From e48c1f2ef990a622722e416c8d301430db4f5081 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 16 Mar 2022 14:42:30 +0100
Subject: Use saemix in help page, typo in vignette

---
 R/dimethenamid_2018.R | 71 ++++++++++++++++++++++++++-------------------------
 1 file changed, 36 insertions(+), 35 deletions(-)

(limited to 'R/dimethenamid_2018.R')

diff --git a/R/dimethenamid_2018.R b/R/dimethenamid_2018.R
index 2bf5fb77..2fdd1981 100644
--- a/R/dimethenamid_2018.R
+++ b/R/dimethenamid_2018.R
@@ -29,41 +29,42 @@
 #' 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
+#' # We don't use DFOP for the parent compound, as this gives numerical
+#' # instabilities in the fits
+#' sfo_sfo3p <- mkinmod(
+#'  DMTA = mkinsub("SFO", 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$nm)
-#' summary(f_dmta_nlmixr_saem)
-#' plot(f_dmta_nlmixr_saem)
+#' dmta_sfo_sfo3p_tc <- mmkin(list("SFO-SFO3+" = sfo_sfo3p),
+#'   dmta_ds, error_model = "tc", quiet = TRUE)
+#' print(dmta_sfo_sfo3p_tc)
+#' # The default (test_log_parms = FALSE) gives an undue
+#' # influence of ill-defined rate constants that have
+#' # extremely small values:
+#' plot(mixed(dmta_sfo_sfo3p_tc), test_log_parms = FALSE)
+#' # If we disregards ill-defined rate constants, the results
+#' # look more plausible, but the truth is likely to be in
+#' # between these variants
+#' plot(mixed(dmta_sfo_sfo3p_tc), test_log_parms = TRUE)
+#' # Therefore we use nonlinear mixed-effects models
+#' # f_dmta_nlme_tc <- nlme(dmta_sfo_sfo3p_tc)
+#' # nlme reaches maxIter = 50 without convergence
+#' f_dmta_saem_tc <- saem(dmta_sfo_sfo3p_tc)
+#' # I am commenting out the convergence plot as rendering them
+#' # with pkgdown fails (at least without further tweaks to the 
+#' # graphics device used)
+#' #saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")
+#' summary(f_dmta_saem_tc)
+#' # As the confidence interval for the random effects of DMTA_0
+#' # includes zero, we could try an alternative model without
+#' # such random effects
+#' # f_dmta_saem_tc_2 <- saem(dmta_sfo_sfo3p_tc,
+#' #   covariance.model = diag(c(0, rep(1, 7))))
+#' # saemix::plot(f_dmta_saem_tc_2$so, plot.type = "convergence")
+#' # This does not perform better judged by AIC and BIC
+#' saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so)
 #' }
 "dimethenamid_2018"
-- 
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