From d6168b0851a52adeaed8099e41a960d79acedae9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 14 Nov 2022 21:05:01 +0100 Subject: Start benchmark vignette for saem fits --- vignettes/web_only/saem_benchmarks.R | 121 +++++++++++++++++++++++++++++++++++ 1 file changed, 121 insertions(+) create mode 100644 vignettes/web_only/saem_benchmarks.R (limited to 'vignettes/web_only/saem_benchmarks.R') diff --git a/vignettes/web_only/saem_benchmarks.R b/vignettes/web_only/saem_benchmarks.R new file mode 100644 index 00000000..210e79e3 --- /dev/null +++ b/vignettes/web_only/saem_benchmarks.R @@ -0,0 +1,121 @@ +## ---- include = FALSE--------------------------------------------------------- +library("knitr") # For the kable() function +opts_chunk$set(tidy = FALSE, cache = FALSE) +library("mkin") + +## ----include = FALSE---------------------------------------------------------- +cpu_model <- benchmarkme::get_cpu()$model_name +# Abbreviate CPU identifiers +cpu_model <- gsub("AMD ", "", cpu_model) +cpu_model <- gsub("Intel\\(R\\) Core\\(TM\\) ", "", cpu_model) +cpu_model <- gsub(" Eight-Core Processor", "", cpu_model) +cpu_model <- gsub(" CPU @ 2.50GHz", "", cpu_model) + +operating_system <- Sys.info()[["sysname"]] +mkin_version <- as.character(packageVersion("mkin")) +saemix_version <- as.character(packageVersion("saemix")) +R_version <- paste0(R.version$major, ".", R.version$minor) +system_string <- paste0(operating_system, ", ", cpu_model, ", mkin ", mkin_version, ", saemix ", saemix_version, ", R ", R_version) + +benchmark_path = normalizePath("~/git/mkin/vignettes/web_only/saem_benchmarks.rda") +load(benchmark_path) + +# Initialization 14 November 2022 +#saem_benchmarks <- data.frame() + +saem_benchmarks[system_string, c("CPU", "OS", "mkin", "saemix", "R")] <- + c(cpu_model, operating_system, mkin_version, saemix_version, R_version) + +## ----setup-------------------------------------------------------------------- +n_cores <- parallel::detectCores() + +## ----dimethenamid_data-------------------------------------------------------- +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 + +## ----parent_only-------------------------------------------------------------- +parent_mods <- c("SFO", "DFOP", "SFORB", "HS") +parent_sep_const <- mmkin(parent_mods, dmta_ds, quiet = TRUE, cores = n_cores) +parent_sep_tc <- update(parent_sep_const, error_model = "tc") + +t1 <- system.time(sfo_const <- saem(parent_sep_const["SFO", ]))[["elapsed"]] +t2 <- system.time(dfop_const <- saem(parent_sep_const["DFOP", ]))[["elapsed"]] +t3 <- system.time(sforb_const <- saem(parent_sep_const["SFORB", ]))[["elapsed"]] +t4 <- system.time(hs_const <- saem(parent_sep_const["HS", ]))[["elapsed"]] +t5 <- system.time(sfo_tc <- saem(parent_sep_tc["SFO", ]))[["elapsed"]] +t6 <- system.time(dfop_tc <- saem(parent_sep_tc["DFOP", ]))[["elapsed"]] +t7 <- system.time(sforb_tc <- saem(parent_sep_tc["SFORB", ]))[["elapsed"]] +t8 <- system.time(hs_tc <- saem(parent_sep_tc["HS", ]))[["elapsed"]] + +## ----------------------------------------------------------------------------- +anova( + sfo_const, dfop_const, sforb_const, hs_const, + sfo_tc, dfop_tc, sforb_tc, hs_tc) |> kable(, digits = 1) + +## ----------------------------------------------------------------------------- +illparms(dfop_tc) +illparms(sforb_tc) + +## ----one_metabolite, message = FALSE------------------------------------------ +one_met_mods <- list( + DFOP_SFO = mkinmod( + DMTA = mkinsub("DFOP", "M23"), + M23 = mkinsub("SFO")), + SFORB_SFO = mkinmod( + DMTA = mkinsub("SFORB", "M23"), + M23 = mkinsub("SFO"))) + +one_met_sep_const <- mmkin(one_met_mods, dmta_ds, error_model = "const", + cores = n_cores, quiet = TRUE) +one_met_sep_tc <- mmkin(one_met_mods, dmta_ds, error_model = "tc", + cores = n_cores, quiet = TRUE) + +t9 <- system.time(dfop_sfo_tc <- saem(one_met_sep_tc["DFOP_SFO", ], + no_random_effect = "log_k2"))[["elapsed"]] +t10 <- system.time(sforb_sfo_tc <- saem(one_met_sep_tc["SFORB_SFO", ], + no_random_effect = "log_k_DMTA_bound_free"))[["elapsed"]] + +## ----------------------------------------------------------------------------- +illparms(sforb_sfo_tc) + +## ----three_metabolites, message = FALSE--------------------------------------- +three_met_mods <- list( + SFORB_SFO3_plus = mkinmod( + DMTA = mkinsub("SFORB", c("M23", "M27", "M31")), + M23 = mkinsub("SFO"), + M27 = mkinsub("SFO"), + M31 = mkinsub("SFO", "M27", sink = FALSE))) + +three_met_sep_tc <- mmkin(three_met_mods, dmta_ds, error_model = "tc", + cores = n_cores, quiet = TRUE) + +t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SFORB_SFO3_plus", ], + no_random_effect = "log_k_DMTA_bound_free"))[["elapsed"]] + +## ----results, include = FALSE------------------------------------------------- +saem_benchmarks[system_string, paste0("t", 1:11)] <- + c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11) +save(saem_benchmarks, file = benchmark_path) +# Hide rownames from kable for results section +rownames(saem_benchmarks) <- NULL + +## ---- echo = FALSE------------------------------------------------------------ +kable(saem_benchmarks[, c(1:4, 6:9)]) + +## ---- echo = FALSE------------------------------------------------------------ +kable(saem_benchmarks[, c(1:4, 10:13)]) + +## ---- echo = FALSE------------------------------------------------------------ +kable(saem_benchmarks[, c(1:4, 14:15)]) + +## ---- echo = FALSE------------------------------------------------------------ +kable(saem_benchmarks[, c(1:4, 16)]) + -- cgit v1.2.1