From 20f235860c3d5a9c6319c516637021e02ecb6cae Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 12 May 2020 17:51:58 +0200 Subject: Update pkgdown --- docs/articles/web_only/benchmarks.html | 195 ++++++++++++++++++++++++++++----- docs/pkgdown.yml | 2 +- 2 files changed, 166 insertions(+), 31 deletions(-) (limited to 'docs') diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index b47df46f..b0bb5196 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -68,6 +68,9 @@
  • Example evaluation of NAFTA SOP Attachment examples
    • +
  • + Some benchmark timings +
  • @@ -168,18 +171,18 @@ 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"] +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"] + error_model = "tc"))[["elapsed"]] t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), - error_model = "tc"))["elapsed"] + error_model = "tc"))[["elapsed"]] t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), - error_model = "obs"))["elapsed"] + error_model = "obs"))[["elapsed"]] t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), - error_model = "obs"))["elapsed"] + 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")
    @@ -188,45 +191,177 @@

    Results

    Currently, we only have benchmark information on one system, therefore only the mkin version is shown with the results below. Timings are in seconds, shorter is better.

    +
    rownames(mkin_benchmarks) <- as.character(mkin_benchmarks$mkin)

    Benchmarks for all available error models are shown.

    Parent only

    Constant variance and two-component error model:

    -
    print(mkin_benchmarks[, c("mkin", "t1", "t2")], row.names = FALSE)
    -
    ##      mkin    t1     t2
-##  0.9.48.1 3.610 11.019
-##  0.9.49.1 8.184 22.889
-##  0.9.49.2 7.064 12.558
-##  0.9.49.3 7.296 21.239
-##  0.9.49.4 5.936 20.545
-##  0.9.50.2 1.697  3.895
    +
    kable(mkin_benchmarks[, c("t1", "t2")])
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    t1t2
    0.9.48.13.61011.019
    0.9.49.18.18422.889
    0.9.49.27.06412.558
    0.9.49.37.29621.239
    0.9.49.45.93620.545
    0.9.50.21.6593.900

    One metabolite

    Constant variance, variance by variable and two-component error model:

    -
    print(mkin_benchmarks[, c("mkin", "t3", "t4", "t5")], row.names = FALSE)
    -
    ##      mkin    t3     t4    t5
-##  0.9.48.1 3.764 14.347 9.495
-##  0.9.49.1 4.649 13.789 6.395
-##  0.9.49.2 4.786  8.461 5.675
-##  0.9.49.3 4.510 13.805 7.386
-##  0.9.49.4 4.446 15.335 6.002
-##  0.9.50.2 1.365  6.105 2.727
    +
    kable(mkin_benchmarks[, c("t3", "t4", "t5")])
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    t3t4t5
    0.9.48.13.76414.3479.495
    0.9.49.14.64913.7896.395
    0.9.49.24.7868.4615.675
    0.9.49.34.51013.8057.386
    0.9.49.44.44615.3356.002
    0.9.50.21.3896.1062.716

    Two metabolites

    Two different datasets, for each constant variance, variance by variable and two-component error model are shown:

    -
    print(mkin_benchmarks[, c("mkin", paste0("t", 6:11))], row.names = FALSE)
    -
    ##      mkin    t6    t7    t8     t9   t10    t11
-##  0.9.48.1 2.623 4.587 7.525 16.621 8.576 31.267
-##  0.9.49.1 2.542 4.128 4.632  8.171 3.676  5.636
-##  0.9.49.2 2.723 4.478 4.862  7.618 3.579  5.574
-##  0.9.49.3 2.643 4.374  7.02 11.124 5.388  7.365
-##  0.9.49.4 2.635 4.259 4.737  7.763 3.427  5.626
-##  0.9.50.2 0.752 1.218 1.273  2.851 2.038  2.968
    +
    kable(mkin_benchmarks[, paste0("t", 6:11)])
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    t6t7t8t9t10t11
    0.9.48.12.6234.5877.52516.6218.57631.267
    0.9.49.12.5424.1284.6328.1713.6765.636
    0.9.49.22.7234.4784.8627.6183.5795.574
    0.9.49.32.6434.3747.02011.1245.3887.365
    0.9.49.42.6354.2594.7377.7633.4275.626
    0.9.50.20.7511.2091.2702.8592.0262.963
    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 18887405..5147a265 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: NAFTA_examples: web_only/NAFTA_examples.html benchmarks: web_only/benchmarks.html compiled_models: web_only/compiled_models.html -last_built: 2020-05-12T14:56Z +last_built: 2020-05-12T15:51Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles -- cgit v1.2.1