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authorJohannes Ranke <jranke@uni-bremen.de>2021-07-23 18:13:14 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2021-07-23 18:13:14 +0200
commit36b67cc7505a0a7f0960d4cb820c527f27e18f9c (patch)
tree389897451f80e8684b2ba6d9bb3da53bd4d5cbff /vignettes/web_only
parent40b78bed232798ecbeb72759cdf8d400ea35b31f (diff)
parent25648577b6d5a4521da7c9d2eb174d292d2d85af (diff)
Merge branch 'master' into nlmixr
After the merge, run make test and accept the new snapshot for the mixed model fit for an nlme object
Diffstat (limited to 'vignettes/web_only')
-rw-r--r--vignettes/web_only/dimethenamid_2018.R66
1 files changed, 0 insertions, 66 deletions
diff --git a/vignettes/web_only/dimethenamid_2018.R b/vignettes/web_only/dimethenamid_2018.R
deleted file mode 100644
index 625cceb8..00000000
--- a/vignettes/web_only/dimethenamid_2018.R
+++ /dev/null
@@ -1,66 +0,0 @@
-## ---- 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)
-

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