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Changelog

Source: NEWS.md

nlmixr2save 0.2.0

CRAN release: 2026-08-04

  • loadFit() (and therefore :=) now restores the fit table’s ID column as a factor. The table round-trips through a plain .csv, so ID came back as an integer while a live fit carries a factor; anything joining the fit table to something derived from the fit then hit a type mismatch, since nlme::augPred() keeps its id a factor. ggPMX::pmx_nlmixr() on a cached fit failed outright with “Incompatible join types: x.ID (factor) and i.ID (integer)”. The repair happens on load, so caches written by earlier versions are fixed too.

  • saveFit() now records the parHistData$type factor levels for fits that store parHistData compressed (the nlmixr2est default). It read the levels straight out of the fit environment, where a compressed fit keeps a raw vector rather than a data frame, so the levels were silently not recorded and loadFit() fell back to a hardcoded level list. nlmixr2est has since added types that list predates (“Analytic Gradient (relaxed)” and friends), and those came back as NA.

  • loadFit() now repairs a parHistData$type that the cache’s own restore script dropped to NA. Those levels are applied by the script stored inside the cache, so a cache written before nlmixr2est added a type has no level for it and coerces it to NA – and re-saving cannot recover it, because by then the string is already gone. loadFit() reads the column back from the -parHistData.csv in the cache and appends whatever the script was missing, so existing caches are repaired in place.

  • Saving or loading a fit no longer disturbs another cache whose base name it is a suffix of. The list of files belonging to a fit was matched with an unanchored pattern, so a cache named fit also matched myfit-env.R – zipping another cache’s files into its own archive and then deleting them from disk. This is reachable whenever unzipped files are lying around, which saveFit(zip=FALSE) leaves by design. The names are now matched literally rather than as a regexp, so a base name holding a metacharacter (my.fit is an ordinary R name, and as a pattern its . also matched my_fit) is matched exactly.

  • saveFit(fit, zip=FALSE) now actually leaves the fit unzipped for a fit table (a nlmixr2FitData). The method wrote the fit .csv and then called the core method with a hardcoded zip=TRUE, so the argument was silently ignored for every fit that carries data.

  • nlmixrDataSimplify() gained est and control arguments and no longer drops the covariate columns that est="vae" searches for. The VAE covariate search picks its covariates out of the data instead of out of the model, so the candidate columns (as identified by nlmixr2est::vaeCovariates(), matched to the vaeControl() search options) are now kept in the simplified data and included in the hash. When the installed nlmixr2est does not export vaeCovariates() the search is skipped rather than erroring.

  • You can now export a fit without the original data so a fitted model can be shared when the subject-level data cannot:

    • saveFit(fit, data = FALSE) (or options(nlmixr2save.data = FALSE)) writes a fit whose origData is omitted from the zip.
    • New nlmixr2saveShare() strips an existing saved fit (a live object or a .zip base name; honors nlmixr2save.dir/nlmixr2save.prefix) into a shareable sibling zip: fit-noData.zip (data removed) or, with noFit = TRUE, fit-noData-noFit.zip (data and the returned prediction/residual table removed, keeping the model, estimates, eta table and parameter history). The original fit is left unchanged.

    See vignette("sharing-fits"), which also documents the side effects (e.g. VPC, residual re-derivation, and re-fitting need the original data).

  • saveFit() no longer stores the redundant model element (the loader always rebuilds it from ui). This removes a spurious “could not determine how to save object of class call for item model” warning when re-saving a previously loaded fit (including via nlmixr2saveShare()).

  • Saved fits now record the nlmixr2est and rxode2 versions they were produced with (including each package’s commit sha when it was installed from a remote such as GitHub). When a fit is later loaded and the installed nlmixr2est or rxode2 differs:

    • loadFit() warns that the fit was run with a different package version (controllable with the new checkVersion argument).
    • the := caching operator, in an interactive session, asks whether to rerun the fit with the currently installed packages; non-interactively it loads the cached fit and warns. (Trusted-cache mode, nlmixr2save.check = FALSE, is left untouched so committed caches stay stable across versions.)

    Fits saved by older nlmixr2save versions (which carry no version metadata) continue to load without any warning. The whole check can be turned off with options(nlmixr2save.checkVersion = FALSE) (or per call via loadFit(..., checkVersion = FALSE)); it is TRUE by default. See vignette("version-tracking").

  • The parHistData$type factor levels are now recorded from the fit at save time and restored on load, so the factor round-trips correctly regardless of which nlmixr2est version produced it (the level set has grown over versions, e.g. "Analytic Gradient"). A hardcoded fallback covers fits saved before this was recorded.

  • The := caching operator gains three options() (mirroring nlmixr2save.quiet):

    • nlmixr2save.prefix (default ""): prepended to the assigned variable name to form the cache file, e.g. with options(nlmixr2save.prefix = "modelPiping-"), fit := nlmixr2(...) caches to modelPiping-fit.zip.
    • nlmixr2save.dir (default "."): the directory the cache files live in.
    • nlmixr2save.check (default TRUE): when TRUE, := keeps verifying the cache against the current model/data/arguments (historical behavior); when FALSE, := simply loads the cache file if it exists (a fit as .zip, a simulation/other value as .rds) and otherwise runs and saves it – the cache is trusted and regenerated only when missing. This keeps a committed cache stable across nlmixr2/rxode2 versions.

  • New nlmixr2saveInvalidate(): deletes every := cache entry under the active nlmixr2save.prefix/nlmixr2save.dir, so cached fits/simulations are re-run on the next render when nlmixr2save.check is FALSE.

  • The saved-fit loader script now quotes its variable name, so a nlmixr2save.prefix containing non-syntactic characters (e.g. -) round-trips correctly.

  • Support both $parFixedDf structures produced by nlmixr2est: the current one (named “Estimate”/“SE” columns) and the upcoming $parFixed refactor (nlmixr2est#645, unnamed columns). The structure of the fit is detected when it is saved and recorded in the restore script, so fits round-trip exactly with either version (nlmixr2saveParFixedDf() gained a named argument; existing saved zip files continue to load unchanged).

  • Additional all-NA numeric columns of $parFixedDf (for example “CI Lower”/“CI Upper” when there is no covariance step) are now coerced back to numeric when a saved fit is loaded, instead of being left as logical columns from the CSV round-trip.

nlmixr2save 0.1.0

CRAN release: 2026-06-17

  • Create zip files that are (mostly) R independent to save nlmixr2 fit items

  • Create a cached assignment operator := to save nlmixr2 fits automatically; if used, it will load a cached fit if function arguments are the same (a sort of disk memoization of the outermost function)

  • Initial CRAN submission.