diff options
Diffstat (limited to 'R/dimethenamid_2018.R')
| -rw-r--r-- | R/dimethenamid_2018.R | 50 |
1 files changed, 49 insertions, 1 deletions
diff --git a/R/dimethenamid_2018.R b/R/dimethenamid_2018.R index 0d8f681f..2bf5fb77 100644 --- a/R/dimethenamid_2018.R +++ b/R/dimethenamid_2018.R @@ -15,7 +15,55 @@ #' @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 -#' \href{https://open.efsa.europa.eu}{https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716} +#' \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" |