diff options
Diffstat (limited to 'man/dimethenamid_2018.Rd')
| -rw-r--r-- | man/dimethenamid_2018.Rd | 33 |
1 files changed, 24 insertions, 9 deletions
diff --git a/man/dimethenamid_2018.Rd b/man/dimethenamid_2018.Rd index 93fcad26..a0e5bbea 100644 --- a/man/dimethenamid_2018.Rd +++ b/man/dimethenamid_2018.Rd @@ -11,7 +11,7 @@ An \link{mkindsg} object grouping eight datasets with some meta information 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} } \usage{ dimethenamid_2018 @@ -56,16 +56,31 @@ f_dmta_mkin_tc <- mmkin( 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) } } \keyword{datasets} |