From a77a10ea6c607346778ba0700b3b66ac393101a2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 27 May 2020 06:06:08 +0200 Subject: Create up to date pkgdown docs in development mode --- docs/dev/articles/web_only/benchmarks.html | 391 +++++++++++++++++++++++++++++ 1 file changed, 391 insertions(+) create mode 100644 docs/dev/articles/web_only/benchmarks.html (limited to 'docs/dev/articles/web_only/benchmarks.html') diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html new file mode 100644 index 00000000..b46b873c --- /dev/null +++ b/docs/dev/articles/web_only/benchmarks.html @@ -0,0 +1,391 @@ + + + + + + + +Benchmark timings for mkin • mkin + + + + + + + + + + + +
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+ + + + +
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+

Benchmark timings for mkin

+

Johannes Ranke

+ +

2020-05-27

+ + Source: vignettes/web_only/benchmarks.rmd + + +
+ + + +

Each system is characterized by its CPU type, the operating system type and the mkin version. Currently only values for one system are available. A compiler was available, so if no analytical solution was available, compiled ODE models are used.

+
+

+Test cases

+

Parent only:

+
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:

+
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:

+
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)
+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. All results were obtained by serial, i.e. not using multiple computing cores.

+

Benchmarks for all available error models are shown.

+
+

+Parent only

+

Constant variance (t1) and two-component error model (t2) for four models fitted to two datasets, i.e. eight fits for each test.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
mkin versiont1 [s]t2 [s]
0.9.48.13.61011.019
0.9.49.18.18422.889
0.9.49.27.06412.558
0.9.49.37.29621.239
0.9.49.45.93620.545
0.9.50.21.7143.971
0.9.50.31.7523.728
+
+
+

+One metabolite

+

Constant variance (t3), two-component error model (t4), and variance by variable (t5) for three models fitted to one dataset, i.e. three fits for each test.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
mkin versiont3 [s]t4 [s]t5 [s]
0.9.48.13.76414.3479.495
0.9.49.14.64913.7896.395
0.9.49.24.7868.4615.675
0.9.49.34.51013.8057.386
0.9.49.44.44615.3356.002
0.9.50.21.4026.1742.764
0.9.50.31.3896.5792.740
+
+
+

+Two metabolites

+

Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
mkin versiont6 [s]t7 [s]t8 [s]t9 [s]t10 [s]t11 [s]
0.9.48.12.6234.5877.52516.6218.57631.267
0.9.49.12.5424.1284.6328.1713.6765.636
0.9.49.22.7234.4784.8627.6183.5795.574
0.9.49.32.6434.3747.02011.1245.3887.365
0.9.49.42.6354.2594.7377.7633.4275.626
0.9.50.20.7771.2361.3322.8722.0692.987
0.9.50.30.7601.2521.4574.2012.0072.979
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