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Diffstat (limited to 'vignettes/web_only/benchmarks.Rmd')
| -rw-r--r-- | vignettes/web_only/benchmarks.Rmd | 97 |
1 files changed, 75 insertions, 22 deletions
diff --git a/vignettes/web_only/benchmarks.Rmd b/vignettes/web_only/benchmarks.Rmd index cc28735a..27f5d366 100644 --- a/vignettes/web_only/benchmarks.Rmd +++ b/vignettes/web_only/benchmarks.Rmd @@ -1,5 +1,5 @@ --- -title: "Benchmark timings for mkin on various systems" +title: "Benchmark timings for mkin" author: "Johannes Ranke" output: html_document: @@ -19,10 +19,8 @@ opts_chunk$set(tidy = FALSE, cache = FALSE) library("mkin") ``` -## Systems - Each system is characterized by its CPU type, the operating system type and the -mkin version. +mkin version. Currently only values for one system are available. ```{r} cpu_model <- benchmarkme::get_cpu()$model_name @@ -30,23 +28,37 @@ operating_system <- Sys.info()[["sysname"]] mkin_version <- as.character(packageVersion("mkin")) system_string <- paste0(operating_system, ", ", cpu_model, ", mkin version ", mkin_version) load("~/git/mkin/vignettes/web_only/mkin_benchmarks.rda") -mkin_benchmarks[system_string, c("CPU", "OS", "mkin")] <- c(cpu_model, operating_system, mkin_version) +mkin_benchmarks[system_string, c("CPU", "OS", "mkin")] <- + c(cpu_model, operating_system, mkin_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) + 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) + mmkin_bench <- function(models, datasets, error_model = NULL) { + mmkin(models, datasets, reweight.method = error_model, cores = 1, quiet = TRUE) + } } ``` -```{r timings} +## Test cases + +Parent only: + +```{r parent_only, warning = FALSE} FOCUS_C <- FOCUS_2006_C FOCUS_D <- subset(FOCUS_2006_D, value != 0) -# Parent only -t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_C, FOCUS_D)))[["elapsed"]] -t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_C, FOCUS_D), error_model = "tc"))[["elapsed"]] +parent_datasets <- list(FOCUS_C, FOCUS_D) -# One metabolite +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: + +```{r one_metabolite} SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) @@ -57,10 +69,15 @@ 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"]] +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, synthetic data +Two metabolites, synthetic data: + +```{r two_metabolites} m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"), M1 = mkinsub("SFO", "M2"), M2 = mkinsub("SFO"), @@ -78,15 +95,51 @@ 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"] +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"] +``` + +```{r 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 = "~/git/mkin/vignettes/web_only/mkin_benchmarks.rda") +``` + +## Results -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"] +Currently, we only have benchmark information on one system, therefore only the mkin +version is shown with the results below. Timings are in seconds, shorter is better. -mkin_benchmarks[system_string, paste0("t", 1:11)] <- c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11) -mkin_benchmarks[, -c(1:3)] +Benchmarks for all available error models are shown. +### Parent only -save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda") +Constant variance and two-component error model: + +```{r} +print(mkin_benchmarks[, c("mkin", "t1", "t2")], row.names = FALSE) +``` + +### One metabolite + +Constant variance, variance by variable and two-component error model: + +```{r} +print(mkin_benchmarks[, c("mkin", "t3", "t4", "t5")], row.names = FALSE) +``` + +### Two metabolites + +Two different datasets, for each constant variance, variance by variable and +two-component error model are shown: + +```{r} +print(mkin_benchmarks[, c("mkin", paste0("t", 6:11))], row.names = FALSE) ``` |