nlmixr2 2.1.0/ rxode2 2.1.1

By Matthew Fidler in rxode2 nlmixr2

January 9, 2024

nlmixr2 2.1.0 was released 9 Jan 2024 which requires the newest (and recently released) engine packages nlmixr2est 2.2.0 (released 12 Dec 2023) and rxode2 2.0.10 (released 13 Dec 2023).

I will be blogging about a few new features but want to mention a few now:

  • More flexible mu referencing
  • User defined functions can now be used with nlmixr2 and rxode2
  • Event handling changes
  • Many new estimation methods for population only fitting

The truncated changelog for these packages are below:

nlmixr2 2.1.0

  • Reexports etExpand(), model()<- and ini()<-; Added required imports for new rxode2/nlmixr2est.

nlmixr2est 2.2.0

New Features

  • Algebraic mu referencing has been implemented in nlme and saem.

  • New estimation method “nlm” has been added to estimate population only likelihoods using stats::nlm and possibly return a standardized nlmixr2 fit.

  • New estimation method “nls” has been added to estimate population only problems. This uses minpack.lm::nlsNM by default if present, or the stats::nls

  • New estimation method “optim” has been added to estimate population only likelihoods. This uses stats::optim and returns a standardized nlmixr2 fit.

  • New estimation method “nlminb” has been added to estimate population only likelihoods. This uses stats::nlminb and returns a standardized nlmixr2 fit.

  • New estimation methods from the minqa package: “bobyqa”, “uobyqa” and “newuoa” have been added to estimate population only likelihoods. These methods returns a standardized nlmixr2 fit.

  • New estimation method “lbfgsb3c” to estimate population only likelihoods. This returns a standardized nlmixr2 fit.

  • New estimation method “n1qn1” to estimate population only likelihoods. This returns a standardized nlmixr2 fit.

  • Added new feature for vpcSim() where a minimum number of subjects are simulated from the model when trying to fill in ODEs that were not solved successfully. By default this is 10. This also works-around a bug when there is only one subject simulated and the data.frame has a slightly different output.

Breaking changes

  • Removed fit$saemTransformedData since it isn’t actually used in saem anymore (but will break anyone’s code who is using it)

  • Now the internal function .foceiPreProcessData() requires the rxode2 control rxControl() because some of the new steady state lag features need to translate the data differently based on rxControl() options.

Bug fixes

  • Printing models with correlated omega values and omega values fixed to zero no longer fails (#359)

  • Add back values for $parHistData (#368)

  • This requires a new rxode2 which will fix multiple endpoint issues observed (#394)

  • Manual back-transformed values in $parFixed are now displaying correctly and are calculated based on the confidence interval in the control instead of 95% confidence no matter what (#397)

Other changes

  • An as.rxUi() method was added for fit models (#377)
Posted on:
January 9, 2024
Length:
2 minute read, 425 words
Categories:
rxode2 nlmixr2
Tags:
new-version
See Also:
nlmixr2 2.1.2/ rxode2 2.1.3
nonmem2rx and babelmixr2
nlmixr2 family releases