R Under development (unstable) (2024-11-22 r87365 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(rxode2) rxode2 3.0.2 using 2 threads (see ?getRxThreads) no cache: create with `rxCreateCache()` > library(nlmixr2est) Loading required package: nlmixr2data Attaching package: 'nlmixr2est' The following objects are masked from 'package:rxode2': boxCox, yeoJohnson > verbose_minimization <- FALSE > test_check("nlmixr2est") R Under development (unstable) (2024-11-22 r87365 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(nlmixr2est) Loading required package: nlmixr2data > rxode2::rxClean() > one.cmt <- function() { + ini({ + tka <- 0.45 + tcl <- log(c(0, 2.7, 100)) + tv <- 3.45 + eta.ka ~ 0.6 + eta.cl ~ 0.3 + eta.v ~ 0.1 + add.sd <- 0.7 + }) + model({ + ka <- exp(tka + eta.ka) + cl <- exp(tcl + eta.cl) + v <- exp(tv + eta.v) + linCmt() ~ add(add.sd) + }) + } > fit <- nlmixr(one.cmt, theo_sd, est = "saem", control = saemControl(print = 0, + nBurn = 1, nEm = 1)) ℹ parameter labels from comments are typically ignored in non-interactive mode ℹ Need to run with the source intact to parse comments → loading into symengine environment... → pruning branches (`if`/`else`) of saem model... ✔ done → finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 ✔ done using C compiler: 'gcc.exe (GCC) 13.3.0' ℹ calculate uninformed etas ℹ done rxode2 3.0.2 using 2 threads (see ?getRxThreads) no cache: create with `rxCreateCache()` Attaching package: 'rxode2' The following objects are masked from 'package:nlmixr2est': boxCox, yeoJohnson Calculating covariance matrix [====|====|====|====|====|====|====|====|====|====] 0:00:00 → loading into symengine environment... → pruning branches (`if`/`else`) of saem model... ✔ done → finding duplicate expressions in saem predOnly model 0... [====|====|====|====|====|====|====|====|====|====] 0:00:00 → finding duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 → finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 ✔ done using C compiler: 'gcc.exe (GCC) 13.3.0' → Calculating residuals/tables ✔ done → compress origData in nlmixr2 object, save 5952 → compress phiM in nlmixr2 object, save 280 → compress parHistData in nlmixr2 object, save 1864 → compress saem0 in nlmixr2 object, save 28224 > saveRDS(fit, "fit.rds") > > proc.time() user system elapsed 10.17 1.45 16.39 Calculating -2LL by Gaussian quadrature (nnodes=3,nsd=1.6) [====|====|====|====|====|====|====|====|====|====] 0:00:00 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.3.0' i calculate uninformed etas i done Calculating covariance matrix [====|====|====|====|====|====|====|====|====|====] 0:00:00 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem predOnly model 0... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.3.0' > compress origData in nlmixr2 object, save 7056 > compress phiM in nlmixr2 object, save 280 > compress parHistData in nlmixr2 object, save 1856 > compress saem0 in nlmixr2 object, save 21256 i change initial estimate of `covwt` to `100` > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.3.0' i calculate uninformed etas i done Calculating covariance matrix [====|====|====|====|====|====|====|====|====|====] 0:00:00 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem predOnly model 0... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.3.0' > compress origData in nlmixr2 object, save 7056 > compress phiM in nlmixr2 object, save 272 > compress parHistData in nlmixr2 object, save 1856 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.3.0' i calculate uninformed etas i done Calculating covariance matrix [====|====|====|====|====|====|====|====|====|====] 0:00:00 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem predOnly model 0... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.3.0' > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 5952 > compress phiM in nlmixr2 object, save 280 > compress parHistData in nlmixr2 object, save 1640 > compress saem0 in nlmixr2 object, save 13032 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done i calculate uninformed etas i done Calculating covariance matrix [====|====|====|====|====|====|====|====|====|====] 0:00:00 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem predOnly model 0... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 5952 > compress phiM in nlmixr2 object, save 280 > compress parHistData in nlmixr2 object, save 1640 > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > calculate jacobian > calculate d(f)/d(eta) [====|====|====|====|====|====|====|====|====|====] 0:00:00 > calculate d(R^2)/d(eta) [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in inner model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in inner model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in EBE model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in EBE model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > compiling inner model... using C compiler: 'gcc.exe (GCC) 13.3.0' v done > finding duplicate expressions in FD model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > compiling EBE model... using C compiler: 'gcc.exe (GCC) 13.3.0' v done > compiling events FD model... using C compiler: 'gcc.exe (GCC) 13.3.0' v done > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 5952 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.3.0' i calculate uninformed etas i done > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem predOnly model 0... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.3.0' > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 5952 > compress phiM in nlmixr2 object, save 1704 > compress parHistData in nlmixr2 object, save 1432 > compress saem0 in nlmixr2 object, save 24104 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem predOnly model 0... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.3.0' > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.3.0' i calculate uninformed etas i done > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem predOnly model 0... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 5952 > compress phiM in nlmixr2 object, save 680 > compress parHistData in nlmixr2 object, save 1440 i parameter labels from comments will be replaced by 'label()' using C compiler: 'gcc.exe (GCC) 13.3.0' i parameter labels from comments will be replaced by 'label()' > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done i calculate uninformed etas i done Calculating covariance matrix [====|====|====|====|====|====|====|====|====|====] 0:00:00 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem predOnly model 0... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.3.0' > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 3696 > compress phiM in nlmixr2 object, save 49608 > compress parHistData in nlmixr2 object, save 14872 > compress saem0 in nlmixr2 object, save 10528 i parameter labels from comments will be replaced by 'label()' > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done Calculating covariance matrix [====|====|====|====|====|====|====|====|====|====] 0:00:00 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem predOnly model 0... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 3696 > compress phiM in nlmixr2 object, save 44008 > compress parHistData in nlmixr2 object, save 14296 i parameter labels from comments will be replaced by 'label()' > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.3.0' i calculate uninformed etas i done Calculating covariance matrix [====|====|====|====|====|====|====|====|====|====] 0:00:00 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem predOnly model 0... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.3.0' > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 3696 > compress phiM in nlmixr2 object, save 48248 > compress parHistData in nlmixr2 object, save 14584 i parameter labels from comments will be replaced by 'label()' > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done Calculating covariance matrix [====|====|====|====|====|====|====|====|====|====] 0:00:00 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem predOnly model 0... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 3696 > compress phiM in nlmixr2 object, save 48664 > compress parHistData in nlmixr2 object, save 14600 [ FAIL 0 | WARN 1 | SKIP 0 | PASS 226 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 226 ] > ## test_check("nlmixr2est", stop_on_failure = FALSE, wrap=TRUE, > ## reporter = testthat::LocationReporter) > > proc.time() user system elapsed 274.67 22.39 377.01