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Diffstat (limited to 'vignettes/web_only/dimethenamid_2018.R')
| -rw-r--r-- | vignettes/web_only/dimethenamid_2018.R | 116 |
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) - |