Store DLL info in mkinmod objects for performance

Thanks to Tomas Kalibera for his analysis of the problem on the
r-package-devel mailing list and for the suggestion on how to
fix it. See the current benchmark vignette for the new data
on mkin 1.1.1 with R 4.2.1, with unprecedented performance.

1 files changed, 0 insertions, 152 deletions

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