intervals() methods, more DFOP/tc variants

1 files changed, 0 insertions, 116 deletions

diff --git a/vignettes/web_only/dimethenamid_2018.R b/vignettes/web_only/dimethenamid_2018.R
deleted file mode 100644
index 2c01bc14..00000000
--- a/vignettes/web_only/dimethenamid_2018.R
+++ /dev/null
@@ -1,116 +0,0 @@
-## ---- 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)
-