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Recent Releases of babelmixr2

babelmixr2 - v0.1.9

i* 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

What's Changed

  • Update rstudio by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/170
  • 171 fme mcmc by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/175
  • Add psuedoOptim method by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/176

Full Changelog: https://github.com/nlmixr2/babelmixr2/compare/v0.1.8...v0.1.9

- R
Published by mattfidler 9 months ago

babelmixr2 - v1.0.8

  • Maintenance fix for upcoming nlmixr2est and rxode2

What's Changed

  • Update PKNCA GitHub repo URL by @billdenney in https://github.com/nlmixr2/babelmixr2/pull/157
  • Update PopED example for now by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/159
  • reexport without nlmixr2 by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/160
  • 161 var babelmixr2 by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/162
  • Add memoise to generated PopED functions by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/163

Full Changelog: https://github.com/nlmixr2/babelmixr2/compare/v0.1.7...v0.1.8

- R
Published by mattfidler 11 months ago

babelmixr2 - v0.1.7

  • Compatibility fixes for upcoming PKNCA

- R
Published by mattfidler about 1 year ago

babelmixr2 - v0.1.6

  • Use new nlmixr2est covariate selection enforcment 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.

- R
Published by mattfidler over 1 year ago

babelmixr2 - v0.1.5

babelmixr2 0.1.5

  • 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 in 'PopED`

  • Fix bug so that shrinkage() calculation works in PopED

  • 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).

What's Changed

  • 124 poped pref by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/125
  • Pull request for lhs by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/128
  • Fix babelmixr2 handling of shrinkage() again by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/132
  • Allow mixing of poped models by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/133
  • Fix doc by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/134
  • Add babelBpopIdx by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/136
  • Add PopED win parallel by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/141
  • Fix G_xt in event table by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/142
  • Update pointers at the beginning of each exported fn by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/143
  • Poped examples tp by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/144

Full Changelog: https://github.com/nlmixr2/babelmixr2/compare/v0.1.4...v0.1.5

- R
Published by mattfidler over 1 year ago

babelmixr2 - v0.1.4

v0.1.4

  • 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.

What's Changed

  • 103 poped interface by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/104
  • 108 dont run nonmem or monolix just create files by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/109
  • 111 remove rxode2parse by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/112
  • Fix the NA runCommand that doesn't work as advertised by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/114
  • Move PopED here by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/117
  • 117 move poped by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/118
  • Support different sampling times per group with separate IDs by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/119
  • Script output for different designs by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/121
  • as.nlmixr2 for monolix2rx objects by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/105
  • rxUiDeparse by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/123

Full Changelog: https://github.com/nlmixr2/babelmixr2/compare/v0.1.2...v0.1.4

- R
Published by mattfidler over 1 year ago

babelmixr2 - v0.1.2

  • 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.

What's Changed

  • 87 safezero=false for nonmem maybe even monolix by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/88
  • 89 bioavailability calculation not set before bioavailability nonmem line of code by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/90
  • Update ssLag by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/93
  • Build fix by @billdenney in https://github.com/nlmixr2/babelmixr2/pull/98
  • Add vignette for PKNCA estimation by @billdenney in https://github.com/nlmixr2/babelmixr2/pull/97

Full Changelog: https://github.com/nlmixr2/babelmixr2/compare/v0.1.1...v0.1.2

- R
Published by mattfidler over 2 years ago

babelmixr2 - v0.1.1

babelmixr2 0.1.1

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

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

What's Changed

  • Centralize the reexports (and fix a documentation warning) by @billdenney in https://github.com/nlmixr2/babelmixr2/pull/61
  • Issue 65 by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/66
  • Change check by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/68
  • Add handle for as.nlmixr2 by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/77
  • Add timing info for as.nlmixr2 by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/79
  • Add the output to the $subroutines record by @mattfidler in https://github.com/nlmixr2/babelmixr2/pull/80

Full Changelog: https://github.com/nlmixr2/babelmixr2/compare/v.0.1.0...v0.1.1

- R
Published by mattfidler almost 3 years ago

babelmixr2 - v0.1.0

Allow multiple methods for submission

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

- R
Published by mattfidler over 3 years ago