From d5ff53448c61134c46cc4df9ea88fd86fa376d66 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 17 Feb 2023 14:44:29 +0100 Subject: Finish adapting to upcoming deSolve --- vignettes/web_only/benchmarks.html | 92 +++++++++++--------------------------- 1 file changed, 27 insertions(+), 65 deletions(-) (limited to 'vignettes/web_only/benchmarks.html') diff --git a/vignettes/web_only/benchmarks.html b/vignettes/web_only/benchmarks.html index fb799462..6cce41e6 100644 --- a/vignettes/web_only/benchmarks.html +++ b/vignettes/web_only/benchmarks.html @@ -1592,7 +1592,7 @@ div.tocify {

Benchmark timings for mkin

Johannes Ranke

-

Last change 14 July 2022 (rebuilt 2023-02-13)

+

Last change 14 July 2022 (rebuilt 2023-02-17)

@@ -1636,31 +1636,11 @@ FOMC_SFO <- mkinmod( DFOP_SFO <- mkinmod( parent = mkinsub("FOMC", "m1"), # erroneously used FOMC twice, not fixed for consistency m1 = mkinsub("SFO")) -t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[["elapsed"]] -
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-
t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
-    error_model = "tc"))[["elapsed"]]
-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-
t5 <- 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"]]
+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"]]
-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable

Two metabolites, synthetic data:

m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
                            M1 = mkinsub("SFO", "M2"),
@@ -1676,36 +1656,18 @@ SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$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"]]
-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-
t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))[["elapsed"]]
-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-
t8 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
-    error_model = "tc"))[["elapsed"]]
-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-
t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
-    error_model = "tc"))[["elapsed"]]
-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-
t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
-    error_model = "obs"))[["elapsed"]]
-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-
t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
+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),
+    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"]]
-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable

Results

@@ -1901,8 +1863,8 @@ models fitted to two datasets, i.e. eight fits for each test.

Ryzen 9 7950X 16-Core Processor 4.2.2 1.3.0 -1.271 -1.787 +1.287 +1.805 @@ -2119,9 +2081,9 @@ for each test.

Ryzen 9 7950X 16-Core Processor 4.2.2 1.3.0 -0.526 -0.623 -0.631 +0.731 +1.984 +1.100 @@ -2404,12 +2366,12 @@ dataset, i.e. one fit for each test.

Ryzen 9 7950X 16-Core Processor 4.2.2 1.3.0 -0.242 -0.237 -0.238 -0.239 -0.237 -0.237 +0.400 +0.518 +0.580 +0.990 +0.701 +0.935 -- cgit v1.2.1