1 files changed, 207 insertions, 0 deletions
diff --git a/vignettes/web_only/saem_benchmarks.rmd b/vignettes/web_only/saem_benchmarks.rmd
new file mode 100644
index 00000000..116713de
--- /dev/null
+++ b/vignettes/web_only/saem_benchmarks.rmd
@@ -0,0 +1,207 @@
+---
+title: "Benchmark timings for saem.mmkin"
+author: "Johannes Ranke"
+date: Last change 14 November 2022 (rebuilt `r Sys.Date()`)
+output:
+  html_document:
+    toc: true
+    toc_float: true
+    code_folding: show
+    fig_retina: null
+vignette: >
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+library("knitr") # For the kable() function
+opts_chunk$set(tidy = FALSE, cache = FALSE)
+library("mkin")
+```
+
+Each system is characterized by operating system type, CPU type,
+mkin version, saemix version and R version. A compiler was available, so if no
+analytical solution was available, compiled ODE models are used.
+
+Every fit is only performed once, so the accuracy of the benchmarks is limited.
+
+```{r include = FALSE}
+cpu_model <- benchmarkme::get_cpu()$model_name
+# Abbreviate CPU identifiers
+cpu_model <- gsub("AMD ", "", cpu_model)
+cpu_model <- gsub("Intel\\(R\\) Core\\(TM\\) ", "", cpu_model)
+cpu_model <- gsub(" Eight-Core Processor", "", cpu_model)
+cpu_model <- gsub(" CPU @ 2.50GHz", "", cpu_model)
+
+operating_system <- Sys.info()[["sysname"]]
+mkin_version <- as.character(packageVersion("mkin"))
+saemix_version <- as.character(packageVersion("saemix"))
+R_version <- paste0(R.version$major, ".", R.version$minor)
+system_string <- paste0(operating_system, ", ", cpu_model, ", mkin ", mkin_version, ", saemix ", saemix_version, ", R ", R_version)
+
+benchmark_path = normalizePath("~/git/mkin/vignettes/web_only/saem_benchmarks.rda")
+load(benchmark_path)
+
+# Initialization 14 November 2022
+#saem_benchmarks <- data.frame()
+
+saem_benchmarks[system_string, c("CPU", "OS", "mkin", "saemix", "R")] <-
+  c(cpu_model, operating_system, mkin_version, saemix_version, R_version)
+```
+
+For the initial mmkin fits, we use all available cores.
+
+```{r setup}
+n_cores <- parallel::detectCores()
+```
+
+## Test data
+
+Please refer to the vignette `dimethenamid_2018` for an explanation
+of the following preprocessing.
+
+```{r dimethenamid_data}
+dmta_ds <- lapply(1:7, function(i) {
+  ds_i <- dimethenamid_2018$ds[[i]]$data
+  ds_i[ds_i$name == "DMTAP", "name"] <-  "DMTA"
+  ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i]
+  ds_i
+})
+names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title)
+dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]])
+dmta_ds[["Elliot 1"]] <- NULL
+dmta_ds[["Elliot 2"]] <- NULL
+```
+
+## Test cases
+
+### Parent only
+
+```{r parent_only}
+parent_mods <- c("SFO", "DFOP", "SFORB", "HS")
+parent_sep_const <- mmkin(parent_mods, dmta_ds, quiet = TRUE, cores = n_cores)
+parent_sep_tc <- update(parent_sep_const, error_model = "tc")
+
+t1 <- system.time(sfo_const <- saem(parent_sep_const["SFO", ]))[["elapsed"]]
+t2 <- system.time(dfop_const <- saem(parent_sep_const["DFOP", ]))[["elapsed"]]
+t3 <- system.time(sforb_const <- saem(parent_sep_const["SFORB", ]))[["elapsed"]]
+t4 <- system.time(hs_const <- saem(parent_sep_const["HS", ]))[["elapsed"]]
+t5 <- system.time(sfo_tc <- saem(parent_sep_tc["SFO", ]))[["elapsed"]]
+t6 <- system.time(dfop_tc <- saem(parent_sep_tc["DFOP", ]))[["elapsed"]]
+t7 <- system.time(sforb_tc <- saem(parent_sep_tc["SFORB", ]))[["elapsed"]]
+t8 <- system.time(hs_tc <- saem(parent_sep_tc["HS", ]))[["elapsed"]]
+```
+
+```{r}
+anova(
+  sfo_const, dfop_const, sforb_const, hs_const,
+  sfo_tc, dfop_tc, sforb_tc, hs_tc) |> kable(, digits = 1)
+```
+
+The above model comparison suggests to use the SFORB model with two-component
+error. For comparison, we keep the DFOP model with two-component error,
+as it competes with SFORB for biphasic curves.
+
+```{r}
+illparms(dfop_tc)
+illparms(sforb_tc)
+```
+
+For these two models, random effects for the transformed parameters `k2` and
+`k_DMTA_bound_free` could not be quantified.
+
+
+### One metabolite
+
+We remove parameters that were found to be ill-defined in the parent only fits.
+
+```{r one_metabolite, message = FALSE}
+one_met_mods <- list(
+  DFOP_SFO = mkinmod(
+    DMTA = mkinsub("DFOP", "M23"),
+    M23 = mkinsub("SFO")),
+  SFORB_SFO = mkinmod(
+    DMTA = mkinsub("SFORB", "M23"),
+    M23 = mkinsub("SFO")))
+
+one_met_sep_const <- mmkin(one_met_mods, dmta_ds, error_model = "const",
+  cores = n_cores, quiet = TRUE)
+one_met_sep_tc <- mmkin(one_met_mods, dmta_ds, error_model = "tc",
+  cores = n_cores, quiet = TRUE)
+
+t9 <- system.time(dfop_sfo_tc <- saem(one_met_sep_tc["DFOP_SFO", ],
+    no_random_effect = "log_k2"))[["elapsed"]]
+t10 <- system.time(sforb_sfo_tc <- saem(one_met_sep_tc["SFORB_SFO", ],
+    no_random_effect = "log_k_DMTA_bound_free"))[["elapsed"]]
+```
+
+### Three metabolites
+
+For the case of three metabolites, we only keep the SFORB model in order
+to limit the time for compiling this vignette, and as fitting in parallel
+may disturb the benchmark. Again, we do not include random effects that
+were ill-defined in previous fits of subsets of the degradation model.
+
+```{r}
+illparms(sforb_sfo_tc)
+```
+
+```{r three_metabolites, message = FALSE}
+three_met_mods <- list(
+  SFORB_SFO3_plus = mkinmod(
+    DMTA = mkinsub("SFORB", c("M23", "M27", "M31")),
+    M23 = mkinsub("SFO"),
+    M27 = mkinsub("SFO"),
+    M31 = mkinsub("SFO", "M27", sink = FALSE)))
+
+three_met_sep_tc <- mmkin(three_met_mods, dmta_ds, error_model = "tc",
+  cores = n_cores, quiet = TRUE)
+
+t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SFORB_SFO3_plus", ],
+    no_random_effect = "log_k_DMTA_bound_free"))[["elapsed"]]
+```
+
+```{r results, include = FALSE}
+saem_benchmarks[system_string, paste0("t", 1:11)] <-
+  c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
+save(saem_benchmarks, file = benchmark_path)
+# Hide rownames from kable for results section
+rownames(saem_benchmarks) <- NULL
+```
+
+## Results
+
+Benchmarks for all available error models are shown. They are intended for
+improving mkin, not for comparing CPUs or operating systems. All trademarks
+belong to their respective owners.
+
+### Parent only
+
+Constant variance for SFO, DFOP, SFORB and HS.
+
+```{r, echo = FALSE}
+kable(saem_benchmarks[, c(1:4, 6:9)])
+```
+
+Two-component error fits for SFO, DFOP, SFORB and HS.
+
+```{r, echo = FALSE}
+kable(saem_benchmarks[, c(1:4, 10:13)])
+```
+
+### One metabolite
+
+Two-component error for DFOP-SFO and SFORB-SFO.
+
+```{r, echo = FALSE}
+kable(saem_benchmarks[, c(1:4, 14:15)])
+```
+
+### Three metabolites
+
+Two-component error for SFORB-SFO3-plus
+
+```{r, echo = FALSE}
+kable(saem_benchmarks[, c(1:4, 16)])
+```
+