v3.0.0

nlmixr2est 3.0.0

• No binary linking to rxode2, lbfgsb3c and n1q1, which means
  that updating these will not make nlmixr2est crash without
  recompiling.

• New mu3 referencing will take context from the model to see if the
  algebraic expression can be completed from defined model variables;
  These variable would have to be unique.

What's Changed

• 451 one rxode2 no longer any sub packages except rxode2ll by @mattfidler in #452
• As observed by babelmixr2 sometimes the ui is not present; handle this by @mattfidler in #457
• Error in saem code generation when all fixed effect parameters are fixed by @mattfidler in #461
• Invalid index warning in nlmixr2 fits by @mattfidler in #463
• It is no longer there. I will add it back. by @mattfidler in #460
• Warnings suppressed when using nlmixr2 with "rxSolve" estimation method. by @mattfidler in #453
• All models created by nlmixr2 should add the model based interpolation (and any other properties) when building other sorts of models by @mattfidler in #456
• tableControl() incompatible options should error with addDosing items by @mattfidler in #464
• Read relevant tableControl() options from nlmixr2 and override control=rxControl() by @mattfidler in #465
• Use lotri nearPD by @mattfidler in #467
• Don't give a warning or error when eta values are NULL or not estimated by @billdenney in #469
• Stop requiring binary linkage by @mattfidler in #466
• Remove abi linkage to lbfgsb3c by @mattfidler in #472
• Add support for levels() by @mattfidler in #474
• Move out PopED by @mattfidler in #476
• Minimum session information by @mattfidler in #480
• mu referencing based on derived variables by @mattfidler in #478

Full Changelog: v2.2.2...v3.0.0

v2.2.2

Breaking changes

• Saem non-mu reference input parameters/covariates were fixed so they
  work correctly with fixed parameters (Issue #445)

• Focei changed back to having a lower bound for standard deviations
  when not specified. This means that best model fits may change. You
  can revert to the old settings by using
  foceiControl(sdLowerFact=0.0). You can also change the factors to
  other values than the default value, that is
  foceiControl(sdLowerFact=0.000001) for instance which would
  multiply the initial value by 0.000001 when either the lower bound
  isn't specified or the lower bound is specified as zero for the
  error estimates related to error-based standard deviations.

• In nlmixr2, expressions are optimized. Because of that
  optimization, numerical rounding differences can cause different
  directions in optimization when fixing parameters in the model
  vs. fixing the parameters manually.

  This means that the fixed parameters in a model vs hard-coded fixed
  parameters could give different values in the final model.

  A new option literalFix was introduced which change the fixed
  population parameters to constants in the model while running the
  optimization. This makes the output of fixing within the model and
  fixing manually the same (which is what is likely expected). The
  default is for this to be turned on (ie. literalFix=TRUE). You
  can get back the old behavior by using the option
  literalFix=FALSE.

• In saem, the monte-carlo sampling occurs for all parameters
  including non-informative ETAs. A fix ensure that non-informative
  etas in saem are fixed to zero while sampling the phi values.
  This may change results for models with uninformative etas. To
  ignore the uninformative etas with saem you ca use use the prior
  saem handling with saemControl(handleUninformativeEtas=FALSE).

New features

• Gracefully degrade when $cov is not in the right form (see #423)

• Add support for PopED in place solving (used in babelmixr2)

• If est=foceiControl() or other nlmixr2 control with the class
  foceiControl infer the estimation method is focei

What's Changed

• No lin b by @mattfidler in #417
• 423 assertion on env$cov failed must be of type matrix not character should gracefully degrade and produce a captured warning by @mattfidler in #425
• fix checkmate assertions by @mattfidler in #426
• Add predict estimation method and test it is the same as predict() by @mattfidler in #437
• 427 single solver per pre loaded by @mattfidler in #430
• Warfarin rik by @mattfidler in #438
• Literal fix by @mattfidler in #439
• amt and evid need to be missing for evid imputation by @mattfidler in #441
• 442 test for uninformative etas by @mattfidler in #444

Full Changelog: v2.2.1...v2.2.2

v2.2.1

nlmixr2est 2.2.1

• Align with the possibility that linCmt sensitivities may not be
  present (like intel c++)

Bug fix

• focei cache needs to be based on the parameter order as well as
  the model information (#415)

What's Changed

• 415 nlmixr2est focei needs to cache based on thetaomega order by @mattfidler in #416

Full Changelog: v2.2.0...v2.2.1

v2.2.0

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)

What's Changed

• Add mu2 processing by @mattfidler in #354
• Fix #359 by @billdenney in #360
• Return fit without table if table step fails by @mattfidler in #364
• Fix 366 by @billdenney in #367
• Only keep $parHistData and calc $parHist and $parHistStacked by @mattfidler in #370
• Clarify keep argument to vpcSim() by @billdenney in #380
• Quieter compile by @billdenney in #381
• 376 make sure and test that fit$eta are non zero by @mattfidler in #383
• With a zero gradient always reset by @mattfidler in #384
• 387 sslag ettrans rxcontrol update by @mattfidler in #388
• 394 error drugmetabolite modeing after zero oder absorption by @mattfidler in #395
• V2.1.7 by @mattfidler in #396
• Fix for #397, needs test still by @mattfidler in #398
• add as.rxUi() method for fit objects by @billdenney in #378
• V2.1.8 by @mattfidler in #401
• 402 nlm by @mattfidler in #403
• 404 nls by @mattfidler in #405
• 406 optim by @mattfidler in #407
• Fix lbfgsb3c documentation by @mattfidler in #408
• Udf by @mattfidler in #409
• 411 cran requests by @mattfidler in #413

Full Changelog: v2.1.8...v2.2.0

v2.1.8

nlmixr2est 2.1.8

• Version bump and a minor documentation update (same as nlmixr2est
  2.1.7). This version bump is to simply allow correct binary linkage
  to rxode2 2.0.14. Otherwise nlmixr2 models will crash R.

nlmixr2est 2.1.7

• As requested by CRAN, remove Rvmmin

• Values in $parFixed for BSV without exponential transformation are now
  correctly shown (#366)

v2.1.7

• As requested by CRAN, remove Rvmmin

• Fix SD calculation typo (#366)

v2.1.6

Breaking changes

• Since rxode2 now allows simulation with omega having diagonal
  zero elements, $omega and $omegaR now reflects this information
  including the zero omega elements in the output. On the other hand,
  the other eta-information and standard error information for zero
  etas are still excluded in $phiR, $phiSE, $eta etc.

Bug fixes

• vpcSim() works when an eta value is fixed to 0 (#341)

• augPred() now consistently uses the simulation model (instead of
  the inner model used for CWRES calculation).

What's Changed

• Add mu ref fix by @mattfidler in #338
• Make addCwres() error clearer for model with no etas by @billdenney in #340
• Update documentation to link parts together (and some minor code formatting changes) by @billdenney in #345
• vpcSim works with etas set to 0 by @billdenney in #342
• Warn on time-varying covariate changes by @mattfidler in #349
• Adds documentation for the nlmixr2 object by @john-harrold in #351
• Aug pred fix by @mattfidler in #352

New Contributors

• @john-harrold made their first contribution in #351

Full Changelog: v2.1.5...v2.1.6

v2.1.5

• Add $fitMergeFull, $fitMergInner, $fitMergeLeft,
  $fitMergeRight as a complement to $dataMergeFull,
  $dataMergInner, $dataMergeLeft, $dataMergeRight. The fit
  variants prefer columns in the fit dataset instead of the original
  dataset. This is useful for goodness of fit plots with censoring
  since the DV in the fit simulates values under the ipred/residual
  assumption and will give more appropriate goodness of fits,
  otherwise these values are the limit of whatever censoring is
  applied

• Moved the mu reference fix for the split mu referenced model here
  (from babelmixr2)

What's Changed

• Add simulation method by @mattfidler in #333
• 335 for $datamerge family prefer fit object instead of original data by @mattfidler in #336

Full Changelog: v2.1.4...v2.1.5

v2.1.4

nlmixr2est 2.1.4

• Breaking change, now calculate condition number based on covariance
  and correlation, the names have changed to be more explicit.
  conditionNumber changed to conditionNumberCov and a new metric
  conditionNumberCor has been added.

• A bug in boundary value detection prevented automatic covariance calculation
  with FOCEi estimation (#318)

• Fix vpcSim so that it will be a bit more robust when it is
  difficult to simulate.

• A bug in model piping which did not allow models to be appended to was fixed
  (rxode2#364)

• An internal change was made in nlmixr2.rxUi() to better support the
  babelmixr2 PKNCA estimation method (babelmixr2#75)

• Fixed bug where $iniUi did not return the initial ui when running
  non focei related methods. Also added alias of $uiIni to the
  same function.

• Dropped Stan headers for this package, also updated to C++17

What's Changed

• 289 issue in obtaining model estimates by @mattfidler in #290
• Fix rxode2 #364 by @billdenney in #292
• Remove debugging statement by @billdenney in #299
• Make some focei methods for simulation that are closer to est model by @mattfidler in #308
• 302 mu reference definition isnt correct for non mu referenced model by @mattfidler in #304
• Fallback to old method by @mattfidler in #310
• drop stan headers and eigen by @mattfidler in #319
• 318 fix bound by @billdenney in #321
• Make package installation consistent; fix typos; use label() by @billdenney in #325
• Speed up some testing by minimizing the fit iterations by @billdenney in #324
• Allow for babelmixr2::pkncaControl() not to set genRxControl by @billdenney in #326
• 311 condition numbers by @mattfidler in #323
• 316 wrong initial values in nlmixr2 object by @mattfidler in #322
• Rebuild documentation by @billdenney in #329

Full Changelog: v2.1.3...v2.1.4

v2.1.3

nlmixr2est 2.1.3

• Allows $etaH and related family to be integrated into a saem fit
  if cwres is calculated.

• Fixed a bug where nlmixrLlikObs in the merged dataset is sometimes
  named llikObs, now it is always named nlmixrLlikObs

• Fixed a bug where nlmixrLlikObs shows up in merged dataset when
  cwres is not calculated (it was always 0), also allow cwres
  calculation to pick up nlmixrLlikObs in merged dataset.

• Dropped dparser dependency

What's Changed

• 282 $etah not available for saem needs cwres but doesnt pull over standard errors by @mattfidler in #283
• 284 include log likelihood per observation when adding cwres by @mattfidler in #285
• Test nonmu and add test case for merge (and unsuccesful merge) by @mattfidler in #288

Full Changelog: https://github.com/nlmixr2/nlmixr2est/compare/v2.1.2...v2.1.3###