v5.1.2

rxode2 5.1.2

• geom_cens() / stat_cens() no longer emit "Ignoring unknown
  aesthetics" warnings when censoring aesthetics are mapped.
  Documentation corrected to describe the two supported lowercase
  forms: lower/upper (both required) or cens (with optional
  limit). The two forms cannot be mixed, lower and upper are
  now required together, and limit without cens is rejected
  rather than silently ignored.

• Checks for is.loaded() before loading a rxode2 model. This helps fix
  the m1 ODR issue shown in nlmixr2est.

• Moved dim.rxEt() here instead of in nlmixr2est

v5.1.1

rxode2 5.1.1

• Various low level fixes to allow nlmixr2est to have parallelized
  focei.

• Parallelized the rxode2 data.frame creation.

• Use ALTREP for id, sim.id, repeated simulation event columns
  (evid, cmt, ss, amt, rate, dur, ii, time),
  covariates and kept variables when blocks are identical across
  simulations; falls back to filled out columns when runtime event
  mutation is detected (evid_() push growth / per-individual event
  reallocation). Also factors cannot currently be represented by
  altrep, so they are forced to be fully represented.

• Change compile flags and compiler directives for rxode2 models to
  speed up how they run.

• Have a pre-allocated context pool for lsoda in both liblsoda and
  lsoda (faster because memory doesn't need to allocated and
  deallocated so often)

• Change OMP scheduling to dynamic to try to help load-balance the ode
  solving per subject.

• Simulation normal random numbers before integrating them into your
  solve.

• Add evid_() function to allow arbitrary doses and observations in
  a rxode2 model.

• Add splitBolus() function to split or relocate doses in the final
  output. This is done at translation time (but is respected by
  evid_()) so in general is a bit faster then arbitrary doses in an
  estimation step for nlmixr2

• Add %% operator to valid rxode2 syntax

• Create per-individual ODE solving tolerances for use in focei.

• Fix potential security and memory-management issues that could lead
  to crashes or undefined behavior including integer overflow

• Change dop853 to allow per state tolerances and parallel solving
  like liblsoda.

• Change dop853 to be able to use dense=TRUE for the 8th order
  dense polynomial interpolation between dosing events.

• Now dop853 can be parallelized per thread.

• Change mtime state-based dosing to use less memory.

• Add plogis() translation inside rxode2 to it's c-based expit()
  functions

• Refactored et() to be mostly in R, fixing many issues (#722 , #725, #858,
  #732, #723, #721, and #724) and allowing dosing/sampling windows to
  use ii, addl and until (realized immediately)

• Add linToOde() convert linCmt() models to ODEs.

• Fix IOV simulation issue observed in #982.

• Fix sticky variable calculation (#1013, #1025)

• More easily identify initial conditions (#948)

• Fix sensitivities in the linCmt() that did not match the ODE (#1018, #1012)

• Added in-solve addition of observations (obs()), bolus doses
  bolus(), infusion doses infuse() or infuseDur(), system resets
  reset(), compartment replacement replace(), multiplicaton events
  multiply(), and phantom/transit compartment events phantom().
  For more granular control you can also use evid_().

• Refactor string comparison in rxode2 so that it is actually doing
  an integer comparison when running the ODE solving routine
  (simulation and estimation) instead of using a string comparison.
  It makes using strings like (sex == "male") run faster.

• Add rxMemoryEstimate() and rxMemSummary() to estimate the amount
  of memory that is required for a rxode2 solve.

• Add tolFactor, a per individual change of the tolerances to be
  used in solving. This is used have individualized tolerances from
  nlmixr2est.

• Add serializeFile as an option to save the rxode2 C fitting data and
  then restore as needed.

What's Changed

• Preserve first error's diagnostic code in op->naTime during parallel solve by @Copilot in #994
• Fix stale documentation in dop853.h after thread-safe refactoring by @Copilot in #995
• Fix integer overflow in nSize causing segfault with large subject counts by @billdenney in #999
• Review by @mattfidler in #1000
• Add C code integration vignette by @mattfidler in #1001
• Use unsigned integer types for non-negative counts (nsub, nsim, nall, nSize) by @billdenney in #1002
• Make rxode2 more thread safe by @billdenney in #992
• Update news by @mattfidler in #1005
• Add some information about the rxUi object by @mattfidler in #586
• Allow individual allocation by @mattfidler in #1007
• Refactor atolRtolFactor_() for thread-safe per-individual sticky tolerances + C-API exposure by @Copilot in #1006
• Par dop853 by @mattfidler in #1009
• Push evid feature by @mattfidler in #1008
• 1012 ode lincmt by @mattfidler in #1018
• 948 identifying non zero initial conditions and setting those to zero by @mattfidler in #1021
• Add mod operator by @mattfidler in #1024
• Add stick vars test by @mattfidler in #1023
• docs: add article on sticky variables by @mattfidler in #1025
• Allow split bolus doses by @mattfidler in #1026
• Add plogis() support inside of a rxode2 model function by @mattfidler in #1027
• Fix and test for issue #982 by @mattfidler in #1028
• Refactor et by @mattfidler in #1015
• 1016 lin cmt by @mattfidler in #1030
• 1035 global struct by @mattfidler in #1036
• Range-check dparse input length to prevent (int)strlen truncation by @billdenney in #1031
• Range-check rc_dup_str length to prevent silent int truncation by @billdenney in #1032
• Per-individual neqOverride C-API + plumb through getSolve/getAdvan by @billdenney in #1038
• Fix OOB read in etTran event loop when id column contains NA by @billdenney in #1037
• Fix/mem sbuf int overflow by @billdenney in #1034
• Use size_t for getLine column accumulator to prevent int overflow by @billdenney in #1033
• Plumb neqOverride through par_solve / iniSubject / indLin by @billdenney in #1040
• Guard convertDvid_ against empty input to prevent OOB read by @billdenney in #1039
• Bolus by @mattfidler in #1041
• Str cmp model variable by @mattfidler in #1043
• Parallel fixes by @mattfidler in #1044
• Memory allocate by @mattfidler in #1045
• Dry sort by @mattfidler in #1046
• Fix dup fn by @mattfidler in #1047
• Add some pool optimization and compiler flag opts by @mattfidler in #1049
• Serialize by @mattfidler in #1048
• Add dense polynomial output for DOP853 (iout=2) by @mattfidler in #1050
• More altrep by @mattfidler in #1051

Full Changelog: v5.0.2...v5.1.1

v5.0.2

rxode2 5.0.2

• Allow state-dependent dur(), rate(), alag(), mtime() now
  allow states to modify their behavior. The state value at the time
  of the event is used to calculate any changes.

• Fix: all six ODE solve loops now use precomputed timeThread values for
  event times instead of recomputing via getTime_() with ypNA, preventing
  NA propagation for any state-dependent lag scenario.

• Export the internal .rxGetSeed() and .rxSetSeed() for use in the
  nlmixr2save package.

• Bug fix for .copyUi() with the new format (5.0+) of rxode2 ui models

• With new versions of R, getOption() is no longer a bottleneck, so
  syncing to local variables is no longer done internally

• Allow transforms to return NA.

• Drop magrittr and use |> instead of %>% in the examples
  (requires R 4.1)

• Change default model serialization to bzip2 and move binary code
  generation inside of C.

• Fix where getting seed saves/modifies the RNG scope, as well as a bug fix
  for restoring the random seed state

What's Changed

• Fix .rxTransform() by @mattfidler in #971
• Change to R's pipe operator by @mattfidler in #973
• Add qs work-around (when it is installed) by @mattfidler in #974
• Codegen of raw binary in C by @mattfidler in #975
• Use %fin% from fastmatch by @mattfidler in #979
• Don't use syncing anymore by @mattfidler in #981
• Fix infinite recursion in .copyEnv() on circular environment references by @Copilot in #987
• Fix copy ui by @mattfidler in #986
• Use (Rf_error) by @mattfidler in #990
• Time dependent dur rate f and mtime by @mattfidler in #991

Full Changelog: v5.0.1...v5.0.2

v5.0.1

• Change random number generation to always return doubles internally as well as no longer take a rxode2 individual structure, this is inferred by the thread number.

• Change string representation of model variables to internal binary C code (to avoid macOS M1 sanitizer issues with strings).

• Allow user to change the internal serialization type with options("rxode2.serialize.type"); Currently can be one of “qs2”, “qdata”, “base”, “bzip2” and “xz”. This option must be set before rxode2 is loaded, once loaded it keeps the option initially set. This is set to xz which is from base R, but could be sped up with either "qs2" (more future proof) or "qdata" (a bit faster).

• Removed lsoda CDIR$ IVDEP directive, as requested by CRAN.

What's Changed

• Fix CRAN issues by @mattfidler in #963
• Use (void*) references for rxbinom() and other random number gen by @mattfidler in #964
• Change random number generators to not include the rxode2 individual patient structure. by @mattfidler in #967
• Add/Use bzip2 by @mattfidler in #968
• Use xz as default serialization/compression by @mattfidler in #969

Full Changelog: v5.0.0...v5.0.1

v5.0.0

rxode2 5.0.0

• Better error for tad(depot) when linCmt() doesn't include a
  depot compartment.

• Remove qs dependency; For rxode2 ui objects, use lists instead of
  serialized objects. The internal C++ code still generates qs2
  sterilization objects (#950)

• Fixed translation for censoring/limit to account for a possible
  CMT variable before the CENS / LIMIT column (#951, #952)

• Added dmexpit() for getting the diagonal Jacobian.

• Added special handling of mixest and mixunif.

What's Changed

• CRAN release by @mattfidler in #941
• Add special handling of mixest and mixunif by @mattfidler in #944
• add dmexpit() by @mattfidler in #946
• Fix grammar in error messages: "in not in" → "is not in" by @Copilot in #953
• Checks for censoring based on name by @mattfidler in #952
• Use qs2 instead of qs by @mattfidler in #957

New Contributors

• @Copilot made their first contribution in #953

Full Changelog: v4.1.1...v5.0.0

v4.1.1

rxode2 4.1.1

• Stacking for multiple-endpoint ipredSim now matches
  multiple-endpoint sim; Issue #929

• Fix occasional $props that threw an error with empty properties
  (when using properties like tad0()); Issue #924

• Allow mixture models mix() to be loaded with rxS() as a step to
  support mixtures in nlmixr2's focei; Issue #933.

• Identify the correct transformation type for iov variables (#936)

• Fix multiple compartment simulation edge cases where simulations
  were not being performed (#939)

• When referencing cmt in models, the variable is forced to be CMT
  (related to #939)

v4.1.0

• Change rxui $ evaluation when completing in rstudio, fixes strange calculations popping up in rstudio (#909)

• Add orphan rxode2 model unloading when using rxUnloadAll(), and change the return type to always be a boolean.

• Add assertRxUiIovNoCor to assert IOVs have no correlations in them.

• Handle the levels for inter-occasion variability in the ui better (#614)

• Create a new function mix() that will allow mixture models to be simulated in preparation of mixture support in nlmixr2. This allows mixture models to be specified as: v = mix(v1, p1, v2, p2, v3) where the probability of having v=v1 is modeled by p1, v=v2 is modeled by p2, and v=v3 is modeled by probability 1-p1-p2.

• Created new functions mlogit() and mexpit() to convert probabilities used in mixture models to log-scaled values. mlogit() converts the probabilities to log-scaled values (using root-finding) and mexpit() converts the log values into probabilities. The equation for the conversion of log to probabilities is $p_i = \frac{exp(x_i)}{1+\sum_{j=1}^{N-1}exp(x_j)}$

• Added new assertion assertRxUiNoMix which throws an error when a mixture model is present (ie mix())

• Fix for label processing when calling rxode2(uiModel)

What's Changed

• 909 rstudio 2025 by @mattfidler in #910
• Try unloading orphan rxode2 dlls by @mattfidler in #911
• Add assertion for new nlmixr2est by @mattfidler in #913
• iov bad cov by @mattfidler in #915
• Fix and test for #919 by @mattfidler in #920
• 918 mix by @mattfidler in #921
• 922 probit probit inv by @mattfidler in #923

Full Changelog: v4.0.3...v4.1.0

v4.0.3

rxode2 4.0.3

• For CRAN's m1 ASAN checks of nlmixr2est, loading and unloading the
  same dll or by deleting the dll and recreating the exact same code,
  and then loading the dll will cause the ASAN check to flag an odr
  violation. Because of this, a mechanism to not unload dlls has been
  added. This allows the next version of nlmixr2est to not have
  issues with Mac m1 san checks.

v4.0.2

rxode2 4.0.2

• At the request of CRAN, be a bit more careful so that names are not
  duplicated. Now include the md5 hash, a global counter and random 4
  digit and number combination. In addition add the name of the
  original function so it will be easier to debug in the future.

• Fall back to data.frame rbind when rbind.rxSolve() fails

What's Changed

• New ODR, as indirectly request by CRAN. by @mattfidler in #904

Full Changelog: v4.0.1...v4.0.2

v4.0.1

rxode2 4.0.1

• Add the ability to use rbind for solved rxode2 frames.

• Fix LTO issue for _rxode2_calcDerived

What's Changed

• Remove more tests for CRAN by @mattfidler in #898
• fix typo by @leovuong in #900
• Another rbind instance by @mattfidler in #899
• Cran update by @mattfidler in #902

Full Changelog: v4.0.0...v4.0.1