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Diffstat (limited to 'vignettes/web_only/benchmarks.R')
| -rw-r--r-- | vignettes/web_only/benchmarks.R | 112 |
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)]) - |