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.

diff --git a/docs/dev/articles/web_only/benchmarks_files/anchor-sections-1.0/anchor-sections.css b/docs/dev/articles/web_only/benchmarks_files/anchor-sections-1.0/anchor-sections.css new file mode 100644 index 00000000..07aee5fc --- /dev/null +++ b/docs/dev/articles/web_only/benchmarks_files/anchor-sections-1.0/anchor-sections.css @@ -0,0 +1,4 @@ +/* Styles for section anchors */ +a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} +a.anchor-section::before {content: '#';} +.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/dev/articles/web_only/benchmarks_files/anchor-sections-1.0/anchor-sections.js b/docs/dev/articles/web_only/benchmarks_files/anchor-sections-1.0/anchor-sections.js new file mode 100644 index 00000000..570f99a0 --- /dev/null +++ b/docs/dev/articles/web_only/benchmarks_files/anchor-sections-1.0/anchor-sections.js @@ -0,0 +1,33 @@ +// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. +document.addEventListener('DOMContentLoaded', function() { + // Do nothing if AnchorJS is used + if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { + return; + } + + const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); + + // Do nothing if sections are already anchored + if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { + return null; + } + + // Use section id when pandoc runs with --section-divs + const section_id = function(x) { + return ((x.classList.contains('section') || (x.tagName === 'SECTION')) + ? x.id : ''); + }; + + // Add anchors + h.forEach(function(x) { + const id = x.id || section_id(x.parentElement); + if (id === '') { + return null; + } + let anchor = document.createElement('a'); + anchor.href = '#' + id; + anchor.classList = ['anchor-section']; + x.classList.add('hasAnchor'); + x.appendChild(anchor); + }); +}); diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 7b186c37..207aaf78 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2020-11-05T22:53Z +last_built: 2020-11-05T23:08Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles -- cgit v1.2.1

Benchmark timings for mkin

Johannes Ranke

2020-10-08

2020-11-06

Test cases