From 679cf716192cdfd91dfd232578cbd4e30d7eac12 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 15 Nov 2022 08:01:52 +0100 Subject: Import saemix for easier profiling, update online docs --- vignettes/web_only/benchmarks.rmd | 2 +- vignettes/web_only/mkin_benchmarks.rda | Bin 1597 -> 1586 bytes vignettes/web_only/saem_benchmarks.R | 121 -------------------------------- vignettes/web_only/saem_benchmarks.html | 22 +++--- vignettes/web_only/saem_benchmarks.rda | Bin 366 -> 359 bytes vignettes/web_only/saem_benchmarks.rmd | 2 +- 6 files changed, 13 insertions(+), 134 deletions(-) delete mode 100644 vignettes/web_only/saem_benchmarks.R (limited to 'vignettes') diff --git a/vignettes/web_only/benchmarks.rmd b/vignettes/web_only/benchmarks.rmd index de8ee723..117dc96a 100644 --- a/vignettes/web_only/benchmarks.rmd +++ b/vignettes/web_only/benchmarks.rmd @@ -141,7 +141,7 @@ t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), ```{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) +save(mkin_benchmarks, file = benchmark_path, version = 2) # Hide rownames from kable for results section rownames(mkin_benchmarks) <- NULL ``` diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda index a0d4c72c..2d3deb26 100644 Binary files a/vignettes/web_only/mkin_benchmarks.rda and b/vignettes/web_only/mkin_benchmarks.rda differ diff --git a/vignettes/web_only/saem_benchmarks.R b/vignettes/web_only/saem_benchmarks.R deleted file mode 100644 index 210e79e3..00000000 --- a/vignettes/web_only/saem_benchmarks.R +++ /dev/null @@ -1,121 +0,0 @@ -## ---- include = FALSE--------------------------------------------------------- -library("knitr") # For the kable() function -opts_chunk$set(tidy = FALSE, cache = FALSE) -library("mkin") - -## ----include = FALSE---------------------------------------------------------- -cpu_model <- benchmarkme::get_cpu()$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) - -## ----setup-------------------------------------------------------------------- -n_cores <- parallel::detectCores() - -## ----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 - -## ----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"]] - -## ----------------------------------------------------------------------------- -anova( - sfo_const, dfop_const, sforb_const, hs_const, - sfo_tc, dfop_tc, sforb_tc, hs_tc) |> kable(, digits = 1) - -## ----------------------------------------------------------------------------- -illparms(dfop_tc) -illparms(sforb_tc) - -## ----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"]] - -## ----------------------------------------------------------------------------- -illparms(sforb_sfo_tc) - -## ----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"]] - -## ----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 - -## ---- echo = FALSE------------------------------------------------------------ -kable(saem_benchmarks[, c(1:4, 6:9)]) - -## ---- echo = FALSE------------------------------------------------------------ -kable(saem_benchmarks[, c(1:4, 10:13)]) - -## ---- echo = FALSE------------------------------------------------------------ -kable(saem_benchmarks[, c(1:4, 14:15)]) - -## ---- echo = FALSE------------------------------------------------------------ -kable(saem_benchmarks[, c(1:4, 16)]) - diff --git a/vignettes/web_only/saem_benchmarks.html b/vignettes/web_only/saem_benchmarks.html index 42d6f71f..4875bb1b 100644 --- a/vignettes/web_only/saem_benchmarks.html +++ b/vignettes/web_only/saem_benchmarks.html @@ -1781,10 +1781,10 @@ t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SF Linux 1.2.0 3.2 -3.025 -5.237 -5.459 -5.218 +2.996 +5.207 +5.317 +5.171 @@ -1808,10 +1808,10 @@ t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SF Linux 1.2.0 3.2 -5.645 -7.726 -7.952 -8.104 +5.671 +7.696 +8.166 +8.168 @@ -1836,8 +1836,8 @@ t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SF Linux 1.2.0 3.2 -24.84 -816.153 +24.883 +818.157 @@ -1861,7 +1861,7 @@ t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SF Linux 1.2.0 3.2 -1323.128 +1355.036 diff --git a/vignettes/web_only/saem_benchmarks.rda b/vignettes/web_only/saem_benchmarks.rda index 1e75b20d..e8b139da 100644 Binary files a/vignettes/web_only/saem_benchmarks.rda and b/vignettes/web_only/saem_benchmarks.rda differ diff --git a/vignettes/web_only/saem_benchmarks.rmd b/vignettes/web_only/saem_benchmarks.rmd index 116713de..6e51fa66 100644 --- a/vignettes/web_only/saem_benchmarks.rmd +++ b/vignettes/web_only/saem_benchmarks.rmd @@ -164,7 +164,7 @@ t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SFORB_SFO3_pl ```{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) +save(saem_benchmarks, file = benchmark_path, version = 2) # Hide rownames from kable for results section rownames(saem_benchmarks) <- NULL ``` -- cgit v1.2.1