1 files changed, 66 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..625cceb8
--- /dev/null
+++ b/vignettes/web_only/dimethenamid_2018.R
@@ -0,0 +1,66 @@
+## ---- include = FALSE---------------------------------------------------------
+require(knitr)
+options(digits = 5)
+opts_chunk$set(
+  comment = "",
+  tidy = FALSE,
+  cache = TRUE
+)
+
+## ----dimethenamid_data--------------------------------------------------------
+library(mkin)
+dmta_ds <- lapply(1:8, function(i) {
+  ds_i <- dimethenamid_2018$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[["Borstel"]] <- rbind(dmta_ds[["Borstel 1"]], dmta_ds[["Borstel 2"]])
+dmta_ds[["Borstel 1"]] <- NULL
+dmta_ds[["Borstel 2"]] <- NULL
+dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]])
+dmta_ds[["Elliot 1"]] <- NULL
+dmta_ds[["Elliot 2"]] <- NULL
+
+## ----f_parent_mkin------------------------------------------------------------
+f_parent_mkin_const <- mmkin(c("SFO", "DFOP"), dmta_ds,
+  error_model = "const", quiet = TRUE)
+f_parent_mkin_tc <- mmkin(c("SFO", "DFOP"), dmta_ds,
+  error_model = "tc", quiet = TRUE)
+
+## ----f_parent_mkin_sfo_const--------------------------------------------------
+plot(mixed(f_parent_mkin_const["SFO", ]))
+
+## ----f_parent_mkin_dfop_const-------------------------------------------------
+plot(mixed(f_parent_mkin_const["DFOP", ]))
+
+## ----f_parent_mkin_dfop_const_test--------------------------------------------
+plot(mixed(f_parent_mkin_const["DFOP", ]), test_log_parms = TRUE)
+
+## ----f_parent_mkin_dfop_tc_test-----------------------------------------------
+plot(mixed(f_parent_mkin_tc["DFOP", ]), test_log_parms = TRUE)
+
+## ----f_parent_nlme, warning = FALSE-------------------------------------------
+f_parent_nlme_sfo_const <- nlme(f_parent_mkin_const["SFO", ])
+#f_parent_nlme_dfop_const <- nlme(f_parent_mkin_const["DFOP", ]) # error
+f_parent_nlme_sfo_tc <- nlme(f_parent_mkin_tc["SFO", ])
+f_parent_nlme_dfop_tc <- nlme(f_parent_mkin_tc["DFOP", ])
+
+## ----f_parent_nlme_logchol, warning = FALSE, eval = FALSE---------------------
+#  f_parent_nlme_sfo_const_logchol <- nlme(f_parent_mkin_const["SFO", ],
+#    random = pdLogChol(list(DMTA_0 ~ 1, log_k_DMTA ~ 1)))
+#  anova(f_parent_nlme_sfo_const, f_parent_nlme_sfo_const_logchol) # not better
+#  f_parent_nlme_dfop_tc_logchol <- update(f_parent_nlme_dfop_tc,
+#    random = pdLogChol(list(DMTA_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)))
+#  # using log Cholesky parameterisation for random effects (nlme default) does
+#  # not converge and gives lots of warnings about the LME step not converging
+
+## ----AIC_parent_nlme----------------------------------------------------------
+anova(
+  f_parent_nlme_sfo_const, f_parent_nlme_sfo_tc, f_parent_nlme_dfop_tc
+)
+
+## ----plot_parent_nlme---------------------------------------------------------
+plot(f_parent_nlme_dfop_tc)
+