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| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-10 21:53:00 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-10 21:53:00 +0200 |
| commit | d113cd79b178fdc91aecb894707ed356129dfb75 (patch) | |
| tree | dc28e049e94eb3ee9745f9cd86387de96a894c93 /vignettes/web_only/benchmarks.Rmd | |
| parent | efab37957381919c21d874906ce870f4941c760a (diff) | |
Default to analytical for coupled models if available
This revealed that transforming rates is necessary for fitting
the analytical solution of the SFO-SFO model to the FOCUS D dataset.
Benchmarks show that fitting coupled models with deSolve got a bit
slower through the latest changes
Diffstat (limited to 'vignettes/web_only/benchmarks.Rmd')
| -rw-r--r-- | vignettes/web_only/benchmarks.Rmd | 14 |
1 files changed, 8 insertions, 6 deletions
diff --git a/vignettes/web_only/benchmarks.Rmd b/vignettes/web_only/benchmarks.Rmd index 4849635f..cc28735a 100644 --- a/vignettes/web_only/benchmarks.Rmd +++ b/vignettes/web_only/benchmarks.Rmd @@ -40,9 +40,11 @@ if (mkin_version > "0.9.48.1") { ``` ```{r timings} +FOCUS_C <- FOCUS_2006_C +FOCUS_D <- subset(FOCUS_2006_D, value != 0) # 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"]] +t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_C, FOCUS_D)))[["elapsed"]] +t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_C, FOCUS_D), error_model = "tc"))[["elapsed"]] # One metabolite SFO_SFO <- mkinmod( @@ -54,9 +56,9 @@ FOMC_SFO <- mkinmod( DFOP_SFO <- mkinmod( parent = mkinsub("FOMC", "m1"), m1 = mkinsub("SFO")) -t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D)))[["elapsed"]] -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"]] +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"), @@ -83,7 +85,7 @@ t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_mod 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 +mkin_benchmarks[, -c(1:3)] save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda") |