From 4eada5fff40493fad77726531e22dd6ad693a662 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 12 May 2020 17:48:07 +0200 Subject: Improve formatting of benchmark vignette --- vignettes/web_only/benchmarks.Rmd | 23 ++++++++++++++--------- 1 file changed, 14 insertions(+), 9 deletions(-) (limited to 'vignettes/web_only/benchmarks.Rmd') diff --git a/vignettes/web_only/benchmarks.Rmd b/vignettes/web_only/benchmarks.Rmd index 27f5d366..990c2fee 100644 --- a/vignettes/web_only/benchmarks.Rmd +++ b/vignettes/web_only/benchmarks.Rmd @@ -92,18 +92,18 @@ 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"] +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"] + error_model = "tc"))[["elapsed"]] t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), - error_model = "tc"))["elapsed"] + error_model = "tc"))[["elapsed"]] t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), - error_model = "obs"))["elapsed"] + error_model = "obs"))[["elapsed"]] t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), - error_model = "obs"))["elapsed"] + error_model = "obs"))[["elapsed"]] ``` ```{r results} @@ -117,6 +117,11 @@ save(mkin_benchmarks, file = "~/git/mkin/vignettes/web_only/mkin_benchmarks.rda" 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. +```{r} +rownames(mkin_benchmarks) <- as.character(mkin_benchmarks$mkin) +``` + + Benchmarks for all available error models are shown. ### Parent only @@ -124,7 +129,7 @@ Benchmarks for all available error models are shown. Constant variance and two-component error model: ```{r} -print(mkin_benchmarks[, c("mkin", "t1", "t2")], row.names = FALSE) +kable(mkin_benchmarks[, c("t1", "t2")]) ``` ### One metabolite @@ -132,7 +137,7 @@ print(mkin_benchmarks[, c("mkin", "t1", "t2")], row.names = FALSE) Constant variance, variance by variable and two-component error model: ```{r} -print(mkin_benchmarks[, c("mkin", "t3", "t4", "t5")], row.names = FALSE) +kable(mkin_benchmarks[, c("t3", "t4", "t5")]) ``` ### Two metabolites @@ -141,5 +146,5 @@ 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) +kable(mkin_benchmarks[, paste0("t", 6:11)]) ``` -- cgit v1.2.1