Import saemix for easier profiling, update online docs

16 files changed, 76 insertions, 180 deletions

diff --git a/NAMESPACE b/NAMESPACE
index 9c85945e..107ffc54 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -160,6 +160,7 @@ importFrom(parallel,detectCores)
 importFrom(parallel,mclapply)
 importFrom(parallel,parLapply)
 importFrom(rlang,"!!!")
+importFrom(saemix,saemix)
 importFrom(stats,AIC)
 importFrom(stats,BIC)
 importFrom(stats,aggregate)
diff --git a/R/saem.R b/R/saem.R
index e980ed1f..696ea0ee 100644
--- a/R/saem.R
+++ b/R/saem.R
@@ -14,6 +14,7 @@ utils::globalVariables(c("predicted", "std"))
 #' using [mmkin].
 #'
 #' @importFrom utils packageVersion
+#' @importFrom saemix saemix
 #' @param object An [mmkin] row object containing several fits of the same
 #' [mkinmod] model to different datasets
 #' @param verbose Should we print information about created objects of
@@ -175,7 +176,7 @@ saem.mmkin <- function(object,
   fit_failed <- FALSE
   FIM_failed <- NULL
   fit_time <- system.time({
-    utils::capture.output(f_saemix <- try(saemix::saemix(m_saemix, d_saemix, control)), split = !quiet)
+    utils::capture.output(f_saemix <- try(saemix(m_saemix, d_saemix, control)), split = !quiet)
     if (inherits(f_saemix, "try-error")) fit_failed <- TRUE
   })
 
diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html
index cb048453..5c7aa3dc 100644
--- a/docs/dev/articles/web_only/benchmarks.html
+++ b/docs/dev/articles/web_only/benchmarks.html
@@ -78,7 +78,10 @@
       <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul>
 </li>
@@ -109,7 +112,7 @@
       <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 14 July 2022 (rebuilt 2022-11-14)</h4>
+            <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-11-15)</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>
@@ -348,8 +351,8 @@
 <td align="left">Ryzen 7 1700</td>
 <td align="left">4.2.2</td>
 <td align="left">1.2.0</td>
-<td align="right">2.030</td>
-<td align="right">3.791</td>
+<td align="right">2.129</td>
+<td align="right">3.784</td>
 </tr>
 </tbody>
 </table>
@@ -527,9 +530,9 @@
 <td align="left">Ryzen 7 1700</td>
 <td align="left">4.2.2</td>
 <td align="left">1.2.0</td>
-<td align="right">1.579</td>
-<td align="right">6.591</td>
-<td align="right">3.107</td>
+<td align="right">1.559</td>
+<td align="right">6.097</td>
+<td align="right">2.841</td>
 </tr>
 </tbody>
 </table>
@@ -761,12 +764,12 @@
 <td align="left">Ryzen 7 1700</td>
 <td align="left">4.2.2</td>
 <td align="left">1.2.0</td>
-<td align="right">0.915</td>
-<td align="right">1.426</td>
-<td align="right">1.613</td>
-<td align="right">3.224</td>
-<td align="right">2.068</td>
-<td align="right">2.962</td>
+<td align="right">0.911</td>
+<td align="right">1.328</td>
+<td align="right">1.519</td>
+<td align="right">2.986</td>
+<td align="right">1.957</td>
+<td align="right">2.769</td>
 </tr>
 </tbody>
 </table>
diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html
index 97ea6fd4..e54bc38c 100644
--- a/docs/dev/articles/web_only/saem_benchmarks.html
+++ b/docs/dev/articles/web_only/saem_benchmarks.html
@@ -78,7 +78,10 @@
       <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul>
 </li>
@@ -109,7 +112,7 @@
       <h1 data-toc-skip>Benchmark timings for saem.mmkin</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-14)</h4>
+            <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-15)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small>
       <div class="hidden name"><code>saem_benchmarks.rmd</code></div>
@@ -306,10 +309,10 @@
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">2.589</td>
-<td align="right">4.945</td>
-<td align="right">4.786</td>
-<td align="right">4.484</td>
+<td align="right">2.11</td>
+<td align="right">4.632</td>
+<td align="right">4.264</td>
+<td align="right">4.93</td>
 </tr></tbody>
 </table>
 <p>Two-component error fits for SFO, DFOP, SFORB and HS.</p>
@@ -329,10 +332,10 @@
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">5.645</td>
-<td align="right">8.115</td>
-<td align="right">7.737</td>
-<td align="right">7.782</td>
+<td align="right">5.602</td>
+<td align="right">7.373</td>
+<td align="right">7.815</td>
+<td align="right">7.831</td>
 </tr></tbody>
 </table>
 </div>
@@ -354,8 +357,8 @@
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">25.921</td>
-<td align="right">766.034</td>
+<td align="right">24.014</td>
+<td align="right">749.699</td>
 </tr></tbody>
 </table>
 </div>
@@ -376,7 +379,7 @@
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">1269.799</td>
+<td align="right">1249.834</td>
 </tr></tbody>
 </table>
 </div>
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index ad0d8b19..e0c11a84 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -13,7 +13,7 @@ articles:
   dimethenamid_2018: web_only/dimethenamid_2018.html
   multistart: web_only/multistart.html
   saem_benchmarks: web_only/saem_benchmarks.html
-last_built: 2022-11-14T20:49Z
+last_built: 2022-11-14T23:45Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index 17a35806..b3448db0 100644
--- a/docs/dev/reference/Rplot001.png
+++ b/docs/dev/reference/Rplot001.png
diff --git a/docs/dev/reference/logLik.saem.mmkin.html b/docs/dev/reference/logLik.saem.mmkin.html
index b1ea22ef..ebef3b10 100644
--- a/docs/dev/reference/logLik.saem.mmkin.html
+++ b/docs/dev/reference/logLik.saem.mmkin.html
@@ -59,7 +59,10 @@
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul></li>
 <li>
diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html
index 14f2b75b..37930912 100644
--- a/docs/dev/reference/mkinpredict.html
+++ b/docs/dev/reference/mkinpredict.html
@@ -61,7 +61,10 @@ kinetic parameters and initial values for the state variables."><meta name="robo
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul></li>
 <li>
@@ -371,10 +374,10 @@ as these always return mapped output.</p></dd>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: rbenchmark</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>               test relative elapsed</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled     1.00   0.004</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4       analytical     5.25   0.021</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1            eigen     6.00   0.024</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3          deSolve    52.50   0.210</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled      1.0   0.005</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1            eigen      4.2   0.021</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4       analytical      4.2   0.021</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3          deSolve     40.8   0.204</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span>  <span class="co"># Predict from a fitted model</span></span></span>
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index 968dc68c..73382cba 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -61,7 +61,10 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul></li>
 <li>
@@ -429,8 +432,8 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting:      3.2 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.2.0 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.2.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Mon Nov 14 21:06:30 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Mon Nov 14 21:06:30 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Tue Nov 15 00:45:58 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Tue Nov 15 00:45:58 2022 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
@@ -445,7 +448,7 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 9.625 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 9.189 s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 10 chains</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Constant variance </span>
diff --git a/log/test.log b/log/test.log
index f20a7f18..7005ac37 100644
--- a/log/test.log
+++ b/log/test.log
@@ -5,7 +5,7 @@
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         3 | Export dataset for reading into CAKE
 ✔ |        12 | Confidence intervals and p-values [1.0s]
-✔ |     1  12 | Dimethenamid data from 2018 [32.1s]
+✔ |     1  12 | Dimethenamid data from 2018 [32.4s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip ('test_dmta.R:98'): Different backends get consistent results for SFO-SFO3+, dimethenamid data
 Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
@@ -14,9 +14,9 @@ Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
 ✔ |         5 | Time step normalisation
 ✔ |         4 | Calculation of FOCUS chi2 error levels [0.6s]
 ✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
-✔ |         4 | Test fitting the decline of metabolites from their maximum [0.3s]
+✔ |         4 | Test fitting the decline of metabolites from their maximum [0.4s]
 ✔ |         1 | Fitting the logistic model [0.2s]
-✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [24.0s]
+✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [24.2s]
 ✔ |     1  12 | Nonlinear mixed-effects models [0.3s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip ('test_mixed.R:74'): saemix results are reproducible for biphasic fits
@@ -26,13 +26,13 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ✔ |        10 | Special cases of mkinfit calls [0.5s]
 ✔ |         3 | mkinfit features [0.7s]
 ✔ |         8 | mkinmod model generation and printing [0.2s]
-✔ |         3 | Model predictions with mkinpredict [0.4s]
-✔ |         7 | Multistart method for saem.mmkin models [36.7s]
+✔ |         3 | Model predictions with mkinpredict [0.3s]
+✔ |         7 | Multistart method for saem.mmkin models [36.9s]
 ✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.3s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.5s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.6s]
 ✔ |        16 | Plotting [9.8s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [66.4s]
+✔ |     1  36 | saemix parent models [66.3s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip ('test_saemix_parent.R:143'): We can also use mkin solution methods for saem
 Reason: This still takes almost 2.5 minutes although we do not solve ODEs
@@ -47,7 +47,7 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs
 ✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 211.1 s
+Duration: 211.7 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
diff --git a/vignettes/web_only/benchmarks.rmd b/vignettes/web_only/benchmarks.rmd
index de8ee723..117dc96a 100644
--- a/vignettes/web_only/benchmarks.rmd
+++ b/vignettes/web_only/benchmarks.rmd
@@ -141,7 +141,7 @@ t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
 ```{r results, include = FALSE}
 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)
+save(mkin_benchmarks, file = benchmark_path, version = 2)
 # Hide rownames from kable for results section
 rownames(mkin_benchmarks) <- NULL
 ```
diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda
index a0d4c72c..2d3deb26 100644
--- a/vignettes/web_only/mkin_benchmarks.rda
+++ b/vignettes/web_only/mkin_benchmarks.rda
diff --git a/vignettes/web_only/saem_benchmarks.R b/vignettes/web_only/saem_benchmarks.R
deleted file mode 100644
index 210e79e3..00000000
--- a/vignettes/web_only/saem_benchmarks.R
+++ /dev/null
@@ -1,121 +0,0 @@
-## ---- include = FALSE---------------------------------------------------------
-library("knitr") # For the kable() function
-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"))
-saemix_version <- as.character(packageVersion("saemix"))
-R_version <- paste0(R.version$major, ".", R.version$minor)
-system_string <- paste0(operating_system, ", ", cpu_model, ", mkin ", mkin_version, ", saemix ", saemix_version, ", R ", R_version)
-
-benchmark_path = normalizePath("~/git/mkin/vignettes/web_only/saem_benchmarks.rda")
-load(benchmark_path)
-
-# Initialization 14 November 2022
-#saem_benchmarks <- data.frame()
-
-saem_benchmarks[system_string, c("CPU", "OS", "mkin", "saemix", "R")] <-
-  c(cpu_model, operating_system, mkin_version, saemix_version, R_version)
-
-## ----setup--------------------------------------------------------------------
-n_cores <- parallel::detectCores()
-
-## ----dimethenamid_data--------------------------------------------------------
-dmta_ds <- lapply(1:7, function(i) {
-  ds_i <- dimethenamid_2018$ds[[i]]$data
-  ds_i[ds_i$name == "DMTAP", "name"] <-  "DMTA"
-  ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i]
-  ds_i
-})
-names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title)
-dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]])
-dmta_ds[["Elliot 1"]] <- NULL
-dmta_ds[["Elliot 2"]] <- NULL
-
-## ----parent_only--------------------------------------------------------------
-parent_mods <- c("SFO", "DFOP", "SFORB", "HS")
-parent_sep_const <- mmkin(parent_mods, dmta_ds, quiet = TRUE, cores = n_cores)
-parent_sep_tc <- update(parent_sep_const, error_model = "tc")
-
-t1 <- system.time(sfo_const <- saem(parent_sep_const["SFO", ]))[["elapsed"]]
-t2 <- system.time(dfop_const <- saem(parent_sep_const["DFOP", ]))[["elapsed"]]
-t3 <- system.time(sforb_const <- saem(parent_sep_const["SFORB", ]))[["elapsed"]]
-t4 <- system.time(hs_const <- saem(parent_sep_const["HS", ]))[["elapsed"]]
-t5 <- system.time(sfo_tc <- saem(parent_sep_tc["SFO", ]))[["elapsed"]]
-t6 <- system.time(dfop_tc <- saem(parent_sep_tc["DFOP", ]))[["elapsed"]]
-t7 <- system.time(sforb_tc <- saem(parent_sep_tc["SFORB", ]))[["elapsed"]]
-t8 <- system.time(hs_tc <- saem(parent_sep_tc["HS", ]))[["elapsed"]]
-
-## -----------------------------------------------------------------------------
-anova(
-  sfo_const, dfop_const, sforb_const, hs_const,
-  sfo_tc, dfop_tc, sforb_tc, hs_tc) |> kable(, digits = 1)
-
-## -----------------------------------------------------------------------------
-illparms(dfop_tc)
-illparms(sforb_tc)
-
-## ----one_metabolite, message = FALSE------------------------------------------
-one_met_mods <- list(
-  DFOP_SFO = mkinmod(
-    DMTA = mkinsub("DFOP", "M23"),
-    M23 = mkinsub("SFO")),
-  SFORB_SFO = mkinmod(
-    DMTA = mkinsub("SFORB", "M23"),
-    M23 = mkinsub("SFO")))
-
-one_met_sep_const <- mmkin(one_met_mods, dmta_ds, error_model = "const",
-  cores = n_cores, quiet = TRUE)
-one_met_sep_tc <- mmkin(one_met_mods, dmta_ds, error_model = "tc",
-  cores = n_cores, quiet = TRUE)
-
-t9 <- system.time(dfop_sfo_tc <- saem(one_met_sep_tc["DFOP_SFO", ],
-    no_random_effect = "log_k2"))[["elapsed"]]
-t10 <- system.time(sforb_sfo_tc <- saem(one_met_sep_tc["SFORB_SFO", ],
-    no_random_effect = "log_k_DMTA_bound_free"))[["elapsed"]]
-
-## -----------------------------------------------------------------------------
-illparms(sforb_sfo_tc)
-
-## ----three_metabolites, message = FALSE---------------------------------------
-three_met_mods <- list(
-  SFORB_SFO3_plus = mkinmod(
-    DMTA = mkinsub("SFORB", c("M23", "M27", "M31")),
-    M23 = mkinsub("SFO"),
-    M27 = mkinsub("SFO"),
-    M31 = mkinsub("SFO", "M27", sink = FALSE)))
-
-three_met_sep_tc <- mmkin(three_met_mods, dmta_ds, error_model = "tc",
-  cores = n_cores, quiet = TRUE)
-
-t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SFORB_SFO3_plus", ],
-    no_random_effect = "log_k_DMTA_bound_free"))[["elapsed"]]
-
-## ----results, include = FALSE-------------------------------------------------
-saem_benchmarks[system_string, paste0("t", 1:11)] <-
-  c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
-save(saem_benchmarks, file = benchmark_path)
-# Hide rownames from kable for results section
-rownames(saem_benchmarks) <- NULL
-
-## ---- echo = FALSE------------------------------------------------------------
-kable(saem_benchmarks[, c(1:4, 6:9)])
-
-## ---- echo = FALSE------------------------------------------------------------
-kable(saem_benchmarks[, c(1:4, 10:13)])
-
-## ---- echo = FALSE------------------------------------------------------------
-kable(saem_benchmarks[, c(1:4, 14:15)])
-
-## ---- echo = FALSE------------------------------------------------------------
-kable(saem_benchmarks[, c(1:4, 16)])
-
diff --git a/vignettes/web_only/saem_benchmarks.html b/vignettes/web_only/saem_benchmarks.html
index 42d6f71f..4875bb1b 100644
--- a/vignettes/web_only/saem_benchmarks.html
+++ b/vignettes/web_only/saem_benchmarks.html
@@ -1781,10 +1781,10 @@ t11 &lt;- system.time(sforb_sfo3_plus_const &lt;- saem(three_met_sep_tc[&quot;SF
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">3.025</td>
-<td align="right">5.237</td>
-<td align="right">5.459</td>
-<td align="right">5.218</td>
+<td align="right">2.996</td>
+<td align="right">5.207</td>
+<td align="right">5.317</td>
+<td align="right">5.171</td>
 </tr>
 </tbody>
 </table>
@@ -1808,10 +1808,10 @@ t11 &lt;- system.time(sforb_sfo3_plus_const &lt;- saem(three_met_sep_tc[&quot;SF
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">5.645</td>
-<td align="right">7.726</td>
-<td align="right">7.952</td>
-<td align="right">8.104</td>
+<td align="right">5.671</td>
+<td align="right">7.696</td>
+<td align="right">8.166</td>
+<td align="right">8.168</td>
 </tr>
 </tbody>
 </table>
@@ -1836,8 +1836,8 @@ t11 &lt;- system.time(sforb_sfo3_plus_const &lt;- saem(three_met_sep_tc[&quot;SF
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">24.84</td>
-<td align="right">816.153</td>
+<td align="right">24.883</td>
+<td align="right">818.157</td>
 </tr>
 </tbody>
 </table>
@@ -1861,7 +1861,7 @@ t11 &lt;- system.time(sforb_sfo3_plus_const &lt;- saem(three_met_sep_tc[&quot;SF
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">1323.128</td>
+<td align="right">1355.036</td>
 </tr>
 </tbody>
 </table>
diff --git a/vignettes/web_only/saem_benchmarks.rda b/vignettes/web_only/saem_benchmarks.rda
index 1e75b20d..e8b139da 100644
--- a/vignettes/web_only/saem_benchmarks.rda
+++ b/vignettes/web_only/saem_benchmarks.rda
diff --git a/vignettes/web_only/saem_benchmarks.rmd b/vignettes/web_only/saem_benchmarks.rmd
index 116713de..6e51fa66 100644
--- a/vignettes/web_only/saem_benchmarks.rmd
+++ b/vignettes/web_only/saem_benchmarks.rmd
@@ -164,7 +164,7 @@ t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SFORB_SFO3_pl
 ```{r results, include = FALSE}
 saem_benchmarks[system_string, paste0("t", 1:11)] <-
   c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
-save(saem_benchmarks, file = benchmark_path)
+save(saem_benchmarks, file = benchmark_path, version = 2)
 # Hide rownames from kable for results section
 rownames(saem_benchmarks) <- NULL
 ```