From db9ae6a0c9cecb92048fde6f06af1da183c09b5f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 19 Nov 2020 15:41:24 +0100 Subject: Depend on parallel, doc improvements By depending on parallel instead of importing it, functions to set up and stop a cluster are always available when mkin is loaded. The use of multicore processing in mmkin on Windows is now documented in the help file, which brings mkin closer to a version 1.0 #9. --- docs/dev/articles/web_only/benchmarks.html | 54 +++++++++++++++--------------- 1 file changed, 27 insertions(+), 27 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 5105afcd..ff70847e 100644 --- a/docs/dev/articles/web_only/benchmarks.html +++ b/docs/dev/articles/web_only/benchmarks.html @@ -102,7 +102,7 @@

Benchmark timings for mkin

Johannes Ranke

-

2020-11-06

+

2020-11-19

Source: vignettes/web_only/benchmarks.rmd @@ -116,17 +116,17 @@

Test cases

Parent only:

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

+    error_model = "tc"))[["elapsed"]]

One metabolite:

-
-SFO_SFO <- mkinmod(
+
+SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))
 FOMC_SFO <- mkinmod(
@@ -137,18 +137,18 @@
   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"]]

+    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]], ...): 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"]]
+
+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)
@@ -173,11 +173,11 @@
 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)] <-
+    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")

+save(mkin_benchmarks, file = "~/git/mkin/vignettes/web_only/mkin_benchmarks.rda")

@@ -232,8 +232,8 @@ 0.9.50.4 -1.753 -3.791 +1.702 +3.717 @@ -294,9 +294,9 @@ 0.9.50.4 -1.374 -6.974 -2.735 +1.355 +7.015 +2.729 @@ -381,12 +381,12 @@ 0.9.50.4 -0.766 -1.250 +0.759 +1.245 1.436 -3.749 -1.878 -2.879 +3.687 +1.886 +3.028 -- cgit v1.2.1