From bc3825ae2d12c18ea3d3caf17eb23c93fef180b8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 8 Oct 2020 09:31:35 +0200 Subject: Fix issues for release --- docs/dev/articles/web_only/benchmarks.html | 46 ++++++++++++++++++------------ 1 file changed, 27 insertions(+), 19 deletions(-) (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 index 9e53f113..30b7a879 100644 --- a/docs/dev/articles/web_only/benchmarks.html +++ b/docs/dev/articles/web_only/benchmarks.html @@ -101,7 +101,7 @@

Benchmark timings for mkin

Johannes Ranke

-

2020-05-27

+

2020-10-08

Source: vignettes/web_only/benchmarks.rmd @@ -132,13 +132,20 @@ 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), +t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[["elapsed"]] +
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Shapiro-Wilk test for standardized residuals: p = 0.0165
+
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Shapiro-Wilk test for standardized residuals: p = 0.0499
+
+## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Shapiro-Wilk test for standardized residuals: p = 0.0499
+
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"),
+
m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
                            M1 = mkinsub("SFO", "M2"),
                            M2 = mkinsub("SFO"),
                            use_of_ff = "max", quiet = TRUE)
@@ -153,9 +160,10 @@
 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),
+t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))[["elapsed"]]

+
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Shapiro-Wilk test for standardized residuals: p = 0.000174

+
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"]]
@@ -164,7 +172,7 @@
     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)] <-
+
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")

 

@@ -216,8 +224,8 @@
 
 
 0.9.50.3
-1.746
-3.716
+1.707
+4.062
 
 
 
@@ -272,9 +280,9 @@
 
 
 0.9.50.3
-1.385
-6.562
-2.736
+1.372
+6.233
+2.779
 
 
 
@@ -350,12 +358,12 @@
 
 
 0.9.50.3
-0.760
-1.226
-1.455
-4.198
-2.007
-2.976
+0.768
+1.235
+1.302
+2.921
+2.078
+3.040
 
 
 
-- 
cgit v1.2.1