From 194659fcaccdd1ee37851725b8c72e99daa3a8cf Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 10 Apr 2019 10:17:35 +0200 Subject: Adapt tests, vignettes and examples - Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit --- vignettes/web_only/benchmarks.html | 1817 ++++++++++++++++++++++++++++++++++++ 1 file changed, 1817 insertions(+) create mode 100644 vignettes/web_only/benchmarks.html (limited to 'vignettes/web_only/benchmarks.html') diff --git a/vignettes/web_only/benchmarks.html b/vignettes/web_only/benchmarks.html new file mode 100644 index 00000000..b35a9695 --- /dev/null +++ b/vignettes/web_only/benchmarks.html @@ -0,0 +1,1817 @@ + + + + + + + + + + + + + + + +Benchmark timings for mkin on various systems + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+

Systems

+

Each system is characterized by its CPU type, the operating system type and the mkin version.

+
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/inst/benchmark_data/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)
+}
+
# Parent only
+t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D)))[["elapsed"]]
+t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D), error_model = "tc"))[["elapsed"]]
+
+# One metabolite
+SFO_SFO <- mkinmod(
+  parent = mkinsub("SFO", "m1"),
+  m1 = mkinsub("SFO"))
+
## Successfully compiled differential equation model from auto-generated C code.
+
FOMC_SFO <- mkinmod(
+  parent = mkinsub("FOMC", "m1"),
+  m1 = mkinsub("SFO"))
+
## Successfully compiled differential equation model from auto-generated C code.
+
DFOP_SFO <- mkinmod(
+  parent = mkinsub("FOMC", "m1"),
+  m1 = mkinsub("SFO"))
+
## Successfully compiled differential equation model from auto-generated C code.
+
t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D)))[["elapsed"]]
+
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Observations with value of zero were removed from the data
+
+## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Observations with value of zero were removed from the data
+
+## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Observations with value of zero were removed from the data
+
t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(subset(FOCUS_2006_D, value != 0)), error_model = "tc"))[["elapsed"]]
+t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D), error_model = "obs"))[["elapsed"]]
+
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Observations with value of zero were removed from the data
+
+## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Observations with value of zero were removed from the data
+
+## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Observations with value of zero were removed from the data
+
# Two metabolites, synthetic data
+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"]
+
+mkin_benchmarks[system_string, paste0("t", 1:11)] <- c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
+mkin_benchmarks
+
##                                                                                                       CPU
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 AMD Ryzen 7 1700 Eight-Core Processor
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 AMD Ryzen 7 1700 Eight-Core Processor
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 AMD Ryzen 7 1700 Eight-Core Processor
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 AMD Ryzen 7 1700 Eight-Core Processor
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 AMD Ryzen 7 1700 Eight-Core Processor
+##                                                                        OS
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 Linux
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 Linux
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 Linux
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 Linux
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 Linux
+##                                                                         mkin
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 0.9.48.1
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 0.9.49.1
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 0.9.49.2
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 0.9.49.3
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 0.9.49.4
+##                                                                        t1
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.610
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.712
+##                                                                         t2
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 23.082
+##                                                                        t3
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.595
+##                                                                         t4
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  8.461
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 11.975
+##                                                                        t5
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.881
+##                                                                        t6
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 1.981
+##                                                                        t7
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  3.32
+##                                                                        t8
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.02
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.309
+##                                                                         t9
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  8.171
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  7.618
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  6.075
+##                                                                       t10
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.518
+##                                                                        t11
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  5.636
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.574
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.365
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  4.289
+
save(mkin_benchmarks, file = "~/git/mkin/inst/benchmark_data/mkin_benchmarks.rda")
+
+ + + +
+
+ +
+ + + + + + + + -- cgit v1.2.1