From 6476f5f49b373cd4cf05f2e73389df83e437d597 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 13 Feb 2025 16:30:31 +0100 Subject: Axis legend formatting, update vignettes --- docs/dev/articles/web_only/saem_benchmarks.html | 639 ------------------------ 1 file changed, 639 deletions(-) delete mode 100644 docs/dev/articles/web_only/saem_benchmarks.html (limited to 'docs/dev/articles/web_only/saem_benchmarks.html') diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html deleted file mode 100644 index 66740a11..00000000 --- a/docs/dev/articles/web_only/saem_benchmarks.html +++ /dev/null @@ -1,639 +0,0 @@ - - - - - - - -Benchmark timings for saem.mmkin • mkin - - - - - - - - - - - - - -
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Benchmark timings for saem.mmkin

-

Johannes -Ranke

- -

Last change 17 February 2023 -(rebuilt 2023-04-16)

- - Source: vignettes/web_only/saem_benchmarks.rmd - - -
- - - -

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.

-

For the initial mmkin fits, we use all available cores.

-
-n_cores <- parallel::detectCores()
-
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Test data -

-

Please refer to the vignette dimethenamid_2018 for an -explanation of the following preprocessing.

-
-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
-
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Test cases -

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Parent only -

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-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)
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nparAICBICLik
sfo_const5796.3795.3-393.2
sfo_tc6798.3797.1-393.2
dfop_const9709.4707.5-345.7
sforb_const9710.0708.1-346.0
hs_const9713.7711.8-347.8
dfop_tc10669.8667.7-324.9
sforb_tc10662.8660.7-321.4
hs_tc10667.3665.2-323.6
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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.

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-illparms(dfop_tc)
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## [1] "sd(log_k2)"
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-illparms(sforb_tc)
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## [1] "sd(log_k_DMTA_bound_free)"
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For these two models, random effects for the transformed parameters -k2 and k_DMTA_bound_free could not be -quantified.

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One metabolite -

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We remove parameters that were found to be ill-defined in the parent -only fits.

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-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"]]
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Three metabolites -

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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.

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-illparms(sforb_sfo_tc)
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-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)))
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-three_met_sep_tc <- mmkin(three_met_mods, dmta_ds, error_model = "tc",
-  cores = n_cores, quiet = TRUE)
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-t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SFORB_SFO3_plus", ],
-    no_random_effect = "log_k_DMTA_bound_free"))[["elapsed"]]
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Results -

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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.

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Parent only -

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Constant variance for SFO, DFOP, SFORB and HS.

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CPUOSmkinsaemixt1t2t3t4
Ryzen 7 1700Linux1.2.03.22.1404.6264.3284.998
Ryzen 7 1700Linux1.2.23.22.4274.5504.2174.851
Ryzen 9 7950XLinux1.2.13.21.3522.8132.4012.074
Ryzen 9 7950XLinux1.2.23.21.3282.7382.3362.023
Ryzen 9 7950XLinux1.2.33.21.1182.0362.0102.088
Ryzen 9 7950XLinux1.2.33.21.3892.3001.8802.355
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Two-component error fits for SFO, DFOP, SFORB and HS.

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CPUOSmkinsaemixt5t6t7t8
Ryzen 7 1700Linux1.2.03.25.6787.4418.0007.980
Ryzen 7 1700Linux1.2.23.25.3527.2018.1748.401
Ryzen 9 7950XLinux1.2.13.22.3883.0333.5323.310
Ryzen 9 7950XLinux1.2.23.22.3412.9683.4653.341
Ryzen 9 7950XLinux1.2.33.22.1593.5843.3073.460
Ryzen 9 7950XLinux1.2.33.22.3003.0753.2063.471
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One metabolite -

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Two-component error for DFOP-SFO and SFORB-SFO.

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CPUOSmkinsaemixt9t10
Ryzen 7 1700Linux1.2.03.224.465800.266
Ryzen 7 1700Linux1.2.23.225.193798.580
Ryzen 9 7950XLinux1.2.13.211.247285.216
Ryzen 9 7950XLinux1.2.23.211.242284.258
Ryzen 9 7950XLinux1.2.33.211.796216.012
Ryzen 9 7950XLinux1.2.33.212.951294.082
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Three metabolites -

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Two-component error for SFORB-SFO3-plus

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CPUOSmkinsaemixt11
Ryzen 7 1700Linux1.2.03.21289.198
Ryzen 7 1700Linux1.2.23.21312.445
Ryzen 9 7950XLinux1.2.13.2489.939
Ryzen 9 7950XLinux1.2.23.2482.970
Ryzen 9 7950XLinux1.2.33.2392.364
Ryzen 9 7950XLinux1.2.33.2477.297
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