Skip to content

v3.0.0
Compare
Choose a tag to compare
@mattfidler mattfidler released this 18 Sep 14:26
· 113 commits to main since this release
v3.0.0
096e100

rxode2 3.0.0

Breaking Changes

  • The model properties was moved from $params to $props so it does
    not conflict with the low level rxode2 model $params

  • Error when specifying wd without modName

  • With Linear and midpoint of a time between two points, how rxode2
    handles missing values has changed. When the missing value is lower
    than the requested time, it will look backward until it finds the
    first non-missing value (or if all are missing start looking
    forward). When the missing value is higher than the requested time,
    the algorithm will look forward until it finds the first non-missing
    value (or if all are missing, start looking backward).

  • The order of ODEs is now only determined by the order of cmt() and
    d/dt(). Compartment properties, tad() and other compartment
    related variables no no longer affect compartment sorting. The
    option rxode2.syntax.require.ode.first no longer does anything.

  • The handling of zeros "safely" has changed (see #775)

    • when safeZero=TRUE and the denominator of a division expression
      is zero, use the Machine's small number/eps (you can see this
      value with .Machine$double.eps)

    • when saveLog=TRUE and the x in the log(x) is less than or
      equal to zero, change this to log(eps)

    • when safePow=TRUE and the expression x^y has a zero for x
      and a negative number for y replace x with eps.

    Since the protection for divide by zero has changed, the results
    will also change. This is a more conservative protection mechanism
    than was applied previously.

  • Random numbers from rxode2 are different when using dop853,
    lsoda or indLin methods. These now seed the random numbers in
    the same way as liblsoda, so the random number provided will be
    the same with different solving methods.

  • The arguments saved in the rxSolve for items like thetaMat will
    be the reduced matrices used in solving, not the full matrices (this
    will likely not break very many items)

Possible breaking changes (though unlikely)

  • iCov is no longer merged to the event dataset. This makes solving
    with iCov slightly faster (#743)

New features

  • You can remove covariances for every omega by piping with %>% ini(diag()) you can be a bit more granular by removing all
    covariances that have either eta.ka or eta.cl by: %>% ini(diag(eta.ka, eta.cl)) or anything with correlations with
    eta.cl with %>% ini(diag(eta.cl))

  • You can also remove individual covariances by %>% ini(-cov(a, b))
    or %>% ini(-cor(a,b)).

  • You can specify the type of interpolation applied for added dosing
    records (or other added records) for columns that are kept with the
    keep= option in rxSolve(). This new option is
    keepInterpolation and can be locf for last observation carried
    forward, nocb which is the next observation carried backward, as
    well as NA which puts a NA in all imputed data rows. See #756.

    • Note: when interpolation is linear/midpoint for
      factors/characters it changes to locf with a warning (#759)

    • Also note, that the default keep interpolation is na

  • Now you can specify the interpolation method per covariate in the model:

    • linear(var1, var2) says both var1 and var2 would use linear
      interpolation when they are a time-varying covariate. You could
      also use linear(var1)

    • locf() declares variables using last observation carried forward

    • nocb() declares variables using next observation carried backward

    • midpoint() declares variables using midpoint interpolation

  • linear(), locf(), locb(), midpoint(), params(), cmt()
    and dvid() declarations are now ignored when loading a rxode2
    model with rxS()

  • Strings can be assigned to variables in rxode2.

  • Strings can now be enclosed with a single quote as well as a double
    quote. This limitation was only in the rxode2 using string since
    the R-parser changes single quotes to double quotes. (This has no
    impact with rxode2({}) and ui/function form).

  • More robust string encoding for symengine (adapted from
    utils::URLencode() and utils::URLdecode())

  • Empty arguments to rxRename() give a warning (#688)

  • Promoting from covariates to parameters with model piping (via ini()) now
    allows setting bounds (#692)

  • Added assertCompartmentName(), assertCompartmentExists(),
    assertCompartmentNew(), testCompartmentExists(),
    assertVariableExists() testVariableExists(),
    assertVariableNew(), assertVariableName(), and
    assertParameterValue() to verify that a value is a valid nlmixr2
    compartment name, nlmixr2 compartment/variable exists in the model,
    variable name, or parameter value (#726; #733)

  • Added assertRxUnbounded(), testRxUnbounded(), warnRxBounded()
    to allow nlmixr2 warn about methods that ignore boundaries #760

  • Added functions tad0(), tafd0(), tlast0() and tfirst0() that
    will give 0 instead of NA when the dose has not been
    administered yet. This is useful for use in ODEs since NAs will
    break the solving (so can be used a bit more robustly with models
    like Weibull absorption).

  • rxode2 is has no more binary link to lotri, which means that
    changes in the lotri package will not require rxode2 to be
    recompiled (in most cases) and will not crash the system.

  • rxode2 also has no more binary linkage to PreciseSums

  • The binary linkage for dparser is reduced to C structures only,
    making changes in dparser less likely to cause segmentation faults
    in rxode2 if it wasn't recompiled.

  • A new model property has been added to $props$cmtProp and
    $statePropDf. Both are data-frames showing which compartment has
    properties (currently ini, f, alag, rate and dur)
    in the rxode2 ui model. This comes from the lower
    level model variable $stateProp which has this information
    encoded in integers for each state.

  • A new generic method rxUiDeparse can be used to deparse meta
    information into more readable expressions; This currently by
    default supports lower triangular matrices by lotri, but can be
    extended to support other types of objects like 'nlmixr2's
    foceiControl() for instance.

Bug fixes

  • Fix ui$props$endpoint when the ui endpoint is defined in terms of
    the ode instead of lhs. See #754

  • Fix ui$props when the ui is a linear compartment model without ka defined.

  • Model extraction modelExtract() will now extract model properties. Note that the model property of alag(cmt) and lag(cmt) will give the same value. See #745

  • When assigning reserved variables, the parser will error. See #744

  • Linear interpolation will now adjust the times as well as the values
    when NA values are observed.

  • Fix when keeping data has NA values that it will not crash R; Also
    fixed some incorrect NA interpolations. See #756

  • When using cmt() sometimes the next statement would be corrupted
    in the normalized syntax (like for instance locf); This bug was
    fixed (#763)

  • keep will now error when trying to keep items that are in the
    rxode2 output data-frame and will be calculated (#764)

Big change

  • At the request of CRAN, combine rxode2parse, rxode2random, and
    rxode2et into this package; The changes in each of the packages are
    now placed here:

rxode2et (no changes before merge)

rxode2et 2.0.13

  • Fix import of data where there are NA times

rxode2et 2.0.12

  • Fix formatting issues identified by m1mac, as requested by CRAN

rxode2et 2.0.11

  • Make the stacking more flexible to help rxode2 have more types of plots

  • Add toTrialDuration by Omar Elashkar to convert event data to trial duration data

  • Fix Issue #23 and prefer variable values over NSE values

rxode2et 2.0.10

  • Fix dollar sign accessing of objects (like data frames), as pointed
    out by @frbrz (issue #16)

  • Use rxode2parse functions for internal event table creation (where
    they were moved to).

  • Dropped C++14 and let the system decide.

rxode2et 2.0.9

  • Split off et(), eventTable() and related functions.

  • Also split off rxStack() and rxCbindStudyIndividual() in this
    package.

  • Added a NEWS.md file to track changes to the package.

rxode2random (before merge)

  • Fix a bug when simulating nested variables (#25)

rxode2random 2.1.0

  • Breaking Change changed distributions from the standard C++
    <random> to boost::random. Since this is not dependent on the
    compiler, it makes the random numbers generated from Mac, Windows
    and Linux the same for every distribution. Unfortunately with a new
    random number transformation, the simulation results will likely be
    different than they were before. The exception to this is the
    uniform number, which was always the same between platforms.

rxode2random 2.0.13

  • Fixed formatting issues (as requested by CRAN and identified on m1mac)

rxode2random 2.0.12

  • Added function dfWishart which gives (by simulation) an
    approximation of the degrees of freedom of a Wishart to match a
    rse value.

  • Added function swapMatListWithCube which swaps omegaList with
    omegaCube values

  • Ensure that the outputs are integers (instead of long integers) as
    requested by CRAN for some checking functions.

rxode2random 2.0.11

  • Fix qassert LTO

rxode2random 2.0.10

  • Moved fast factor to rxode2parse to allow etTrans to be moved there

rxode2random 2.0.9

  • Initial release of rxode2random, which separates the parallel
    safe, random number generation from 'rxode2' into a separate package to
    reduce 'rxode2' compilation time. This should make CRAN maintenance
    a bit easier.

  • Added a NEWS.md file to track changes to the package.

rxode2parse (fixed before merging)

  • As requested by CRAN remove the C code SET_TYPEOF which is no
    longer part of the C R API.

rxode2parse 2.0.19

  • Added a evid suffix of 60 for cases where evid=2 adds an on event
    (fixes tad() calculation in certain edge cases)

  • Initialize all variables to NA

rxode2parse 2.0.18

  • Removed linear compartment solutions with gradients from rxode2parse
    (and rxode2) when compiled with intel c++ compiler (since it crashes
    while compiling).

  • Fixed m1mac string issues as requested by CRAN

rxode2parse 2.0.17

  • Added ability to query R user functions in a rxode2 model (will
    force single threaded solve)

  • Moved core rxFunParse and rxRmFunParse here so that C and R user
    function clashes can be handled

  • Model variables now tracks which compartments have a lag-time
    defined

  • For compartment with steady state doses (NONMEM equivalent SS=1,
    SS=2), an additional tracking time-point is added at to track the
    time when the lagged dose is given. As an upshot, the lagged dose
    will start at the steady state concentration shifted by + ii - lag
    in rxode2 (currently for ode systems only)

  • This release calculates non bio-availability adjusted duration for
    all rates instead of trying to figure the rate duration during
    solving.

  • Make double assignment an error, ie a <- b <-

  • NA times are ignored (with warning)

  • Steady state bolus doses with addl are treated as non steady state
    events (like what is observed in NONMEM)

  • Timsort was upgraded; drop radix support in rxode2 structure

  • etTrans now supports keeping logical vectors (with the appropriate
    version of rxode2).

  • Security fixes were applied as requested by CRAN

rxode2parse 2.0.16

  • Import data.table explicitly in the R code (before was imported only in C/C++ code)

rxode2parse 2.0.15

  • Updates the make flags to support CXX17.

rxode2parse 2.0.14

  • 'linCmt()' translations of 'alpha', 'beta', 'gamma', 'k21', 'k31',
    'vc' now error instead of ignoring 'gamma' and 'k31' to give 2 cmt
    solution

  • transit compartment internal code now changes dose to 0.0 when no
    dose has been administered to the depot compartment. This way dosing
    to the central compartment (without dosing to the transit
    compartment) will not give a NA for the depot compartment (and
    consequently for the central compartment)

  • Moved rxDerived here and added tests for it here as well.

  • Moved etTransParse here and added tests for it here as well (makes
    up most of etTrans). In addition the following changes were made
    to etTransParse()/etTrans():

    • The internal translation (etTrans()) will not drop times when
      infusions stop. Before, if the infusion stopped after the last
      observation the time when the infusion stopped would be dropped.
      This interferes with linCmt() models.

    • Breaking change/bug fix evid=2 are considered observations when
      translating data to internal rxode2 event structure

    • Fix edge case to find infusion duration when it is the first item
      of the dosing record at time 0.

  • Fixed a bug for certain infusions where the rate, ii and/or
    ss data items were dropped from the output when addDosing=TRUE

  • Also have internal functions to convert between classic NONMEM
    events and rxode2 events

  • Have an internal function that gives information on the linear
    compartmental model translation type, which could be useful for
    babelmixr2

  • 'time' in model is now case insensitive

  • Use function declaration in rxode2parseGetTranslation() to
    determine thread safety of functions available to rxode2

  • Add check for correct number of function arguments to parser.

  • Like R, known functions can be assigned as a variable and the
    function can still be called (while not changing the variable
    value). For example you can have a variable gamma as well as a
    function gamma().

  • Fix garbled error messages that occur with certain messages.

  • Fixed errors that occurred when using capitalized AMT variables in
    the model.

rxode2parse 2.0.13

  • Version bump for dparser (so binaries will be built correctly)

rxode2parse 2.0.12

  • Bug fix for strict prototypes

  • Removed sprintf as noted by CRAN

  • Made rxode2parse dll binary independent of rxode2()

rxode2parse 2.0.11

  • Bug fix for strict aliasing as requested by CRAN

rxode2parse 2.0.10

  • Use strict aliasing as requested by CRAN

What's Changed

Full Changelog: v2.1.3...v3.0.0

Contributors

mattfidler, billdenney, and frbrz
Assets 2
Loading