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---
title: "Benchmark timings for mkin on various systems"
author: "Johannes Ranke"
output:
html_document:
toc: true
toc_float: true
code_folding: show
fig_retina: null
date: "`r Sys.Date()`"
vignette: >
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
library(knitr)
opts_chunk$set(tidy = FALSE, cache = FALSE)
library("mkin")
```
## Systems
Each system is characterized by its CPU type, the operating system type and the
mkin version.
```{r}
cpu_model <- benchmarkme::get_cpu()$model_name
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)
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)
}
```
```{r timings}
# Parent only
t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D)))[["elapsed"]]
t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D), error_model = "tc"))[["elapsed"]]
# One metabolite
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_2006_D)))[["elapsed"]]
t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(subset(FOCUS_2006_D, value != 0)), error_model = "tc"))[["elapsed"]]
t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D), error_model = "obs"))[["elapsed"]]
# Two metabolites, synthetic data
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"]
mkin_benchmarks[system_string, paste0("t", 1:11)] <- c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
mkin_benchmarks
save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")
```
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