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Changelog

Source: NEWS.md

babelmixr2 0.1.11.9000

  • Each estimation method now carries type and description attributes so it appears in the category-grouped method list nlmixr2est prints for an unsupported est= (or a bare nlmixr2() call): nonmem, monolix, pknca, fmeMcmc and pseudoOptim under “External”, saemix under “Stochastic EM”, nlmer under “Integral approximation”, and poped under “Optimal Design”.

  • The mu-referenced covariate algorithm (muRefCovAlg) is now applied through the nlmixr2est preprocessing/post-final-object hooks instead of explicit nlmixr2est::.uiApplyMu2()/.uiFinalizeMu2() calls in the saemix, nonmem, monolix, and nlmer estimation methods (#184). The nonmem and monolix methods gained the mu method attribute so the hooks fire for them.

  • The nlmer estimation method now prints its iterations during the lme4::nlmer optimization and records a parameter history, both driven by the shared nlmixr2est nlm machinery (not lme4). Each recorded nlmerSolveGrad() evaluation logs the population parameter estimate (per-subject mean of the phi columns) into the resident nlm scale; the accumulated history is recovered via nlmixr2est::nlmGetParHist() and stored on the fit as parHistData. No objective column is shown (lme4 owns the deviance). Iteration printing defaults on (nlmerControl(print = 1L)). Requires nlmixr2est (>= 6.2.0).

  • The pseudoOptimControl() and fmeMcmcControl() functions now accept either the legacy scalar print / printNcol / useColor arguments or a pre-built nlmixr2est::iterPrintControl() object via print. Internally the control list stores a single iterPrintControl sub-list (matching the upstream nlmixr2est unification in nlmixr2est PR #651), so iteration output from these estimators uses the same shared C++ formatter as every other nlmixr2est estimator. Requires nlmixr2est (>= 6.0.1).

  • The iterPrintControl unification now also covers nlmerControl() and saemixControl(). nlmerControl() gains the standard print / printNcol / useColor arguments (or a pre-built nlmixr2est::iterPrintControl() object) and feeds the resulting iterPrintControl sub-list to the nlm C solving engine instead of a hard-coded print = 0L. saemixControl() absorbs its legacy print (logical), printNcol and useColor arguments into the same iterPrintControl sub-list; a nonzero every enables the saemix progress output.

  • Fix NONMEM export silently dropping the absorption lag (#190). A lag(depot)/alag(depot) assignment computed the lag parameter in $PK but never emitted the corresponding ALAG<n>= statement, so NONMEM fit the model without any lag. The lag value is now assigned to ALAG<n> in $PK.

  • NONMEM export now announces when a model variable is renamed because it collides with a NONMEM reserved name (e.g. a variable named alag becomes RXR1). The rename was previously silent (#190).

  • Added nlmer estimation method: fits nlmixr2 models via lme4::nlmer using analytical gradients from rxode2 sensitivity equations. Supports mu-referenced and non-mu-referenced random-effects models. Access via nlmixr(model, data, est = "nlmer"). The underlying lme4 fit is stored as fit$nlmer.

  • Fix integer type safety in C++ source: loop variables and size variables now use R_xlen_t (signed) or size_t (unsigned) instead of int/unsigned int where appropriate, preventing potential integer overflow and segfaults for vectors with more than 2^31 elements. The specific crash: in getDvid(), int j = cmtDvid.size() when cmtDvid.size() ≥ 2^31 wraps to INT_MIN, the subsequent decrement jumps to INT_MAX, and cmtDvid[INT_MAX] accesses memory far out of bounds.

  • Add bounds check in popedSolveIdME() and popedSolveIdME2() to verify that modelSwitch values are within the allocated matrix column dimensions (nend), in addition to the existing check against the number of unique IDs in the global time indexer.

  • Remove qs since it will be archived and replace with qs2.

  • Added saemix estimation method

babelmixr2 0.1.10

CRAN release: 2025-10-14

  • Bug fix for the new version of units (#179)

babelmixr2 0.1.9

CRAN release: 2025-08-31

  • Added estimation method fmeMcmc which runs FME::modMCMC(). It is also compatible with the coda package; you can convert with as.mcmc(fit) and then run coda tools like coda::raftery.diag(coda::as.mcmc(fit2)).

  • Added estimation method pseudoOptim which runs FME::pseudoOptim(). This estimation method requires all parameters to be bound.

  • Added bug fix for rstudio completion

babelmixr2 0.1.8

CRAN release: 2025-07-15

  • Maintenance fix for upcoming nlmixr2est and rxode2

babelmixr2 0.1.7

CRAN release: 2025-05-07

  • Maintenance fix for upcoming PKNCA

babelmixr2 0.1.6

CRAN release: 2025-01-20

  • Use new nlmixr2est covariate selection enforcement for babelmixr2

  • Fix a bug where the NONMEM export isn’t working well (#839)

  • Check loaded rxode2 information and compare to what the loaded model information should be. This allows better checking of which model is loaded and even more robust stability. It requires rxode2 > 3.0.2.

babelmixr2 0.1.5

CRAN release: 2024-11-06

  • Fix bug where PopED could error with certain dvid values

  • Fix bug where if/else clauses in the model could cause the model to not predict the values correctly.

  • Fix bug so that shrinkage() calculation works

  • Fix bug so that you can mix 2 different PopED data bases in an analysis without crashing R. While this didn’t occur with every database clash, it more frequently occurred when you interleaved PopED code between two different PopED databases, like in issue #131.

  • Added a new function babelBpopIdx(poped.db, "par") which will get the poped index for a model generated from babelmixr2, which is useful when calculating the power (as in example 11).

babelmixr2 0.1.4

CRAN release: 2024-09-23

  • Added experimental PopED integration

  • Removed dependence on rxode2parse

  • Imported monolix2rx from the monolix2rx package

  • Also allow conversion of a model imported from monolix to a nlmixr2 fit.

babelmixr2 0.1.3

  • Changed default NONMEM rounding protection to FALSE

  • Added a run option to the monolixControl() and nonemControl() in case you only want to export the modeling files and not run the models.

babelmixr2 0.1.2

CRAN release: 2023-12-12

  • Handle algebraic mu expressions

  • PKNCA controller now contains rxControl since it is used for some translation options

  • This revision will load the pruned ui model to query the compartment properties (i.e. bioavailability, lag time, etc) when writing out the NONMEM model. It should fix issues where the PK block does not define some of the variables and will have a larger calculated variable that can be used in the model instead.

  • When nonmem2rx has a different lst file, as long as nonmem2rx::nminfo(file) works, then a successful conversion to a nlmixr2 fit object will occur.

  • Fix to save parameter history into $parHistData to accommodate changes in focei’s output ($parHist is now derived).

  • Changed the solving options to match the new steady state options in rxode2 and how NONMEM implements them. Also changed the iwres model to account for the rxerr. instead of the err. which was updated in rxode2 as well.

babelmixr2 0.1.1

CRAN release: 2023-05-27

  • Add new method as.nlmixr2 to convert nonmem2rx methods to nlmixr fits

  • Dropped pmxTools in favor of nonmem2rx to conserve some of the methods

babelmixr2 0.1.0

CRAN release: 2022-10-28

  • Babelmixr has support for “monolix”, “nonmem”, and “pknca” methods on release.

  • Added a NEWS.md file to track changes to the package.