diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/dimethenamid_2018.R | 33 | ||||
| -rw-r--r-- | R/mkinsub.R | 5 |
2 files changed, 24 insertions, 14 deletions
diff --git a/R/dimethenamid_2018.R b/R/dimethenamid_2018.R index 6e0bda0c..770649e2 100644 --- a/R/dimethenamid_2018.R +++ b/R/dimethenamid_2018.R @@ -15,7 +15,7 @@ #' @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{http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-5211} +#' \url{https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716} #' @examples #' print(dimethenamid_2018) #' dmta_ds <- lapply(1:8, function(i) { @@ -43,15 +43,30 @@ #' list("DFOP-SFO3+" = dfop_sfo3_plus), #' dmta_ds, quiet = TRUE, error_model = "tc") #' nlmixr_model(f_dmta_mkin_tc) -#' f_dmta_nlmixr_focei <- nlmixr(f_dmta_mkin_tc, est = "focei", -#' control = nlmixr::foceiControl(print = 500)) +#' # 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) -#' # saem has a problem with this model/data combination, maybe because of the -#' # overparameterised error model, to be investigated -#' #f_dmta_nlmixr_saem <- nlmixr(f_dmta_mkin_tc, est = "saem", -#' # control = saemControl(print = 500)) -#' #summary(f_dmta_nlmixr_saem) -#' #plot(f_dmta_nlmixr_saem) +#' # 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" diff --git a/R/mkinsub.R b/R/mkinsub.R index 886f712c..93af3f16 100644 --- a/R/mkinsub.R +++ b/R/mkinsub.R @@ -1,8 +1,3 @@ -#' Function to set up a kinetic submodel for one state variable -#' -#' This is a convenience function to set up the lists used as arguments for -#' \code{\link{mkinmod}}. -#' #' @rdname mkinmod #' @param submodel Character vector of length one to specify the submodel type. #' See \code{\link{mkinmod}} for the list of allowed submodel names. |