diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-10 21:53:00 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-10 21:53:00 +0200 |
| commit | d113cd79b178fdc91aecb894707ed356129dfb75 (patch) | |
| tree | dc28e049e94eb3ee9745f9cd86387de96a894c93 | |
| parent | efab37957381919c21d874906ce870f4941c760a (diff) | |
Default to analytical for coupled models if available
This revealed that transforming rates is necessary for fitting
the analytical solution of the SFO-SFO model to the FOCUS D dataset.
Benchmarks show that fitting coupled models with deSolve got a bit
slower through the latest changes
| -rw-r--r-- | R/create_deg_func.R | 3 | ||||
| -rw-r--r-- | R/mkinfit.R | 4 | ||||
| -rw-r--r-- | test.log | 20 | ||||
| -rw-r--r-- | tests/testthat/FOCUS_2006_D.csf | 2 | ||||
| -rw-r--r-- | tests/testthat/test_FOCUS_D_UBA_expertise.R | 21 | ||||
| -rw-r--r-- | vignettes/mkin_benchmarks.rda | bin | 871 -> 871 bytes | |||
| -rw-r--r-- | vignettes/web_only/benchmarks.Rmd | 14 | ||||
| -rw-r--r-- | vignettes/web_only/benchmarks.html | 243 |
8 files changed, 150 insertions, 157 deletions
diff --git a/R/create_deg_func.R b/R/create_deg_func.R index 886c5e8b..6c0ae40b 100644 --- a/R/create_deg_func.R +++ b/R/create_deg_func.R @@ -51,7 +51,8 @@ create_deg_func <- function(spec, use_of_ff = c("min", "max")) { n10 <- paste0("odeini['", parent, "']") n20 <- paste0("odeini['", n2, "']") - if (all(use_of_ff == "max", spec[[1]]$sink == TRUE, length(obs_vars) == 2, spec[[2]]$type == "SFO")) { + if (all(use_of_ff == "max", spec[[1]]$sink == TRUE, length(obs_vars) == 2, + spec[[1]]$type == "SFO", spec[[2]]$type == "SFO")) { supported <- TRUE k1 <- paste0("k_", n1) k2 <- paste0("k_", n2) diff --git a/R/mkinfit.R b/R/mkinfit.R index c33afbf0..e1089673 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -464,7 +464,7 @@ mkinfit <- function(mkinmod, observed, if (solution_type == "eigen" && !is.matrix(mkinmod$coefmat)) stop("Eigenvalue based solution not possible, coefficient matrix not present.") if (solution_type == "auto") { - if (length(mkinmod$spec) == 1) { + if (length(mkinmod$spec) == 1 || is.function(mkinmod$deg_func)) { solution_type = "analytical" } else { if (!is.null(mkinmod$cf) & use_compiled[1] != FALSE) { @@ -694,7 +694,7 @@ mkinfit <- function(mkinmod, observed, # Show parameter names if tracing is requested if(trace_parms) cat(names_optim, "\n") - # browser() + #browser() # Do the fit and take the time until the hessians are calculated fit_time <- system.time({ @@ -2,33 +2,33 @@ Loading mkin Testing mkin ✔ | OK F W S | Context ✔ | 2 | Export dataset for reading into CAKE -✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.3 s] -✔ | 4 | Calculation of FOCUS chi2 error levels [2.0 s] -✔ | 7 | Fitting the SFORB model [9.1 s] -✔ | 1 | Analytical solutions for coupled models [1.1 s] +✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [2.5 s] +✔ | 4 | Calculation of FOCUS chi2 error levels [0.4 s] +✔ | 7 | Fitting the SFORB model [9.0 s] +✔ | 1 | Analytical solutions for coupled models [0.2 s] ✔ | 5 | Calculation of Akaike weights ✔ | 10 | Confidence intervals and p-values [1.0 s] -✔ | 14 | Error model fitting [3.7 s] +✔ | 14 | Error model fitting [3.8 s] ✔ | 6 | Test fitting the decline of metabolites from their maximum [0.2 s] ✔ | 1 | Fitting the logistic model [0.2 s] ✔ | 1 | Test dataset class mkinds used in gmkin ✔ | 12 | Special cases of mkinfit calls [0.6 s] ✔ | 8 | mkinmod model generation and printing [0.2 s] ✔ | 3 | Model predictions with mkinpredict [0.4 s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.4 s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.3 s] ✔ | 9 | Nonlinear mixed-effects models [12.1 s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s] ✔ | 3 | Summary -✔ | 14 | Plotting [3.5 s] +✔ | 14 | Plotting [3.6 s] ✔ | 4 | AIC calculation ✔ | 4 | Residuals extracted from mkinfit models ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [4.2 s] ✔ | 1 | Summaries of old mkinfit objects -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [6.4 s] -✔ | 9 | Hypothesis tests [17.8 s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [6.3 s] +✔ | 9 | Hypothesis tests [17.7 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 69.9 s +Duration: 66.3 s OK: 157 Failed: 0 diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf index f113a668..d41f0a9f 100644 --- a/tests/testthat/FOCUS_2006_D.csf +++ b/tests/testthat/FOCUS_2006_D.csf @@ -5,7 +5,7 @@ Description: MeasurementUnits: % AR TimeUnits: days Comments: Created using mkin::CAKE_export -Date: 2020-05-09 +Date: 2020-05-10 Optimiser: IRLS [Data] diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R index f3b12bd9..be2806de 100644 --- a/tests/testthat/test_FOCUS_D_UBA_expertise.R +++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R @@ -2,19 +2,22 @@ context("Results for FOCUS D established in expertise for UBA (Ranke 2014)") # Results are from p. 40 +# Avoid warnings due to the zero value in the data for m1 at time zero +FOCUS_D <- subset(FOCUS_2006_D, value != 0) + test_that("Fits without formation fractions are correct for FOCUS D", { - fit.default <- expect_warning(mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE), "value of zero") + fit.noff <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE) - expect_equal(round(as.numeric(endpoints(fit.default)$distimes["parent", ]), 2), + expect_equal(round(as.numeric(endpoints(fit.noff)$distimes["parent", ]), 2), c(7.02, 23.33)) - expect_equal(round(as.numeric(endpoints(fit.default)$distimes["m1", ]), 1), + expect_equal(round(as.numeric(endpoints(fit.noff)$distimes["m1", ]), 1), c(131.8, 437.7)) }) test_that("Fits with formation fractions are correct for FOCUS D", { skip_on_cran() - fit.ff <- expect_warning(mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE), "value of zero") + fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_D, quiet = TRUE) expect_equivalent(round(fit.ff$bparms.optim, c(2, 4, 4, 4)), c(99.60, 0.0987, 0.0053, 0.5145)) @@ -30,8 +33,15 @@ test_that("Fits with formation fractions are correct for FOCUS D", { test_that("Fits without internal transformations are correct for FOCUS D", { skip_on_cran() expect_warning( + # Analytical solutions (now the default for SFO_SFO with formation fractions) + # return NA at some point not internally transforming rates + expect_error(fit.ff.notrans <- mkinfit(SFO_SFO.ff, FOCUS_D, + transform_fractions = FALSE, transform_rates = FALSE, quiet = TRUE))) + + expect_warning( fit.ff.notrans <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, - transform_fractions = FALSE, transform_rates = FALSE, quiet = TRUE), + transform_fractions = FALSE, transform_rates = FALSE, + quiet = TRUE, solution_type = "deSolve"), "sum of formation fractions") expect_equivalent(round(fit.ff.notrans$bparms.optim, c(2, 4, 4, 4)), @@ -40,7 +50,6 @@ test_that("Fits without internal transformations are correct for FOCUS D", { expect_equivalent(round(100 * mkinerrmin(fit.ff.notrans)$err.min, 2), c(6.40, 6.46, 4.69)) - expect_equal(round(as.numeric(endpoints(fit.ff.notrans)$distimes["parent", ]), 2), c(7.02, 23.33)) expect_equal(round(as.numeric(endpoints(fit.ff.notrans)$distimes["m1", ]), 1), diff --git a/vignettes/mkin_benchmarks.rda b/vignettes/mkin_benchmarks.rda Binary files differindex 1190d924..32223710 100644 --- a/vignettes/mkin_benchmarks.rda +++ b/vignettes/mkin_benchmarks.rda diff --git a/vignettes/web_only/benchmarks.Rmd b/vignettes/web_only/benchmarks.Rmd index 4849635f..cc28735a 100644 --- a/vignettes/web_only/benchmarks.Rmd +++ b/vignettes/web_only/benchmarks.Rmd @@ -40,9 +40,11 @@ if (mkin_version > "0.9.48.1") { ``` ```{r timings} +FOCUS_C <- FOCUS_2006_C +FOCUS_D <- subset(FOCUS_2006_D, value != 0) # Parent only -t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D)))[["elapsed"]] -t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D), error_model = "tc"))[["elapsed"]] +t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_C, FOCUS_D)))[["elapsed"]] +t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_C, FOCUS_D), error_model = "tc"))[["elapsed"]] # One metabolite SFO_SFO <- mkinmod( @@ -54,9 +56,9 @@ FOMC_SFO <- mkinmod( DFOP_SFO <- mkinmod( parent = mkinsub("FOMC", "m1"), m1 = mkinsub("SFO")) -t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D)))[["elapsed"]] -t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(subset(FOCUS_2006_D, value != 0)), error_model = "tc"))[["elapsed"]] -t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D), error_model = "obs"))[["elapsed"]] +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"]] # Two metabolites, synthetic data m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"), @@ -83,7 +85,7 @@ t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_mod 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) -mkin_benchmarks +mkin_benchmarks[, -c(1:3)] save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda") diff --git a/vignettes/web_only/benchmarks.html b/vignettes/web_only/benchmarks.html index 054b4afc..c80a7e44 100644 --- a/vignettes/web_only/benchmarks.html +++ b/vignettes/web_only/benchmarks.html @@ -1,17 +1,17 @@ <!DOCTYPE html> -<html xmlns="http://www.w3.org/1999/xhtml"> +<html> <head> <meta charset="utf-8" /> -<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <meta name="generator" content="pandoc" /> +<meta http-equiv="X-UA-Compatible" content="IE=EDGE" /> <meta name="author" content="Johannes Ranke" /> -<meta name="date" content="2019-05-02" /> +<meta name="date" content="2020-05-10" /> <title>Benchmark timings for mkin on various systems</title> @@ -69,8 +69,6 @@ overflow: auto; margin-left: 2%; position: fixed; border: 1px solid #ccc; -webkit-border-radius: 6px; -moz-border-radius: 6px; border-radius: 6px; } @@ -98,10 +96,15 @@ font-size: 12px; .tocify-subheader .tocify-subheader { text-indent: 30px; } - .tocify-subheader .tocify-subheader .tocify-subheader { text-indent: 40px; } +.tocify-subheader .tocify-subheader .tocify-subheader .tocify-subheader { +text-indent: 50px; +} +.tocify-subheader .tocify-subheader .tocify-subheader .tocify-subheader .tocify-subheader { +text-indent: 60px; +} .tocify .tocify-item > a, .tocify .nav-list .nav-header { margin: 0px; @@ -504,13 +507,13 @@ float: none; item.append($("<a/>", { - "text": self.text() + "html": self.html() })); } else { - item.text(self.text()); + item.html(self.html()); } @@ -1285,7 +1288,7 @@ window.initializeCodeFolding = function(show) { // create a collapsable div to wrap the code in var div = $('<div class="collapse r-code-collapse"></div>'); - if (show) + if (show || $(this)[0].classList.contains('fold-show')) div.addClass('in'); var id = 'rcode-643E0F36' + currentIndex++; div.attr('id', id); @@ -1401,7 +1404,6 @@ code { } img { max-width:100%; - height: auto; } .tabbed-pane { padding-top: 12px; @@ -1463,6 +1465,7 @@ summary { border: none; display: inline-block; border-radius: 4px; + background-color: transparent; } .tabset-dropdown > .nav-tabs.nav-tabs-open > li { @@ -1475,56 +1478,12 @@ summary { } </style> -<script> -$(document).ready(function () { - window.buildTabsets("TOC"); -}); - -$(document).ready(function () { - $('.tabset-dropdown > .nav-tabs > li').click(function () { - $(this).parent().toggleClass('nav-tabs-open') - }); -}); -</script> - <!-- code folding --> <style type="text/css"> .code-folding-btn { margin-bottom: 4px; } </style> -<script> -$(document).ready(function () { - window.initializeCodeFolding("show" === "show"); -}); -</script> - - - -<script> -$(document).ready(function () { - // move toc-ignore selectors from section div to header - $('div.section.toc-ignore') - .removeClass('toc-ignore') - .children('h1,h2,h3,h4,h5').addClass('toc-ignore'); - // establish options - var options = { - selectors: "h1,h2,h3", - theme: "bootstrap3", - context: '.toc-content', - hashGenerator: function (text) { - return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase(); - }, - ignoreSelector: ".toc-ignore", - scrollTo: 0 - }; - options.showAndHide = true; - options.smoothScroll = true; - - // tocify - var toc = $("#TOC").tocify(options).data("toc-tocify"); -}); -</script> <style type="text/css"> @@ -1538,6 +1497,12 @@ $(document).ready(function () { } } +@media print { +.toc-content { + /* see https://github.com/w3c/csswg-drafts/issues/4434 */ + float: right; +} +} .toc-content { padding-left: 30px; @@ -1573,8 +1538,6 @@ div.tocify { .tocify-subheader .tocify-item { font-size: 0.90em; - padding-left: 25px; - text-indent: 0; } .tocify .list-group-item { @@ -1620,7 +1583,7 @@ div.tocify { <h1 class="title toc-ignore">Benchmark timings for mkin on various systems</h1> <h4 class="author">Johannes Ranke</h4> -<h4 class="date">2019-05-02</h4> +<h4 class="date">2020-05-10</h4> </div> @@ -1640,11 +1603,16 @@ if (mkin_version > "0.9.48.1") { } else { mmkin_bench <- function(models, datasets, error_model = NULL) mmkin(models, datasets, reweight.method = error_model, cores = 1, quiet = TRUE) }</code></pre> -<pre class="r"><code># Parent only -t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D)))[["elapsed"]] -t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D), error_model = "tc"))[["elapsed"]]</code></pre> +<pre class="r"><code>FOCUS_C <- FOCUS_2006_C +FOCUS_D <- subset(FOCUS_2006_D, value != 0) +# Parent only +t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_C, FOCUS_D)))[["elapsed"]] +t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_C, FOCUS_D), error_model = "tc"))[["elapsed"]]</code></pre> <pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge: -## false convergence (8)</code></pre> +## 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)</code></pre> <pre class="r"><code># One metabolite SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), @@ -1658,25 +1626,11 @@ SFO_SFO <- mkinmod( parent = mkinsub("FOMC", "m1"), m1 = mkinsub("SFO"))</code></pre> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<pre class="r"><code>t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D)))[["elapsed"]]</code></pre> -<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data</code></pre> -<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data - -## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data</code></pre> -<pre class="r"><code>t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(subset(FOCUS_2006_D, value != 0)), error_model = "tc"))[["elapsed"]] -t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D), error_model = "obs"))[["elapsed"]]</code></pre> -<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data - -## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data - -## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data</code></pre> -<pre class="r"><code># Two metabolites, synthetic data +<pre class="r"><code>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"]] + +# Two metabolites, synthetic data m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"), M1 = mkinsub("SFO", "M2"), M2 = mkinsub("SFO"), @@ -1701,91 +1655,70 @@ t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_ 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) -mkin_benchmarks</code></pre> -<pre><code>## CPU -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 AMD Ryzen 7 1700 Eight-Core Processor -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 AMD Ryzen 7 1700 Eight-Core Processor -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 AMD Ryzen 7 1700 Eight-Core Processor -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 AMD Ryzen 7 1700 Eight-Core Processor -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 AMD Ryzen 7 1700 Eight-Core Processor -## OS -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 Linux -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 Linux -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 Linux -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 Linux -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 Linux -## mkin -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 0.9.48.1 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 0.9.49.1 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 0.9.49.2 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 0.9.49.3 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 0.9.49.4 -## t1 +mkin_benchmarks[, -c(1:3)]</code></pre> +<pre><code>## t1 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.610 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.023 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 1.658 ## t2 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.409 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 3.820 ## t3 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.283 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 3.424 ## t4 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 8.461 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 14.531 -## t5 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.744 -## t6 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.518 -## t7 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.211 -## t8 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.02 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.557 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 18.375 +## t5 t6 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 2.623 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 2.542 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 2.723 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 2.643 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002 2.635 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 7.480 2.188 +## t7 t8 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 7.525 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 4.632 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 4.862 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374 7.02 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259 4.737 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 3.69 3.87 ## t9 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.171 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.618 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.739 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.763 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 8.872 ## t10 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.413 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 6.257 ## t11 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 5.636 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.574 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.365 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.588</code></pre> +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.626 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50 9.289</code></pre> <pre class="r"><code>save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")</code></pre> </div> @@ -1809,6 +1742,54 @@ $(document).ready(function () { </script> +<!-- tabsets --> + +<script> +$(document).ready(function () { + window.buildTabsets("TOC"); +}); + +$(document).ready(function () { + $('.tabset-dropdown > .nav-tabs > li').click(function () { + $(this).parent().toggleClass('nav-tabs-open') + }); +}); +</script> + +<!-- code folding --> +<script> +$(document).ready(function () { + window.initializeCodeFolding("show" === "show"); +}); +</script> + +<script> +$(document).ready(function () { + + // move toc-ignore selectors from section div to header + $('div.section.toc-ignore') + .removeClass('toc-ignore') + .children('h1,h2,h3,h4,h5').addClass('toc-ignore'); + + // establish options + var options = { + selectors: "h1,h2,h3", + theme: "bootstrap3", + context: '.toc-content', + hashGenerator: function (text) { + return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase(); + }, + ignoreSelector: ".toc-ignore", + scrollTo: 0 + }; + options.showAndHide = true; + options.smoothScroll = true; + + // tocify + var toc = $("#TOC").tocify(options).data("toc-tocify"); +}); +</script> + <!-- dynamically load mathjax for compatibility with self-contained --> <script> (function () { |