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Changelog

Source: NEWS.md

babelmixr2 0.1.11.9000

  • Monolix: a mu-referenced parameter that stays inside exp() in the model (like cl <- exp(tcl + eta.cl) * (CRCL/100)^cl.crcl, or f(depot) <- exp(lfdepot)) was given a log-normal distribution while the model still took exp() of it, so exp() was applied twice. It is now a normal parameter on nlmixr2’s scale (its initial value, estimate and covariance too).

  • When lixoftConnectors cannot load or run a Monolix project, the error now includes Monolix’s reason (its [ERROR] lines) instead of “see Monolix’s [ERROR] above”.

  • Fixes found by running the NONMEM/Monolix stress kit with NONMEM 7.4:

    • nonmemControl(est="imp") and est="its" fits were always reported as unsuccessful; NONMEM ends them with “OPTIMIZATION WAS NOT TESTED FOR CONVERGENCE”, which is now read as finished.
    • nonmemControl(est="posthoc") fits could not be read (no #TERM: block and no parameter history).
    • Box-Cox, Yeo-Johnson and logit + Yeo-Johnson residual errors were rejected by NM-TRAN (IPRED redefined in nested/ELSE IF structures); the transformations are now written without nested IFs. They are still transform-both-sides (DV in CCONTR, IPRED in $ERROR). Predictions at or below sqrt(DBL_EPSILON) are floored like rxode2 instead of being set to -1000000000 (which gave lnorm() fits a huge objective function), and Box-Cox no longer divides by zero when lambda is 0.
    • The IPRED/PRED comparison with NONMEM now undoes the residual transformation first (NONMEM’s predictions are on the transformed scale).
    • Censored (CENS, CENS + LIMIT, LIMIT only) models were rejected by NM-TRAN (“random variable is defined in a nested IF structure”).
    • A $PK parameter changed later in the model (like if (SEX == 1) cl <- cl * 1.2) was changed in $DES, which NONMEM does not allow, and used undefined in $ERROR; it is now defined as RXPK_<name> in $PK.
    • Models without random effects are refused (NONMEM treats them as single-subject data, where METHOD=COND is invalid).

  • Monolix fixes found by running the NONMEM/Monolix stress kit:

    • Infusions given by rate (RATE) or duration (TINF) were written to the data but not declared in [CONTENT], so Monolix gave them as bolus doses.
    • Endpoints with dotted names (like concentration.in.plasma) kept the dots in the Monolix project (OUTPUT, observation names, predictions), which Monolix cannot load.
    • Reading a fit with a fixed parameter (like tfdepot <- fix(0.8)) failed with “subscript out of bounds”; Monolix’s covariance has only the estimated parameters.
    • A monolixControl(runCommand=) command that finished without writing Monolix’s output now stops with an error instead of waiting for it forever.

  • nonmemControl(cov="") now skips the covariance step as documented; before it gave an error because match.arg() cannot match "".

  • The NONMEM/Monolix stress test (inst/stress) is now a kit to run on a machine with NONMEM and/or Monolix: install-kit.R installs the versions to test, run-stress.R --check finds NONMEM/Monolix, and run-stress.R --kit runs every case end to end, checks that rxode2 reproduces the NONMEM/Monolix predictions and that a second fit reads the saved output, and zips the results to send back. New cases cover missing observations, evid=2, character IDs, time not starting at zero, extra data columns, a single subject, oral plus iv doses, ODE infusions (rate, steady state, modeled duration), two endpoints, bounded thetas, several covariates, models without random effects and the NONMEM/Monolix estimation options.

  • NONMEM control streams now use $ABBR PROTECT so NM-TRAN replaces LOG, EXP, SQRT, division and powers with NONMEM’s protected functions (NONMEM 7.4 or later). Turn it off with nonmemControl(protect=FALSE) or options(babelmixr2.nmProtect=FALSE). Since NM-TRAN writes B**E as PEXP(E*PLOG(B)), integer powers are written as products (or powers of x*x, which is never negative) and powers of a positive number with DEXP(). Functions of numbers (like exp(0), log(2*pi) or expit(0)) and divisions of numbers are written as numbers, and model variables named like a protected function (like plog) are renamed. babelmixr2’s own zero protection (protectZeros) is now only used with protect=FALSE, like for NONMEM before 7.4 (#62).

  • NONMEM control streams now explain the zero-protection code babelmixr2 adds: each RXDZ### IF block is preceded by a comment saying what it keeps the variable away from and why, as is the IF (W1 .EQ. 0.0) residual variance protection (#91). The protection for lfactorial()/lgamma1p() now keeps its argument above -1 (it previously clamped it just below -1, making x+1 negative), log(x) and 1/x no longer share one protected variable, so 1/x keeps the sign of a negative x, and a variable reassigned in the model is protected again instead of reusing the protection of its old value. Zero protection needed by f(), alag(), rate() or dur() (written in $PK) is no longer shared with other lines, which could use it before (or without) it being calculated.

  • est="pknca" now works with covariates in the data and with a mix of intravascular and extravascular doses (#102). Doses into a compartment that the observations are calculated from are intravascular. With both routes, ka is estimated from the extravascular doses and vc and cl from the intravascular doses. Intravascular bolus doses have the concentration at the time of dosing back-extrapolated (replacing a predose concentration at the first dose), and other doses have it imputed (as the predose concentration, or zero for the first dose). When no doses are only extravascular, ka is not updated. Multiple-dose data no longer need a concentration at each dose time; each dose until the next (with at least 2 concentrations) is used, with vc from the first dose of each route and cl from dosing intervals mostly covered by concentrations. Doses at the same time are combined.

  • When a NONMEM run fails, est="nonmem" now says why and where to look instead of failing with an unclear error: a run command that was not found or wrote no output, a NONMEM license problem, an NM-TRAN error in the control stream or the data, NONMEM not starting (for example a compiler problem), NONMEM crashing or stopping during estimation, and output babelmixr2 cannot read (#46).

  • est="pknca" now updates the initial estimates of models that are not mu-referenced, like ka <- tka * exp(eta.ka), instead of failing with “Must have names” (#101). When there is no vc, a central volume named v, V, Vc, VC, v1 or V1 (only one of them) now gets the NCA central volume estimate. Parameters defined as expit() of a theta are now transformed back correctly. A message lists the parameters that could not be updated.

  • NONMEM models can now use nested if/else if/else statements (and ifelse()): their branches are pruned with rxode2’s branch pruning before the model is translated to NONMEM (#11). With the default nonmemControl(prune="auto") a model whose if blocks are simple is still written with NONMEM IF blocks and only a model that needs it is pruned; prune=TRUE always prunes and prune=FALSE never prunes (the error for unsupported if/else statements suggests prune=TRUE).

  • monolixControl(prune=) has the same option for Monolix. Monolix writes if/elseif/else (and nested if) statements directly, so prune="auto" (the default) only prunes a model that uses ifelse(), which Monolix cannot write; prune=TRUE always prunes and prune=FALSE never prunes. A logical expression used as a number in a Monolix model is written as a 0/1 indicator variable (#11).

  • A logical expression used as a number in a NONMEM model (like cl <- tcl * (WT > 70)) is now written as a 0/1 indicator variable, since NONMEM cannot use a logical expression as a number. A numeric if () condition is written as not equal to zero.

  • est="nonmem" and est="monolix" fits with table=tableControl(cwres=TRUE) no longer fail with “objective function ‘FOCEi’ already present”. The fit keeps both the NONMEM (or Monolix) objective, which stays in use, and nlmixr2’s FOCEi objective (#94). as.nlmixr2() of a nonmem2rx or monolix2rx model now also keeps the imported objective in use with cwres=TRUE, and no longer fails after an earlier import with cwres=TRUE (it started from that fit’s etas).

  • est="monolix" now translates compartment properties (f(), alag(), rate() and dur()) that are expressions, like f(depot) <- exp(lfdepot), instead of erroring with “the complex F is not supported by babelmixr2” (#115). The expression is calculated in a new variable (like rx_f_depot) that the PK: macro uses. A property set only inside an if now keeps rxode2’s default otherwise (1 for f(), 0 for alag()) instead of being applied unconditionally.

  • The ACoP 2024 babelmixr2/PopED abstract (doi:10.70534/XUMG6226) is now in citation("babelmixr2"), the package description and the PopED article (#155).

  • as.nlmixr2() of a nonmem2rx model now stops with an informative error when the model still contains untranslated NONMEM residual variables (eps# or err#) instead of failing inside the estimation routine (#95).

  • popedControl(sigdig=) now sets the ODE solver tolerances itself (atol = rtol = 0.5*10^(-sigdig-2), the same values as before) instead of using rxode2::rxControl(sigdig=). rxode2 5.1.5 loosened the tolerances that rxControl(sigdig=) gives, which made the finite-difference FIM, and so the design OFV and RSEs, less accurate (#223).

  • est="nonmem" now fits censored data the way nlmixr2 does (#92). M3 (CENS), M4 (CENS with a finite LIMIT) and M2 (CENS=0 with a finite LIMIT, including data with a LIMIT but no CENS column) use F_FLAG likelihoods in $ERROR with LAPLACIAN estimation. A missing LIMIT is now written as NONMEM’s infinity instead of 0, CENS/LIMIT columns that do not censor anything are dropped, the objective function is adjusted so the log-likelihood includes the censored observations correctly, and censoring with a transformed endpoint (like lnorm()) is refused instead of giving the wrong likelihood. The censored observations are left out of the NONMEM PRED comparison since NONMEM’s PRED is their likelihood.

  • est="nonmem" and est="monolix" now fit linCmt() models. A pure linCmt() model uses NONMEM’s closed-form solutions (ADVAN1-ADVAN4, ADVAN11 or ADVAN12 with TRANS1 micro-constants) or Monolix’s pkmodel(); a model the closed form cannot represent (other ODEs, parameters that change with time, and for Monolix modeled rates or durations, doses into more than one compartment or amounts used in the model) is translated to ODEs with rxode2::linToOde(). nonmemControl(linCmt="ode") and monolixControl(linCmt="ode") always use ODEs. The closed-form solutions need an rxode2 with linCmtMicro(); with an older rxode2, linCmt() models use ODEs.

  • est="poped" now designs linCmt() models (translated to ODEs). est="nlmer", est="fmeMcmc" and est="pseudoOptim" are now tested with linCmt() models.

  • New NONMEM/Monolix stress test (inst/stress/), shared by the package tests and a command line runner (run-stress.R). The runner can also fit every case with NONMEM and/or Monolix end to end on a machine that has them, and optionally translate the nlmixr2lib models; see inst/stress/README.md.

  • The NONMEM data dropped the RATE, SS and II items: which items were written was decided from settings made only after the data were converted, so infusions, steady state doses and modeled rates or durations were written as plain bolus doses. The items are now kept when the data use them.

  • A steady state dose with a lag time (which rxode2 splits in two) is now written as one SS dose for NONMEM and Monolix, not as two bolus doses.

  • NONMEM now writes a modeled duration as Dn (it was DURn, which NONMEM does not know) and a modeled rate as Rn (it was dropped).

  • NONMEM now uses the NONMEM name of a mu-referenced covariate in $PK (like NLMIXRMUDERCOV1), matching $INPUT.

  • probitInv() (which rxode2 writes with erf()) now translates to NONMEM (PHI()) and Monolix (normcdf()).

  • est="monolix" now refuses models without between-subject variability, residual errors other than add(), prop() and add() + prop(), and transformations other than lnorm() and logitNorm() up front with a clear error. Before, a boxCox(), yeoJohnson() or logitNorm() residual stopped with “argument must be a character string”.

  • Monolix now separates the arguments of the empty() macro and the logitNormal distribution with commas.

  • rxode2’s normalized powers (Rx_pow_di(), Rx_pow()) now translate to NONMEM (**) and Monolix (^).

  • NONMEM and Monolix data without doses (like a $PRED model with the dose as a covariate) no longer stop with “undefined columns selected”.

  • est="nonmem" now refuses residual transformations it cannot write (like probitNorm()) up front; before, writing the files stopped with “can only write character objects”.

  • Monolix now applies a bioavailability or lag time to the doses of that compartment only; a property of a compartment without doses no longer stops with “values must be length 1”. A parameter written with brackets (like v <- (tv + eta.v)) is now a normal parameter, and an unsupported parameter transformation (like log10()) gives a clear error.

  • est="monolix" now spells a mu-referenced parameter with a . in its name (like the tainted rx__cl.wt, or ka.x <- exp(tka + eta.ka)) the same way in every section of the Monolix model (#220). The EQUATION: block already wrote it as rx__cl__wt, but input=, [INDIVIDUAL], <PARAMETER> and the output readers used rx__cl.wt, so Monolix saw an undeclared variable.

  • est="saemix" now fits linCmt() models. The prediction was looked up in a column named after the endpoint (rxLinCmt), which the solved model does not output, so saemix stopped with non-numeric argument to function (#212).

  • est="saemix" now fits models where a structural theta has no between-subject variability (e.g. v <- exp(tv)). Collecting the individual etas after the fit failed with invalid subscript type 'list' (#212).

  • est="saemix" now refuses a model it cannot fit, instead of fitting it with a different residual error. saemix fits one endpoint with an add(), prop(), add() + prop() (combined2, the only combination saemix has) or lnorm() residual error, or an ll() likelihood. A model with more than one endpoint (previously fit against predictions of zero), a combined1 add() + prop() (including saemixControl(addProp="combined1")), pow(), boxCox(), yeoJohnson(), a logit/probit transformation, lnorm() + prop() or a non-normal residual distribution now stops with an error, as does a fixed residual error or between-subject variability, which saemix would otherwise estimate anyway. The checks use the new rxode2 assertions assertRxUiTransform(), assertRxUiErrType(), assertRxUiAddProp(), assertRxUiNoFixedResiduals() and assertRxUiNoFixedOmega(), so this requires rxode2 5.1.8 (#212).

  • est="saemix" now fits lnorm() residual errors with saemix’s exponential error model; they were previously fit as an additive error with a missing starting value (#212).

  • est="monolix" now accepts normal priors from ini({}) and writes them as Monolix MAP estimation (#207). A parameter with a prior is estimated with method=MAP, and its prior is written to a [POPULATION] section of <MODEL>. Monolix’s prior on a typical value has the same distribution as the parameter itself, with its sd in the Gaussian space, so the prior mean is back-transformed like the estimate (exp(), expit(), probitInv()) while the prior sd is written as is: prior(tka) ~ dnorm(log(1.5), 0.5) becomes ka_pop = {distribution=logNormal, typical=1.5, sd=0.5}, the same distribution with no approximation. Covariate effects get a normal prior. Checked with Monolix 2024R1: tight priors pin ka_pop, cl_pop, a covariate effect and a logit-normal parameter at the prior mean, and a vague prior leaves the estimate at the MLE. Priors Monolix cannot honour are errors rather than being dropped: priors on omega elements or omega blocks, multivariate normal priors, non-normal priors, priors on a probitInv() parameter with bounds other than (0, 1), and priors on residual error parameters – Monolix accepts a MAP prior on add__sd but ignores it (every estimate identical to the run without it).

  • The “PRED absolute difference compared to Monolix PRED” line of a Monolix fit’s message is now an absolute difference (it printed a relative one). The covariance of a fit from Monolix 2020 or later now carries nlmixr2’s parameter names (tka, cl.wt) instead of Monolix’s (ka_pop, beta_cl_lWT), like fits from older Monolix versions already did.

  • Monolix projects with mu-referenced covariates (cl <- exp(tcl + eta.cl + cl.wt * lWT)) now load in Monolix. The covariate was missing from the [INDIVIDUAL] inputs (Monolix: Undefined variable 'lWT'), and when every covariate was mu-referenced the structural model got a regressor line with no name (= {use=regressor}, a syntax error). Reading the results of such a fit back failed with subscript out of bounds: the covariance looked up the covariate effect as NA_pop instead of beta_cl_lWT. The tests now replay Monolix 2024R1 runs, with and without MAP priors. When lixoftConnectors cannot load or run the project, nlmixr2() now stops with an error instead of waiting forever for output Monolix never writes.

  • est="nonmem" now runs models with ini({}) priors, translating them to NONMEM’s $PRIOR NWPRI (#205). Normal priors on population parameters (dnorm(), stdNormal(), the tcl + tv ~ c(...) joint normal) become $THETAP/$THETAPV, and invWishart(nu) degrees of freedom on an omega block become $OMEGAP/$OMEGAPD, with the block’s own initial estimate as the prior scale. NWPRI gives its priors to the first THETAs and the first omega blocks, so the parameters with a prior have to come first in ini({}); otherwise, and for priors NWPRI cannot express (dcauchy(), a normal prior directly on an omega element, which is TNPRI), the model is refused before any file is written instead of fitting a different prior. When the output is read back, the prior values NM-TRAN adds as extra THETAs and OMEGAs are dropped, and the objective function type says nwpri because NONMEM’s objective includes the prior.

  • $OMEGA BLOCK() records of 3 or more etas are now written in the order NONMEM reads them (row by row down the lower triangle). They used to be written column by column, so NONMEM started from the wrong initial omega values.

  • The $PROBLEM record of a generated NONMEM control stream now carries the model name ($PROBLEM one.cmt translated from babelmixr2). It read a misspelled getter and was always blank (#209). Because the control stream changes, an existing NONMEM export that has a .md5 hash file will not match and is re-run once in a new numbered directory. Moving past a second stale export (-001-nonmem also not matching) no longer hangs: the export directory kept its cached number and the hash check looped forever.

  • est="fmeMcmc" now uses priors declared in the model’s ini({}) block (for example prior(tka) ~ dnorm(0, 10)) instead of refusing the model. They become the prior function FME::modMCMC() samples with, evaluated with rxode2’s shared prior kernel on the natural parameter scale, even when scaleType makes FME sample a rescaled space. Supplying fmeMcmcControl(prior=) as well is an error rather than silently preferring one of them (#208).

  • nonmemControl(est="its") now writes $ESTIMATION METHOD=ITS INTERACTION (iterative two stage). It wrote METHOD=IMP, so NONMEM ran importance sampling while the returned fit was labelled with the nonmem its objective function type (#211).

  • A PopED design dataset that gives cmt as a compartment number (et(amt=180, cmt=1)) now doses the right compartment. et() keeps cmt as a character column, so rxode2::etTrans() read "1" as a compartment name, found no match and quietly moved the dose to an extra compartment; the design built without a warning but every prediction was zero and the FIM was degenerate (#201). This also works when the column mixes names and numbers, which is what a multiple endpoint design looks like when it names the endpoint on its observation records. A dosing record that still cannot be matched to a model compartment is now an error instead of a silently empty design.

  • A multiple endpoint PopED design can now name its endpoints with cmt (cmt="cp", cmt="eff") instead of dvid. The cmt fallback was already written but unreachable: a dataset without a dvid column stopped with attempt to select less than one element in get1index before it was tried. This applies to the usual design space; a design that gives per-ID sampling through popedControl(a=) still needs dvid.

  • The PopED model translation no longer drops the if () condition that guards an adaptive dosing call (evid_(), bolus(), infuse(), infuseDur(), reset(), …). The branch pruner used to flatten the model unconditionally, so a model like if (t <= 0) infuseDur(DOSE, TINF, cmt=1) pushed a dose at every design point instead of once (#131). The pruner’s capture protocol is now used and the guarded call is restored after the branches are flattened.

  • Added two PopED examples showing how to make the dosing regimen itself optimizable (#131):

    • inst/poped/ex.10.PKPD.HCV.dose-and-tinf.babelmixr2.R keeps the dose record and makes the amount and infusion duration design (a) variables via f(depot) <- DOSE (with amt=1) and dur(depot) <- TINF (with rate=-2).

    • inst/poped/ex.10.PKPD.HCV.adaptive-dosing.babelmixr2.R drops the dose records entirely and pushes the regimen from inside the model with infuseDur(), which makes the dosing interval a design variable as well. This one needs rxode2 > 5.1.7 (rxode2#1214).

    Both are optimized with poped_optim(..., opt_a=TRUE) and agree on the reference design (OFV 88.27).

  • The NONMEM/Monolix fit cache is now written with saveRDS() as <model>.rds / nlmixr.rds instead of qs2, so qs2 moved from Imports to Suggests. Existing run directories keep working: a .qs2 cache is read once (when qs2 is installed) and rewritten as the .rds, and if it cannot be read the fit is rebuilt from the run output as it would be for any missing cache.

  • 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.