Test cases

Parent only:

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

## 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
++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"]]
+## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
+## iteration limit reached without convergence (10)
 
-## 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"]]
+## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
+## iteration limit reached without convergence (10)

+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_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)
+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]]$data
+SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
 
-DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
+DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$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"]]
-## 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"]]
+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"]]
 
-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")
+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")

@@ -224,8 +227,13 @@ 0.9.50.3 -1.707 -4.062 +1.752 +4.156 + + +0.9.50.4 +1.753 +3.791 @@ -280,9 +288,15 @@ 0.9.50.3 -1.372 -6.233 -2.779 +1.430 +6.615 +2.878 + + +0.9.50.4 +1.374 +6.974 +2.735 @@ -358,12 +372,21 @@ 0.9.50.3 -0.768 -1.235 -1.302 -2.921 -2.078 -3.040 +0.858 +1.264 +1.333 +2.984 +2.113 +3.073 + + +0.9.50.4 +0.766 +1.250 +1.436 +3.749 +1.878 +2.879 @@ -386,7 +409,7 @@

Site built with pkgdown 1.5.1.

Site built with pkgdown 1.6.1.

-- cgit v1.2.1

Benchmark timings for mkin

Johannes Ranke

2020-10-08

2020-11-06

Test cases