Merge branch 'nlmixr'

1 files changed, 49 insertions, 1 deletions

diff --git a/man/dimethenamid_2018.Rd b/man/dimethenamid_2018.Rd
index 31a05a26..0d1265be 100644
--- a/man/dimethenamid_2018.Rd
+++ b/man/dimethenamid_2018.Rd
@@ -11,7 +11,7 @@ An \link{mkindsg} object grouping seven 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
-\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}
 }
 \usage{
 dimethenamid_2018
@@ -31,5 +31,53 @@ specific pieces of information in the comments.
 }
 \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)
+}
 }
 \keyword{datasets}