diff options
Diffstat (limited to 'vignettes/web_only/benchmarks.rmd')
| -rw-r--r-- | vignettes/web_only/benchmarks.rmd | 33 |
1 files changed, 21 insertions, 12 deletions
diff --git a/vignettes/web_only/benchmarks.rmd b/vignettes/web_only/benchmarks.rmd index 420bef27..9c8c10b7 100644 --- a/vignettes/web_only/benchmarks.rmd +++ b/vignettes/web_only/benchmarks.rmd @@ -1,7 +1,7 @@ --- title: "Benchmark timings for mkin" author: "Johannes Ranke" -date: Last change 1 July 2022 (rebuilt `r Sys.Date()`) +date: Last change 14 July 2022 (rebuilt `r Sys.Date()`) output: html_document: toc: true @@ -26,6 +26,21 @@ solution was available, compiled ODE models are used. Every fit is only performed once, so the accuracy of the benchmarks is limited. +The following wrapper function for `mmkin` is used because the way the error +model is specified was changed in mkin version 0.9.49.1. + +```{r} +if (packageVersion("mkin") > "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 include = FALSE} cpu_model <- benchmarkme::get_cpu()$model_name # Abbreviate CPU identifiers @@ -53,18 +68,11 @@ load(benchmark_path) 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) - } -} ``` + + + ## Test cases Parent only: @@ -74,6 +82,7 @@ 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"]] @@ -129,7 +138,7 @@ t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "obs"))[["elapsed"]] ``` -```{r results} +```{r results, include = FALSE} 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) |