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, 112 deletions

diff --git a/vignettes/web_only/benchmarks.R b/vignettes/web_only/benchmarks.R
deleted file mode 100644
index c9ba5be3..00000000
--- a/vignettes/web_only/benchmarks.R
+++ /dev/null
@@ -1,112 +0,0 @@
-## ---- include = FALSE---------------------------------------------------------
-library(knitr)
-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"))
-R_version <- paste0(R.version$major, ".", R.version$minor)
-system_string <- paste0(operating_system, ", ", cpu_model, ", mkin ", mkin_version, ", R ", R_version)
-
-benchmark_path = normalizePath("~/git/mkin/vignettes/web_only/mkin_benchmarks.rda")
-load(benchmark_path)
-
-# Used for reformatting the data on 2022-06-30
-# mkin_benchmarks[, "R"] <- NA
-# mkin_benchmarks <- mkin_benchmarks[c(2, 1, 15, 3, 4:14)]
-# mkin_benchmarks[, "CPU"] <- gsub("AMD.*", "Ryzen 7 1700", mkin_benchmarks[, "CPU"])
-# mkin_benchmarks[, "CPU"] <- gsub("Intel.*", "i7-4710MQ", mkin_benchmarks[, "CPU"])
-# rownames(mkin_benchmarks) <- gsub("AMD Ryzen 7 1700 Eight-Core Processor", "Ryzen 7 1700", rownames(mkin_benchmarks))
-# rownames(mkin_benchmarks) <- gsub("Intel\\(R\\) Core\\(TM\\) i7-4710MQ CPU @ 2.50GHz", "i7-4710MQ", rownames(mkin_benchmarks))
-# rownames(mkin_benchmarks) <- gsub(" version", "", rownames(mkin_benchmarks))
-
-mkin_benchmarks[system_string, c("CPU", "OS", "mkin", "R")] <-
-  c(cpu_model, operating_system, mkin_version, R_version)
-
-if (mkin_version > "0.9.48.1") {
-  mmkin_bench <- function(models, datasets, error_model = "const") {
-    mmkin(models, datasets, error_model = error_model, cores = 1, quiet = TRUE)
-  }
-} else {
-  mmkin_bench <- function(models, datasets, error_model = NULL) {
-    mmkin(models, datasets, reweight.method = error_model, cores = 1, quiet = TRUE)
-  }
-}
-
-## ----parent_only, warning = FALSE---------------------------------------------
-FOCUS_C <- FOCUS_2006_C
-FOCUS_D <- subset(FOCUS_2006_D, value != 0)
-parent_datasets <- list(FOCUS_C, FOCUS_D)
-
-t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), parent_datasets))[["elapsed"]]
-t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), parent_datasets,
-    error_model = "tc"))[["elapsed"]]
-
-## ----one_metabolite, message = FALSE------------------------------------------
-SFO_SFO <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
-FOMC_SFO <- mkinmod(
-  parent = mkinsub("FOMC", "m1"),
-  m1 = mkinsub("SFO"))
-DFOP_SFO <- mkinmod(
-  parent = mkinsub("FOMC", "m1"),
-  m1 = mkinsub("SFO"))
-t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[["elapsed"]]
-t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
-    error_model = "tc"))[["elapsed"]]
-t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
-    error_model = "obs"))[["elapsed"]]
-
-## ----two_metabolites, message = FALSE-----------------------------------------
-m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
-                           M1 = mkinsub("SFO", "M2"),
-                           M2 = mkinsub("SFO"),
-                           use_of_ff = "max", quiet = TRUE)
-
-m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
-                           M1 = mkinsub("SFO"),
-                           M2 = mkinsub("SFO"),
-                           use_of_ff = "max", quiet = TRUE)
-
-SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
-
-DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
-
-t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))[["elapsed"]]
-t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))[["elapsed"]]
-
-t8 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
-    error_model = "tc"))[["elapsed"]]
-t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
-    error_model = "tc"))[["elapsed"]]
-
-t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
-    error_model = "obs"))[["elapsed"]]
-t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
-    error_model = "obs"))[["elapsed"]]
-
-## ----results------------------------------------------------------------------
-mkin_benchmarks[system_string, paste0("t", 1:11)] <-
-  c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
-save(mkin_benchmarks, file = benchmark_path)
-# Hide rownames from kable for results section
-rownames(mkin_benchmarks) <- NULL
-
-## ---- echo = FALSE------------------------------------------------------------
-kable(mkin_benchmarks[, c(1:4, 5:6)])
-
-## ---- echo = FALSE------------------------------------------------------------
-kable(mkin_benchmarks[, c(1:4, 7:9)])
-
-## ---- echo = FALSE------------------------------------------------------------
-kable(mkin_benchmarks[, c(1:4, 10:15)])
-