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| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-12 17:48:07 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-12 17:48:07 +0200 |
| commit | 4eada5fff40493fad77726531e22dd6ad693a662 (patch) | |
| tree | a45299476f0f801788d5e524ce494b286caff916 /vignettes/web_only/benchmarks.Rmd | |
| parent | e364bbc05bb3e0fab7b35aae7a7c4ad479a1aa92 (diff) | |
Improve formatting of benchmark vignette
Diffstat (limited to 'vignettes/web_only/benchmarks.Rmd')
| -rw-r--r-- | vignettes/web_only/benchmarks.Rmd | 23 |
1 files changed, 14 insertions, 9 deletions
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)]) ``` |