Merge branch 'main' into custom_lsoda_call

1 files changed, 152 insertions, 0 deletions

diff --git a/vignettes/web_only/dimethenamid_2018.R b/vignettes/web_only/dimethenamid_2018.R
new file mode 100644
index 00000000..2554cd13
--- /dev/null
+++ b/vignettes/web_only/dimethenamid_2018.R
@@ -0,0 +1,152 @@
+## ---- 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()
+