Rerun benchmarks on desktop computer

6 files changed, 193 insertions, 15 deletions

diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 2f7730bd..4e0cbba7 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -105,7 +105,7 @@
       <h1 data-toc-skip>Benchmark timings for mkin</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 1 July 2022 (rebuilt 2022-07-08)</h4>
+            <h4 data-toc-skip class="date">Last change 1 July 2022 (rebuilt 2022-07-12)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small>
       <div class="hidden name"><code>benchmarks.rmd</code></div>
@@ -317,6 +317,14 @@
 <td align="right">1.644</td>
 <td align="right">3.172</td>
 </tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Ryzen 7 1700</td>
+<td align="left">4.2.1</td>
+<td align="left">1.1.1</td>
+<td align="right">1.809</td>
+<td align="right">3.468</td>
+</tr>
 </tbody>
 </table>
 </div>
@@ -470,6 +478,15 @@
 <td align="right">5.839</td>
 <td align="right">2.444</td>
 </tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Ryzen 7 1700</td>
+<td align="left">4.2.1</td>
+<td align="left">1.1.1</td>
+<td align="right">1.336</td>
+<td align="right">5.820</td>
+<td align="right">2.621</td>
+</tr>
 </tbody>
 </table>
 </div>
@@ -671,6 +688,18 @@
 <td align="right">1.658</td>
 <td align="right">2.472</td>
 </tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Ryzen 7 1700</td>
+<td align="left">4.2.1</td>
+<td align="left">1.1.1</td>
+<td align="right">0.707</td>
+<td align="right">1.148</td>
+<td align="right">1.339</td>
+<td align="right">2.812</td>
+<td align="right">1.752</td>
+<td align="right">2.594</td>
+</tr>
 </tbody>
 </table>
 </div>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 19332d6b..87309c06 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
   benchmarks: web_only/benchmarks.html
   compiled_models: web_only/compiled_models.html
   dimethenamid_2018: web_only/dimethenamid_2018.html
-last_built: 2022-07-08T15:33Z
+last_built: 2022-07-12T10:10Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/vignettes/mkin.html b/vignettes/mkin.html
index 1f35e9bd..0d5ed6fc 100644
--- a/vignettes/mkin.html
+++ b/vignettes/mkin.html
@@ -1303,6 +1303,8 @@ window.initializeCodeFolding = function(show) {
   // select all R code blocks
   var rCodeBlocks = $('pre.r, pre.python, pre.bash, pre.sql, pre.cpp, pre.stan, pre.julia, pre.foldable');
   rCodeBlocks.each(function() {
+    // skip if the block has fold-none class
+    if ($(this).hasClass('fold-none')) return;
 
     // create a collapsable div to wrap the code in
     var div = $('<div class="collapse r-code-collapse"></div>');
@@ -1318,7 +1320,9 @@ window.initializeCodeFolding = function(show) {
     showCodeButton.append(showCodeText);
     showCodeButton
         .attr('data-toggle', 'collapse')
+        .attr('data-bs-toggle', 'collapse') // BS5
         .attr('data-target', '#' + id)
+        .attr('data-bs-target', '#' + id)   // BS5
         .attr('aria-expanded', showThis)
         .attr('aria-controls', id);
 
@@ -1402,6 +1406,7 @@ if (window.hljs) {
 
 
 
+
 <style type="text/css">
 .main-container {
   max-width: 940px;
@@ -1423,6 +1428,9 @@ button.code-folding-btn:focus {
 summary {
   display: list-item;
 }
+details > summary > p:only-child {
+  display: inline;
+}
 pre code {
   padding: 0;
 }
@@ -1580,7 +1588,7 @@ div.tocify {
 <div id="header">
 
 <div class="btn-group pull-right float-right">
-<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>
+<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm dropdown-toggle" data-toggle="dropdown" data-bs-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>
 <ul class="dropdown-menu dropdown-menu-right" style="min-width: 50px;">
 <li><a id="rmd-show-all-code" href="#">Show All Code</a></li>
 <li><a id="rmd-hide-all-code" href="#">Hide All Code</a></li>
@@ -1591,7 +1599,7 @@ div.tocify {
 
 <h1 class="title toc-ignore">Introduction to mkin</h1>
 <h4 class="author">Johannes Ranke</h4>
-<h4 class="date">Last change 15 February 2021 (rebuilt 2022-03-02)</h4>
+<h4 class="date">Last change 15 February 2021 (rebuilt 2022-07-12)</h4>
 
 </div>
 
diff --git a/vignettes/web_only/benchmarks.R b/vignettes/web_only/benchmarks.R
new file mode 100644
index 00000000..c9ba5be3
--- /dev/null
+++ b/vignettes/web_only/benchmarks.R
@@ -0,0 +1,112 @@
+## ---- include = FALSE---------------------------------------------------------
+library(knitr)
+opts_chunk$set(tidy = FALSE, cache = FALSE)
+library("mkin")
+
+## ----include = FALSE----------------------------------------------------------
+cpu_model <- benchmarkme::get_cpu()$model_name
+# Abbreviate CPU identifiers
+cpu_model <- gsub("AMD ", "", cpu_model)
+cpu_model <- gsub("Intel\\(R\\) Core\\(TM\\) ", "", cpu_model)
+cpu_model <- gsub(" Eight-Core Processor", "", cpu_model)
+cpu_model <- gsub(" CPU @ 2.50GHz", "", cpu_model)
+
+operating_system <- Sys.info()[["sysname"]]
+mkin_version <- as.character(packageVersion("mkin"))
+R_version <- paste0(R.version$major, ".", R.version$minor)
+system_string <- paste0(operating_system, ", ", cpu_model, ", mkin ", mkin_version, ", R ", R_version)
+
+benchmark_path = normalizePath("~/git/mkin/vignettes/web_only/mkin_benchmarks.rda")
+load(benchmark_path)
+
+# Used for reformatting the data on 2022-06-30
+# mkin_benchmarks[, "R"] <- NA
+# mkin_benchmarks <- mkin_benchmarks[c(2, 1, 15, 3, 4:14)]
+# mkin_benchmarks[, "CPU"] <- gsub("AMD.*", "Ryzen 7 1700", mkin_benchmarks[, "CPU"])
+# mkin_benchmarks[, "CPU"] <- gsub("Intel.*", "i7-4710MQ", mkin_benchmarks[, "CPU"])
+# rownames(mkin_benchmarks) <- gsub("AMD Ryzen 7 1700 Eight-Core Processor", "Ryzen 7 1700", rownames(mkin_benchmarks))
+# rownames(mkin_benchmarks) <- gsub("Intel\\(R\\) Core\\(TM\\) i7-4710MQ CPU @ 2.50GHz", "i7-4710MQ", rownames(mkin_benchmarks))
+# rownames(mkin_benchmarks) <- gsub(" version", "", rownames(mkin_benchmarks))
+
+mkin_benchmarks[system_string, c("CPU", "OS", "mkin", "R")] <-
+  c(cpu_model, operating_system, mkin_version, R_version)
+
+if (mkin_version > "0.9.48.1") {
+  mmkin_bench <- function(models, datasets, error_model = "const") {
+    mmkin(models, datasets, error_model = error_model, cores = 1, quiet = TRUE)
+  }
+} else {
+  mmkin_bench <- function(models, datasets, error_model = NULL) {
+    mmkin(models, datasets, reweight.method = error_model, cores = 1, quiet = TRUE)
+  }
+}
+
+## ----parent_only, warning = FALSE---------------------------------------------
+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"]]
+
+## ----one_metabolite, message = FALSE------------------------------------------
+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"]]
+t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
+    error_model = "obs"))[["elapsed"]]
+
+## ----two_metabolites, message = FALSE-----------------------------------------
+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)
+
+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"]]
+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"]]
+
+## ----results------------------------------------------------------------------
+mkin_benchmarks[system_string, paste0("t", 1:11)] <-
+  c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
+save(mkin_benchmarks, file = benchmark_path)
+# Hide rownames from kable for results section
+rownames(mkin_benchmarks) <- NULL
+
+## ---- echo = FALSE------------------------------------------------------------
+kable(mkin_benchmarks[, c(1:4, 5:6)])
+
+## ---- echo = FALSE------------------------------------------------------------
+kable(mkin_benchmarks[, c(1:4, 7:9)])
+
+## ---- echo = FALSE------------------------------------------------------------
+kable(mkin_benchmarks[, c(1:4, 10:15)])
+
diff --git a/vignettes/web_only/benchmarks.html b/vignettes/web_only/benchmarks.html
index 9923a8fa..4afe49c4 100644
--- a/vignettes/web_only/benchmarks.html
+++ b/vignettes/web_only/benchmarks.html
@@ -1599,7 +1599,7 @@ div.tocify {
 
 <h1 class="title toc-ignore">Benchmark timings for mkin</h1>
 <h4 class="author">Johannes Ranke</h4>
-<h4 class="date">Last change 1 July 2022 (rebuilt 2022-07-08)</h4>
+<h4 class="date">Last change 1 July 2022 (rebuilt 2022-07-12)</h4>
 
 </div>
 
@@ -1799,8 +1799,16 @@ rownames(mkin_benchmarks) &lt;- NULL</code></pre>
 <td align="left">i7-4710MQ</td>
 <td align="left">4.2.1</td>
 <td align="left">1.1.1</td>
-<td align="right">1.592</td>
-<td align="right">3.101</td>
+<td align="right">1.644</td>
+<td align="right">3.172</td>
+</tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Ryzen 7 1700</td>
+<td align="left">4.2.1</td>
+<td align="left">1.1.1</td>
+<td align="right">1.767</td>
+<td align="right">3.396</td>
 </tr>
 </tbody>
 </table>
@@ -1952,9 +1960,18 @@ rownames(mkin_benchmarks) &lt;- NULL</code></pre>
 <td align="left">i7-4710MQ</td>
 <td align="left">4.2.1</td>
 <td align="left">1.1.1</td>
-<td align="right">1.198</td>
-<td align="right">5.740</td>
-<td align="right">2.388</td>
+<td align="right">1.230</td>
+<td align="right">5.839</td>
+<td align="right">2.444</td>
+</tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Ryzen 7 1700</td>
+<td align="left">4.2.1</td>
+<td align="left">1.1.1</td>
+<td align="right">1.320</td>
+<td align="right">5.774</td>
+<td align="right">2.575</td>
 </tr>
 </tbody>
 </table>
@@ -2151,12 +2168,24 @@ rownames(mkin_benchmarks) &lt;- NULL</code></pre>
 <td align="left">i7-4710MQ</td>
 <td align="left">4.2.1</td>
 <td align="left">1.1.1</td>
-<td align="right">0.652</td>
-<td align="right">1.089</td>
+<td align="right">0.678</td>
+<td align="right">1.095</td>
 <td align="right">1.149</td>
-<td align="right">3.205</td>
-<td align="right">1.635</td>
-<td align="right">2.444</td>
+<td align="right">3.247</td>
+<td align="right">1.658</td>
+<td align="right">2.472</td>
+</tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Ryzen 7 1700</td>
+<td align="left">4.2.1</td>
+<td align="left">1.1.1</td>
+<td align="right">0.700</td>
+<td align="right">1.146</td>
+<td align="right">1.334</td>
+<td align="right">2.807</td>
+<td align="right">1.750</td>
+<td align="right">2.593</td>
 </tr>
 </tbody>
 </table>
diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda
index 3687ab8e..49a91664 100644
--- a/vignettes/web_only/mkin_benchmarks.rda
+++ b/vignettes/web_only/mkin_benchmarks.rda