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Diffstat (limited to 'vignettes/web_only/benchmarks.R')
| -rw-r--r-- | vignettes/web_only/benchmarks.R | 112 |
1 files changed, 112 insertions, 0 deletions
diff --git a/vignettes/web_only/benchmarks.R b/vignettes/web_only/benchmarks.R new file mode 100644 index 00000000..c9ba5be3 --- /dev/null +++ b/vignettes/web_only/benchmarks.R @@ -0,0 +1,112 @@ +## ---- 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)]) + |