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authorJohannes Ranke <jranke@uni-bremen.de>2023-01-09 06:22:04 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2023-01-09 06:22:04 +0100
commit24eb77216700cf8b2f2bde3abad84c1f83f9e32a (patch)
tree1fecd5557499ea0e5d9a651f3a27fc602c0431cc /vignettes/web_only/dimethenamid_2018.R
parenta5903e74d9cf54c764d5bbc48e461cecd5f56e72 (diff)
Prebuilt PDF vignettes, summary_listing
Diffstat (limited to 'vignettes/web_only/dimethenamid_2018.R')
-rw-r--r--vignettes/web_only/dimethenamid_2018.R152
1 files changed, 152 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)
+require(mkin)
+require(nlme)
+options(digits = 5)
+opts_chunk$set(
+ comment = "",
+ tidy = FALSE,
+ cache = TRUE
+)
+
+## ----dimethenamid_data--------------------------------------------------------
+library(mkin, quietly = TRUE)
+dmta_ds <- lapply(1:7, function(i) {
+ ds_i <- dimethenamid_2018$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[["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_mkin_dfop_tc_print----------------------------------------------
+print(f_parent_mkin_tc["DFOP", ])
+
+## ----f_parent_nlme, warning = FALSE-------------------------------------------
+library(nlme)
+f_parent_nlme_sfo_const <- nlme(f_parent_mkin_const["SFO", ])
+# f_parent_nlme_dfop_const <- nlme(f_parent_mkin_const["DFOP", ])
+f_parent_nlme_sfo_tc <- nlme(f_parent_mkin_tc["SFO", ])
+f_parent_nlme_dfop_tc <- nlme(f_parent_mkin_tc["DFOP", ])
+
+## ----AIC_parent_nlme----------------------------------------------------------
+anova(
+ f_parent_nlme_sfo_const, f_parent_nlme_sfo_tc, f_parent_nlme_dfop_tc
+)
+
+## ----f_parent_nlme_logchol, warning = FALSE, eval = FALSE---------------------
+# f_parent_nlme_sfo_const_logchol <- nlme(f_parent_mkin_const["SFO", ],
+# random = nlme::pdLogChol(list(DMTA_0 ~ 1, log_k_DMTA ~ 1)))
+# anova(f_parent_nlme_sfo_const, f_parent_nlme_sfo_const_logchol)
+# f_parent_nlme_sfo_tc_logchol <- nlme(f_parent_mkin_tc["SFO", ],
+# random = nlme::pdLogChol(list(DMTA_0 ~ 1, log_k_DMTA ~ 1)))
+# anova(f_parent_nlme_sfo_tc, f_parent_nlme_sfo_tc_logchol)
+# f_parent_nlme_dfop_tc_logchol <- nlme(f_parent_mkin_const["DFOP", ],
+# random = nlme::pdLogChol(list(DMTA_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)))
+# anova(f_parent_nlme_dfop_tc, f_parent_nlme_dfop_tc_logchol)
+
+## ----plot_parent_nlme---------------------------------------------------------
+plot(f_parent_nlme_dfop_tc)
+
+## ----saemix_control, results='hide'-------------------------------------------
+library(saemix)
+saemix_control <- saemixControl(nbiter.saemix = c(800, 300), nb.chains = 15,
+ print = FALSE, save = FALSE, save.graphs = FALSE, displayProgress = FALSE)
+saemix_control_moreiter <- saemixControl(nbiter.saemix = c(1600, 300), nb.chains = 15,
+ print = FALSE, save = FALSE, save.graphs = FALSE, displayProgress = FALSE)
+saemix_control_10k <- saemixControl(nbiter.saemix = c(10000, 300), 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$so, plot.type = "convergence")
+
+## ----f_parent_saemix_dfop_const, results = 'show', dependson = "saemix_control"----
+f_parent_saemix_dfop_const <- mkin::saem(f_parent_mkin_const["DFOP", ], quiet = TRUE,
+ control = saemix_control, transformations = "saemix")
+plot(f_parent_saemix_dfop_const$so, plot.type = "convergence")
+print(f_parent_saemix_dfop_const)
+
+## ----f_parent_saemix_dfop_tc, results = 'show', dependson = "saemix_control"----
+f_parent_saemix_dfop_tc <- mkin::saem(f_parent_mkin_tc["DFOP", ], quiet = TRUE,
+ control = saemix_control, transformations = "saemix")
+f_parent_saemix_dfop_tc_moreiter <- mkin::saem(f_parent_mkin_tc["DFOP", ], quiet = TRUE,
+ control = saemix_control_moreiter, transformations = "saemix")
+plot(f_parent_saemix_dfop_tc$so, plot.type = "convergence")
+print(f_parent_saemix_dfop_tc)
+
+## ----AIC_parent_saemix, cache = FALSE-----------------------------------------
+AIC_parent_saemix <- saemix::compare.saemix(
+ f_parent_saemix_sfo_const$so,
+ f_parent_saemix_sfo_tc$so,
+ f_parent_saemix_dfop_const$so,
+ f_parent_saemix_dfop_tc$so,
+ f_parent_saemix_dfop_tc_moreiter$so)
+rownames(AIC_parent_saemix) <- c(
+ "SFO const", "SFO tc", "DFOP const", "DFOP tc", "DFOP tc more iterations")
+print(AIC_parent_saemix)
+
+## ----AIC_parent_saemix_methods, cache = FALSE---------------------------------
+f_parent_saemix_dfop_tc$so <-
+ saemix::llgq.saemix(f_parent_saemix_dfop_tc$so)
+AIC_parent_saemix_methods <- c(
+ is = AIC(f_parent_saemix_dfop_tc$so, method = "is"),
+ gq = AIC(f_parent_saemix_dfop_tc$so, method = "gq"),
+ lin = AIC(f_parent_saemix_dfop_tc$so, method = "lin")
+)
+print(AIC_parent_saemix_methods)
+
+## ----AIC_parent_saemix_methods_defaults, cache = FALSE------------------------
+f_parent_saemix_dfop_tc_defaults <- mkin::saem(f_parent_mkin_tc["DFOP", ])
+f_parent_saemix_dfop_tc_defaults$so <-
+ saemix::llgq.saemix(f_parent_saemix_dfop_tc_defaults$so)
+AIC_parent_saemix_methods_defaults <- c(
+ is = AIC(f_parent_saemix_dfop_tc_defaults$so, method = "is"),
+ gq = AIC(f_parent_saemix_dfop_tc_defaults$so, method = "gq"),
+ lin = AIC(f_parent_saemix_dfop_tc_defaults$so, method = "lin")
+)
+print(AIC_parent_saemix_methods_defaults)
+
+## ----AIC_all, cache = FALSE---------------------------------------------------
+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)),
+ saemix_lin = 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, method = "lin"),
+ saemix_is = 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, method = "is")
+)
+kable(AIC_all)
+
+## ----sessionInfo, cache = FALSE-----------------------------------------------
+sessionInfo()
+

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