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authorJohannes Ranke <jranke@uni-bremen.de>2021-09-16 15:31:13 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2021-09-16 17:36:26 +0200
commitc41381a961263c28d60976e68923157916c78b15 (patch)
tree8259a2dd4a374734a5521b9bd1b10dbdf8c39a0e /vignettes/web_only/dimethenamid_2018.R
parente0ca5972b4a300b93a9fe6b44345eeb19d574149 (diff)
Adapt and improve the dimethenamid vignette
Adapt to the corrected data and unify control parameters for saemix and nlmixr with saem. Update docs
Diffstat (limited to 'vignettes/web_only/dimethenamid_2018.R')
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1 files changed, 116 insertions, 0 deletions
diff --git a/vignettes/web_only/dimethenamid_2018.R b/vignettes/web_only/dimethenamid_2018.R
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+## ---- 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)
+

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