aboutsummaryrefslogtreecommitdiff
path: root/vignettes/web_only/dimethenamid_2018.R
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2021-09-27 20:10:01 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2021-09-27 20:10:01 +0200
commit5c15ef747568b3a9a9c094b6aa546dc80e3aa87a (patch)
tree70f86619437fb8f1bc1f144b847fc4dacbcba128 /vignettes/web_only/dimethenamid_2018.R
parent047d048b89e167fb354b45cd7c6b719b9f4cdd28 (diff)
intervals() methods, more DFOP/tc variants
Diffstat (limited to 'vignettes/web_only/dimethenamid_2018.R')
-rw-r--r--vignettes/web_only/dimethenamid_2018.R116
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)
-

Contact - Imprint