diff options
Diffstat (limited to 'man')
-rw-r--r-- | man/experimental_data_for_UBA.Rd | 120 | ||||
-rw-r--r-- | man/mkinerrplot.Rd | 2 | ||||
-rw-r--r-- | man/mkinfit.Rd | 40 | ||||
-rw-r--r-- | man/plot.mkinfit.Rd | 2 |
4 files changed, 164 insertions, 0 deletions
diff --git a/man/experimental_data_for_UBA.Rd b/man/experimental_data_for_UBA.Rd new file mode 100644 index 00000000..e3386a2f --- /dev/null +++ b/man/experimental_data_for_UBA.Rd @@ -0,0 +1,120 @@ +\name{experimental_data_for_UBA_2019} +\alias{experimental_data_for_UBA_2019} +\docType{data} +\title{ + Experimental datasets used for development and testing of error models +} +\description{ + 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. + + 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). + +} +\usage{experimental_data_for_UBA_2019} +\format{ + A list containing twelve datasets as an R6 class defined by \code{\link{mkinds}}, + each containing, among others, the following components + \describe{ + \item{\code{title}}{The name of the dataset, e.g. \code{Soil 1}} + \item{\code{data}}{A data frame with the data in the form expected by \code{\link{mkinfit}}} + } +} +\source{ + + 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) \dQuote{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 + \url{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{\dontrun{ + +# Model definitions +sfo_sfo <- mkinmod( + parent = mkinsub("SFO", to = "A1"), + A1 = mkinsub("SFO"), + use_of_ff = "max" +) + +dfop_sfo <- mkinmod( + parent = mkinsub("DFOP", to = "A1"), + A1 = mkinsub("SFO"), + use_of_ff = "max" +) + +sfo_sfo_sfo <- mkinmod( + parent = mkinsub("SFO", to = "A1"), + A1 = mkinsub("SFO", to = "A2"), + A2 = mkinsub("SFO"), + use_of_ff = "max" +) + +dfop_sfo_sfo <- mkinmod( + parent = mkinsub("DFOP", to = "A1"), + A1 = mkinsub("SFO", to = "A2"), + A2 = mkinsub("SFO"), + use_of_ff = "max" +) +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") + +}} +\keyword{datasets} diff --git a/man/mkinerrplot.Rd b/man/mkinerrplot.Rd index 4cbb5eb7..3b557b0a 100644 --- a/man/mkinerrplot.Rd +++ b/man/mkinerrplot.Rd @@ -68,8 +68,10 @@ \code{\link{mkinplot}}, for a way to plot the data and the fitted lines of the mkinfit object. } \examples{ +\dontrun{ model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) fit <- mkinfit(model, FOCUS_2006_D, error_model = "tc", quiet = TRUE) mkinerrplot(fit) } +} \keyword{ hplot } diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index 78a53ee0..975eace8 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -31,6 +31,8 @@ mkinfit(mkinmod, observed, quiet = FALSE, atol = 1e-8, rtol = 1e-10, n.outtimes = 100, error_model = c("const", "obs", "tc"), + error_model_algorithm = c("d_3", "direct", "twostep", "threestep", "fourstep", "IRLS"), + reweight.tol = 1e-8, reweight.max.iter = 10, trace_parms = FALSE, ...) } \arguments{ @@ -171,6 +173,44 @@ mkinfit(mkinmod, observed, errors follow a lognormal distribution for large values, not a normal distribution as assumed by this method. } + \item{error_model_algorithm}{ + If the error model is "const", the error model algorithm is ignored, + because no special algorithm is needed and unweighted (also known as + ordinary) least squares fitting can be applied. + + The default algorithm "d_3" will directly minimize the negative + log-likelihood and - independently - also use the three step algorithm + described below. The fit with the higher likelihood is returned. + + The algorithm "direct" will directly minimize the negative + log-likelihood. + + The algorithm "twostep" will minimize the negative log-likelihood + after an initial unweighted leas squares optimisation step. + + The algorithm "threestep" starts with unweighted least squares, + then optimizes only the error model using the degradation model + parameters found, and then minimizes the negative log-likelihood + with free degradation and error model parameters. + + The algorithm "fourstep" starts with unweighted least squares, + then optimizes only the error model using the degradation model + parameters found, then optimizes the degradation model again + with fixed error model parameters, and finally minimizes the negative + log-likelihood with free degradation and error model parameters. + + The algorithm "IRLS" starts with unweighted least squares, + and then iterates optimization of the error model parameters and subsequent + optimization of the degradation model using those error model parameters, + until the error model parameters converge. + } + \item{reweight.tol}{ + Tolerance for the convergence criterion calculated from the error model + parameters in IRLS fits. + } + \item{reweight.max.iter}{ + Maximum number of iterations in IRLS fits. + } \item{trace_parms}{ Should a trace of the parameter values be listed? } diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd index 9514c5e5..5e20ad90 100644 --- a/man/plot.mkinfit.Rd +++ b/man/plot.mkinfit.Rd @@ -115,6 +115,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, \dots) \examples{ # One parent compound, one metabolite, both single first order, path from # parent to sink included +\dontrun{ SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"), m1 = mkinsub("SFO", full = "Metabolite M1" )) fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc") @@ -136,6 +137,7 @@ plot_sep(fit, lpos = c("topright", "bottomright")) plot(fit, sep_obs = TRUE, show_errplot = TRUE, lpos = c("topright", "bottomright"), show_errmin = TRUE) } +} \author{ Johannes Ranke } |