From 679cf716192cdfd91dfd232578cbd4e30d7eac12 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 15 Nov 2022 08:01:52 +0100 Subject: Import saemix for easier profiling, update online docs --- NAMESPACE | 1 + R/saem.R | 3 +- docs/dev/articles/web_only/benchmarks.html | 29 +++--- docs/dev/articles/web_only/saem_benchmarks.html | 29 +++--- docs/dev/pkgdown.yml | 2 +- docs/dev/reference/Rplot001.png | Bin 1011 -> 22432 bytes docs/dev/reference/logLik.saem.mmkin.html | 5 +- docs/dev/reference/mkinpredict.html | 13 ++- docs/dev/reference/saem.html | 11 ++- log/test.log | 16 ++-- vignettes/web_only/benchmarks.rmd | 2 +- vignettes/web_only/mkin_benchmarks.rda | Bin 1597 -> 1586 bytes vignettes/web_only/saem_benchmarks.R | 121 ------------------------ vignettes/web_only/saem_benchmarks.html | 22 ++--- vignettes/web_only/saem_benchmarks.rda | Bin 366 -> 359 bytes vignettes/web_only/saem_benchmarks.rmd | 2 +- 16 files changed, 76 insertions(+), 180 deletions(-) delete mode 100644 vignettes/web_only/saem_benchmarks.R 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 @@ Example evaluation of NAFTA SOP Attachment examples
  • - Some benchmark timings + Benchmark timings for mkin +
    • +
  • + Benchmark timings for saem.mmkin
    • @@ -109,7 +112,7 @@

    Benchmark timings for mkin

    Johannes Ranke

    -

    Last change 14 July 2022 (rebuilt 2022-11-14)

    +

    Last change 14 July 2022 (rebuilt 2022-11-15)

    Source: vignettes/web_only/benchmarks.rmd @@ -348,8 +351,8 @@ Ryzen 7 1700 4.2.2 1.2.0 -2.030 -3.791 +2.129 +3.784 @@ -527,9 +530,9 @@ Ryzen 7 1700 4.2.2 1.2.0 -1.579 -6.591 -3.107 +1.559 +6.097 +2.841 @@ -761,12 +764,12 @@ Ryzen 7 1700 4.2.2 1.2.0 -0.915 -1.426 -1.613 -3.224 -2.068 -2.962 +0.911 +1.328 +1.519 +2.986 +1.957 +2.769 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 @@ Example evaluation of NAFTA SOP Attachment examples
  • - Some benchmark timings + Benchmark timings for mkin +
    • +
  • + Benchmark timings for saem.mmkin
    • @@ -109,7 +112,7 @@

    Benchmark timings for saem.mmkin

    Johannes Ranke

    -

    Last change 14 November 2022 (rebuilt 2022-11-14)

    +

    Last change 14 November 2022 (rebuilt 2022-11-15)

    Source: vignettes/web_only/saem_benchmarks.rmd @@ -306,10 +309,10 @@ Linux 1.2.0 3.2 -2.589 -4.945 -4.786 -4.484 +2.11 +4.632 +4.264 +4.93

    Two-component error fits for SFO, DFOP, SFORB and HS.

    @@ -329,10 +332,10 @@ Linux 1.2.0 3.2 -5.645 -8.115 -7.737 -7.782 +5.602 +7.373 +7.815 +7.831 @@ -354,8 +357,8 @@ Linux 1.2.0 3.2 -25.921 -766.034 +24.014 +749.699 @@ -376,7 +379,7 @@ Linux 1.2.0 3.2 -1269.799 +1249.834 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 Binary files a/docs/dev/reference/Rplot001.png and b/docs/dev/reference/Rplot001.png differ 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 @@ Example evaluation of NAFTA SOP Attachment examples
  • - Some benchmark timings + Benchmark timings for mkin +
    • +
  • + Benchmark timings for saem.mmkin
  • 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.">Example evaluation of NAFTA SOP Attachment examples
  • - Some benchmark timings + Benchmark timings for mkin +
    • +
  • + Benchmark timings for saem.mmkin
  • @@ -371,10 +374,10 @@ as these always return mapped output.

    } #> Loading required package: rbenchmark #> test relative elapsed -#> 2 deSolve_compiled 1.00 0.004 -#> 4 analytical 5.25 0.021 -#> 1 eigen 6.00 0.024 -#> 3 deSolve 52.50 0.210 +#> 2 deSolve_compiled 1.0 0.005 +#> 1 eigen 4.2 0.021 +#> 4 analytical 4.2 0.021 +#> 3 deSolve 40.8 0.204 # \dontrun{ # Predict from a fitted model 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).">Example evaluation of NAFTA SOP Attachment examples
  • - Some benchmark timings + Benchmark timings for mkin +
    • +
  • + Benchmark timings for saem.mmkin
  • @@ -429,8 +432,8 @@ using mmkin.

    #> saemix version used for fitting: 3.2 #> mkin version used for pre-fitting: 1.2.0 #> R version used for fitting: 4.2.2 -#> Date of fit: Mon Nov 14 21:06:30 2022 -#> Date of summary: Mon Nov 14 21:06:30 2022 +#> Date of fit: Tue Nov 15 00:45:58 2022 +#> Date of summary: Tue Nov 15 00:45:58 2022 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -445,7 +448,7 @@ using mmkin.

    #> #> Model predictions using solution type analytical #> -#> Fitted in 9.625 s +#> Fitted in 9.189 s #> Using 300, 100 iterations and 10 chains #> #> Variance model: Constant variance 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 Binary files a/vignettes/web_only/mkin_benchmarks.rda and b/vignettes/web_only/mkin_benchmarks.rda differ 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 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SF Linux 1.2.0 3.2 -3.025 -5.237 -5.459 -5.218 +2.996 +5.207 +5.317 +5.171 @@ -1808,10 +1808,10 @@ t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SF Linux 1.2.0 3.2 -5.645 -7.726 -7.952 -8.104 +5.671 +7.696 +8.166 +8.168 @@ -1836,8 +1836,8 @@ t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SF Linux 1.2.0 3.2 -24.84 -816.153 +24.883 +818.157 @@ -1861,7 +1861,7 @@ t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc["SF Linux 1.2.0 3.2 -1323.128 +1355.036 diff --git a/vignettes/web_only/saem_benchmarks.rda b/vignettes/web_only/saem_benchmarks.rda index 1e75b20d..e8b139da 100644 Binary files a/vignettes/web_only/saem_benchmarks.rda and b/vignettes/web_only/saem_benchmarks.rda differ 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 ``` -- cgit v1.2.1