 @@ For the definition of model types and their parameters, the equations given SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB filebbe6b539c4f.c 2> filebbe6b539c4f.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file50a55c3108b2.c 2> file50a55c3108b2.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index f339b26a..7e71ec27 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -328,17 +328,17 @@ c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "eigen")[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.003 0.000 0.003
system.time( +#> 0.004 0.000 0.004
system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve")[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.002 0.000 0.002
system.time( +#> 0.003 0.000 0.002
system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve", use_compiled = FALSE)[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.021 0.000 0.022
+#> 0.022 0.000 0.022
# Predict from a fitted model f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Ordinary least squares optimisation
#> Sum of squared residuals at call 1: 552.5739 #> Sum of squared residuals at call 3: 552.5739 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index a830646f..61a029fc 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -194,8 +194,8 @@ time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default
#> User System verstrichen -#> 0.046 0.032 5.094
time_1
#> User System verstrichen -#> 19.798 0.004 19.814
+#> 0.038 0.050 6.779
time_1
#> User System verstrichen +#> 27.209 0.004 27.278
endpoints(fits.0[["SFO_lin", 2]])
#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340481 0.2659519 0.7505684 0.2494316 diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index ffe1edb1..68b36542 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -211,18 +211,19 @@

Examples

  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Tue Jun  4 15:03:02 2019 
-#> Date of summary: Tue Jun  4 15:03:02 2019 
+#> Date of fit:     Wed Jun  5 15:10:34 2019 
+#> Date of summary: Wed Jun  5 15:10:34 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 131 model solutions performed in 0.266 s
+#> Fitted using 131 model solutions performed in 0.268 s
 #> 
-#> Error model:
-#> Constant variance 
+#> Error model: Constant variance 
+#> 
+#> Error model algorithm: d_3 
 #> 
 #> Starting values for parameters to be optimised:
 #>                    value   type
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