From 91c5db736a4d3f2290a0cc5698fb4e35ae7bda59 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 May 2022 21:26:17 +0200 Subject: Remove outdated comment in FOCUS L vignette, update docs This also adds the first benchmark results obtained on my laptop system --- vignettes/web_only/benchmarks.html | 2005 ------------------------------------ 1 file changed, 2005 deletions(-) delete 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 deleted file mode 100644 index a591dc06..00000000 --- a/vignettes/web_only/benchmarks.html +++ /dev/null @@ -1,2005 +0,0 @@ - - - - - - - - - - - - - - -Benchmark timings for mkin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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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.

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Test cases

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Parent only:

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FOCUS_C <- FOCUS_2006_C
-FOCUS_D <- subset(FOCUS_2006_D, value != 0)
-parent_datasets <- list(FOCUS_C, FOCUS_D)
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-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"]]
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One metabolite:

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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"]]
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Two metabolites, synthetic data:

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m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
-                           M1 = mkinsub("SFO", "M2"),
-                           M2 = mkinsub("SFO"),
-                           use_of_ff = "max", quiet = TRUE)
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-m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
-                           M1 = mkinsub("SFO"),
-                           M2 = mkinsub("SFO"),
-                           use_of_ff = "max", quiet = TRUE)
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-SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
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-DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
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-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"]]
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-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"]]
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-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"]]
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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")
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Results

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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.

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Benchmarks for all available error models are shown.

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Parent only

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

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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
0.9.50.31.7524.156
0.9.50.41.7863.729
1.0.01.7703.703
1.0.31.5823.476
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One metabolite

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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.

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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
0.9.50.31.4306.6152.878
0.9.50.41.3977.2512.810
1.0.01.3737.1272.762
1.0.31.4176.4182.823
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Two metabolites

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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.

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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
0.9.50.30.8581.2641.3332.9842.1133.073
0.9.50.40.7831.2821.4863.8151.9583.105
1.0.00.7751.2691.4673.7671.9192.942
1.0.30.7831.2581.6113.0951.9512.859
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