From a9427a09abdf7ce9aaeae7c7190f90c8f2e5ef52 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 15 Feb 2021 14:08:13 +0100 Subject: Improve README, introductory vignette and some other docs Also bump version to 1.0.3. --- docs/articles/web_only/benchmarks.html | 50 +++++++++++++++------------------- 1 file changed, 22 insertions(+), 28 deletions(-) (limited to 'docs/articles/web_only/benchmarks.html') diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index e15358a0..d7b81f20 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -31,7 +31,7 @@ mkin - 1.0.0 + 1.0.3 @@ -94,13 +94,13 @@ -
+

Benchmark timings for mkin

Johannes Ranke

-

2021-02-03

+

Last change 13 May 2020 (rebuilt 2021-02-15)

Source: vignettes/web_only/benchmarks.rmd @@ -135,17 +135,11 @@ 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]], ...): 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 = "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"),
                            M1 = mkinsub("SFO", "M2"),
                            M2 = mkinsub("SFO"),
@@ -172,7 +166,7 @@
     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)] <-
   c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
 save(mkin_benchmarks, file = "~/git/mkin/vignettes/web_only/mkin_benchmarks.rda")

@@ -234,9 +228,9 @@
 3.729
 
 
-1.0.0
-1.770
-3.703
+1.0.3
+1.722
+3.419
 
 
 
@@ -302,10 +296,10 @@
 2.810
 
 
-1.0.0
-1.373
-7.127
-2.762
+1.0.3
+1.402
+6.343
+2.802
 
 
 
@@ -313,7 +307,7 @@
 

 

 Two metabolites

-
Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.

+
Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.

 
@@ -398,13 +392,13 @@
 
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 mkin version3.105
 

 
1.0.00.7751.2691.4673.7671.9192.9421.0.30.7711.2511.4643.0741.9402.831
 

 
 

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