Adapt and improve the dimethenamid vignette

Adapt to the corrected data and unify control parameters for saemix and
nlmixr with saem. Update docs

1 files changed, 116 insertions, 0 deletions

diff --git a/vignettes/web_only/dimethenamid_2018.R b/vignettes/web_only/dimethenamid_2018.R
new file mode 100644
index 00000000..2c01bc14
--- /dev/null
+++ b/vignettes/web_only/dimethenamid_2018.R
@@ -0,0 +1,116 @@
+## ---- include = FALSE---------------------------------------------------------
+require(knitr)
+options(digits = 5)
+opts_chunk$set(
+  comment = "",
+  tidy = FALSE,
+  cache = TRUE
+)
+
+## ----saemix_control-----------------------------------------------------------
+library(saemix)
+saemix_control <- saemixControl(nbiter.saemix = c(800, 200), nb.chains = 15,
+    print = FALSE, save = FALSE, save.graphs = FALSE, displayProgress = FALSE)
+
+## ----f_parent_saemix_sfo_const, results = 'hide', dependson = "saemix_control"----
+f_parent_saemix_sfo_const <- mkin::saem(f_parent_mkin_const["SFO", ], quiet = TRUE,
+  control = saemix_control, transformations = "saemix")
+plot(f_parent_saemix_sfo_const$so, plot.type = "convergence")
+
+## ----f_parent_saemix_sfo_tc, results = 'hide', dependson = "saemix_control"----
+f_parent_saemix_sfo_tc <- mkin::saem(f_parent_mkin_tc["SFO", ], quiet = TRUE,
+  control = saemix_control, transformations = "saemix")
+plot(f_parent_saemix_sfo_tc$so, plot.type = "convergence")
+
+## ----f_parent_saemix_dfop_const, results = 'hide', dependson = "saemix_control"----
+f_parent_saemix_dfop_const <- mkin::saem(f_parent_mkin_const["DFOP", ], quiet = TRUE,
+  control = saemix_control, transformations = "saemix")
+plot(f_parent_saemix_dfop_const$so, plot.type = "convergence")
+
+## ----f_parent_saemix_dfop_tc, results = 'hide', dependson = "saemix_control"----
+f_parent_saemix_dfop_tc <- mkin::saem(f_parent_mkin_tc["DFOP", ], quiet = TRUE,
+  control = saemix_control, transformations = "saemix")
+plot(f_parent_saemix_dfop_tc$so, plot.type = "convergence")
+
+## ----AIC_parent_saemix--------------------------------------------------------
+compare.saemix(
+  f_parent_saemix_sfo_const$so,
+  f_parent_saemix_sfo_tc$so,
+  f_parent_saemix_dfop_const$so,
+  f_parent_saemix_dfop_tc$so)
+
+## ----AIC_parent_saemix_methods------------------------------------------------
+f_parent_saemix_dfop_tc$so <-
+  llgq.saemix(f_parent_saemix_dfop_tc$so)
+AIC(f_parent_saemix_dfop_tc$so)
+AIC(f_parent_saemix_dfop_tc$so, method = "gq")
+AIC(f_parent_saemix_dfop_tc$so, method = "lin")
+
+## ----f_parent_nlmixr_focei, results = "hide", message = FALSE, warning = FALSE----
+library(nlmixr)
+f_parent_nlmixr_focei_sfo_const <- nlmixr(f_parent_mkin_const["SFO", ], est = "focei")
+f_parent_nlmixr_focei_sfo_tc <- nlmixr(f_parent_mkin_tc["SFO", ], est = "focei")
+f_parent_nlmixr_focei_dfop_const <- nlmixr(f_parent_mkin_const["DFOP", ], est = "focei")
+f_parent_nlmixr_focei_dfop_tc<- nlmixr(f_parent_mkin_tc["DFOP", ], est = "focei")
+
+## ----AIC_parent_nlmixr_focei--------------------------------------------------
+aic_nlmixr_focei <- sapply(
+  list(f_parent_nlmixr_focei_sfo_const$nm, f_parent_nlmixr_focei_sfo_tc$nm,
+    f_parent_nlmixr_focei_dfop_const$nm, f_parent_nlmixr_focei_dfop_tc$nm),
+  AIC)
+
+## ----AIC_parent_nlme_rep------------------------------------------------------
+aic_nlme <- sapply(
+  list(f_parent_nlme_sfo_const, NA, f_parent_nlme_sfo_tc, f_parent_nlme_dfop_tc),
+  function(x) if (is.na(x[1])) NA else AIC(x))
+aic_nlme_nlmixr_focei <- data.frame(
+  "Degradation model" = c("SFO", "SFO", "DFOP", "DFOP"),
+  "Error model" = rep(c("constant variance", "two-component"), 2),
+  "AIC (nlme)" = aic_nlme,
+  "AIC (nlmixr with FOCEI)" = aic_nlmixr_focei,
+  check.names = FALSE
+)
+
+## ----nlmixr_saem_control------------------------------------------------------
+nlmixr_saem_control <- saemControl(logLik = TRUE,
+  nBurn = 800, nEm = 200, nmc = 15)
+
+## ----f_parent_nlmixr_saem_sfo_const, results = "hide", warning = FALSE, message = FALSE, dependson = "nlmixr_saem_control"----
+f_parent_nlmixr_saem_sfo_const <- nlmixr(f_parent_mkin_const["SFO", ], est = "saem",
+  control = nlmixr_saem_control)
+traceplot(f_parent_nlmixr_saem_sfo_const$nm)
+
+## ----f_parent_nlmixr_saem_sfo_tc, results = "hide", warning = FALSE, message = FALSE, dependson = "nlmixr_saem_control"----
+f_parent_nlmixr_saem_sfo_tc <- nlmixr(f_parent_mkin_tc["SFO", ], est = "saem",
+  control = nlmixr_saem_control)
+traceplot(f_parent_nlmixr_saem_sfo_tc$nm)
+
+## ----f_parent_nlmixr_saem_dfop_const, results = "hide", warning = FALSE, message = FALSE, dependson = "nlmixr_saem_control"----
+f_parent_nlmixr_saem_dfop_const <- nlmixr(f_parent_mkin_const["DFOP", ], est = "saem",
+  control = nlmixr_saem_control)
+traceplot(f_parent_nlmixr_saem_dfop_const$nm)
+
+## ----f_parent_nlmixr_saem_dfop_tc, results = "hide", warning = FALSE, message = FALSE, dependson = "nlmixr_saem_control"----
+f_parent_nlmixr_saem_dfop_tc <- nlmixr(f_parent_mkin_tc["DFOP", ], est = "saem",
+  control = nlmixr_saem_control)
+traceplot(f_parent_nlmixr_saem_dfop_tc$nm)
+
+## ----AIC_parent_nlmixr_saem---------------------------------------------------
+AIC(f_parent_nlmixr_saem_sfo_const$nm, f_parent_nlmixr_saem_sfo_tc$nm,
+  f_parent_nlmixr_saem_dfop_const$nm, f_parent_nlmixr_saem_dfop_tc$nm)
+
+## ----AIC_all------------------------------------------------------------------
+AIC_all <- data.frame(
+  check.names = FALSE,
+  "Degradation model" = c("SFO", "SFO", "DFOP", "DFOP"),
+  "Error model" = c("const", "tc", "const", "tc"),
+  nlme = c(AIC(f_parent_nlme_sfo_const), AIC(f_parent_nlme_sfo_tc), NA, AIC(f_parent_nlme_dfop_tc)),
+  nlmixr_focei = sapply(list(f_parent_nlmixr_focei_sfo_const$nm, f_parent_nlmixr_focei_sfo_tc$nm,
+  f_parent_nlmixr_focei_dfop_const$nm, f_parent_nlmixr_focei_dfop_tc$nm), AIC),
+  saemix = sapply(list(f_parent_saemix_sfo_const$so, f_parent_saemix_sfo_tc$so,
+    f_parent_saemix_dfop_const$so, f_parent_saemix_dfop_tc$so), AIC),
+  nlmixr_saem = sapply(list(f_parent_nlmixr_saem_sfo_const$nm, f_parent_nlmixr_saem_sfo_tc$nm,
+  f_parent_nlmixr_saem_dfop_const$nm, f_parent_nlmixr_saem_dfop_tc$nm), AIC)
+)
+kable(AIC_all)
+