#' Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 #' #' The datasets were extracted from the active substance evaluation dossier #' published by EFSA. Kinetic evaluations shown for these datasets are intended #' to illustrate and advance kinetic modelling. The fact that these data and #' some results are shown here does 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. #' #' 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 #' specific pieces of information in the comments. #' #' @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{https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716} #' @examples #' print(dimethenamid_2018) #' dmta_ds <- lapply(1:7, function(i) { #' ds_i <- dimethenamid_2018$ds[[i]]$data #' ds_i[ds_i$name == "DMTAP", "name"] <- "DMTA" #' ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i] #' ds_i #' }) #' names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title) #' dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]]) #' dmta_ds[["Elliot 1"]] <- NULL #' dmta_ds[["Elliot 2"]] <- NULL #' \dontrun{ #' dfop_sfo3_plus <- mkinmod( #' DMTA = mkinsub("DFOP", c("M23", "M27", "M31")), #' M23 = mkinsub("SFO"), #' M27 = mkinsub("SFO"), #' M31 = mkinsub("SFO", "M27", sink = FALSE), #' quiet = TRUE #' ) #' f_dmta_mkin_tc <- mmkin( #' list("DFOP-SFO3+" = dfop_sfo3_plus), #' dmta_ds, quiet = TRUE, error_model = "tc") #' nlmixr_model(f_dmta_mkin_tc) #' # The focei fit takes about four minutes on my system #' system.time( #' f_dmta_nlmixr_focei <- nlmixr(f_dmta_mkin_tc, est = "focei", #' control = nlmixr::foceiControl(print = 500)) #' ) #' summary(f_dmta_nlmixr_focei) #' plot(f_dmta_nlmixr_focei) #' # Using saemix takes about 18 minutes #' system.time( #' f_dmta_saemix <- saem(f_dmta_mkin_tc, test_log_parms = TRUE) #' ) #' #' # nlmixr with est = "saem" is pretty fast with default iteration numbers, most #' # of the time (about 2.5 minutes) is spent for calculating the log likelihood at the end #' # The likelihood calculated for the nlmixr fit is much lower than that found by saemix #' # Also, the trace plot and the plot of the individual predictions is not #' # convincing for the parent. It seems we are fitting an overparameterised #' # model, so the result we get strongly depends on starting parameters and control settings. #' system.time( #' f_dmta_nlmixr_saem <- nlmixr(f_dmta_mkin_tc, est = "saem", #' control = nlmixr::saemControl(print = 500, logLik = TRUE, nmc = 9)) #' ) #' traceplot(f_dmta_nlmixr_saem$nm) #' summary(f_dmta_nlmixr_saem) #' plot(f_dmta_nlmixr_saem) #' } "dimethenamid_2018"