Import saemix for easier profiling, update online docs

6 files changed, 13 insertions, 134 deletions

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
 ```