Further formatting improvement of benchmark vignette

Also, use .rmd extension instead of .Rmd for vignettes.

1 files changed, 0 insertions, 150 deletions

diff --git a/vignettes/web_only/benchmarks.Rmd b/vignettes/web_only/benchmarks.Rmd
deleted file mode 100644
index 990c2fee..00000000
--- a/vignettes/web_only/benchmarks.Rmd
+++ /dev/null
@@ -1,150 +0,0 @@
----
-title: "Benchmark timings for mkin"
-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$set(tidy = FALSE, cache = FALSE)
-library("mkin")
-```
-
-Each system is characterized by its CPU type, the operating system type and the
-mkin version. Currently only values for one system are available.
-
-```{r}
-cpu_model <- benchmarkme::get_cpu()$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)
-  }
-}
-```
-
-## Test cases
-
-Parent only:
-
-```{r parent_only, warning = FALSE}
-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"]]
-```
-
-One metabolite:
-
-```{r 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_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"]]
-```
-
-Two metabolites, synthetic data:
-
-```{r two_metabolites}
-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"]]
-```
-
-```{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
-
-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
-
-Constant variance and two-component error model:
-
-```{r}
-kable(mkin_benchmarks[, c("t1", "t2")])
-```
-
-### One metabolite
-
-Constant variance, variance by variable and two-component error model:
-
-```{r}
-kable(mkin_benchmarks[, c("t3", "t4", "t5")])
-```
-
-### Two metabolites
-
-Two different datasets, for each constant variance, variance by variable and
-two-component error model are shown:
-
-```{r}
-kable(mkin_benchmarks[, paste0("t", 6:11)])
-```