v3.0.4

rxode2 3.0.4

• Add stable hashes for rxUi objects (#838, #689)

• Fix for iov simulation (#842)

• Fix for rxnbinom() called directly from R (#847) and expand it to
  match more close with R's rnbinom() including allowing named mu=
  calls. In rxode2 ui, these are also now allowed.

What's Changed

• rebuild documentation by @billdenney in #830
• Create a rxUi method for digest by @mattfidler in #838
• Fix nesting by @mattfidler in #844
• Fixes for rxnbinom by @mattfidler in #849

Full Changelog: v3.0.3...v3.0.4

v3.0.3

rxode2 3.0.3

• Add logit/expit named expressions, that is logit(x, high=20)
  becomes logit(x, 0, 20) in ui models.

• Updated random ui models like rxnorm(sd=10) to accept complex
  numeric expressions like rxnorm(sd=10+1).

• Updated random ui models to accept complex non-numeric expressions
  like rxnorm(sd=a+b)

• Rework the tad() and related functions so they use the same
  interface as compartments (this way they do not depend on the order
  of compartments); See #815. For mu-referencing, Also allow dummy
  variables to ignore state requirements (ie podo(depot) in a single
  line will not error when parsing mu-referenced equations).

• Add getRxNpars to api. This allows the development version of
  babelmixr2 to better check what model is loaded and unload/reload
  as necessary.

• Add rxUdfUiControl() to rxode2 user function to get control
  information from something like nlmixr2

• Bug fix for tracking time after dose when dosing to 2 compartments
  occur at the exact same time (#804, #819)

• Change transit() model so that it uses tad0(), podo0() and
  related functions for a bit more stable simulation and estimation

• Fix compile flags to work with BH 1.87 (#826)

What's Changed

• Add getRxNpars to api by @mattfidler in #802
• add rxUdfUiControl() by @mattfidler in #807
• White list PopOS with isystem by @mattfidler in #809
• simplify repeated ifelse by @billdenney in #800
• Add NN activation fns by @mattfidler in #811
• Create R NN activation interface by @mattfidler in #813
• Fix parsing for tad() and podo() by @mattfidler in #817
• Change the tlast handling to be based on tlast per cmt by @mattfidler in #819
• Named logit/expit by @mattfidler in #824
• Fix BH flags to work with BH 1.87.0 by @mattfidler in #826

Full Changelog: v3.0.2...v3.0.3

v3.0.2

rxode2 3.0.2

• Bug fix for api, the censoring function pointer has been updated
  (#801).

• Query rxode2.verbose.pipe at run time instead of requiring it to
  be set before loading rxode2.

• Have correct values at boundaries for logit, expit, probit,
  and probitInv (instead of NA). For most cases this does not
  break anything.

• Add a new style of user function that modifies the ui while
  parsing or just before using the function (in the presence of
  data).

• Used the new user function interface to allow all random functions
  in rxode2 ui functions to be named. For example, you can use
  rxnorm(sd=3) instead of having to use rxnorm(0, 3), although
  rxnorm() still works.

What's Changed

• CRAN issues by @mattfidler in #795
• Handle logit/expit probit/probitInv at boundaries similar to log by @mattfidler in #796
• rxode2.verbose.pipe by @mattfidler in #797
• Add user function in rxode2 ui that can change code when evaluating by @mattfidler in #782
• Documentation and pkgdown fix by @billdenney in #799
• API for censoring points to wrong function by @mattfidler in #801

Full Changelog: v3.0.1...v3.0.2

v3.0.1

rxode2 3.0.1

• Explicitly initialize the order vector to stop valgrind warning
  (requested from CRAN)

Full Changelog: v3.0.0...v3.0.1

v3.0.0

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. Th...

v2.1.3

rxode2 2.1.3

Bug fixes

• Make sure that the object is a uncompressed rxode2 ui for solving with rxSolve (See #661)

• Fix #670 by using the last simulated observation residual when there
  are trailing doses.

New features

• Create a function to see if a rxode2 solve is loaded in memory
  (rxode2::rxSolveSetup())

• Create a new function that fixes the rxode2 population values in the
  model (and drops them in the initial estimates); rxFixPop()

Other changes

• Pendantic no-remap (as requested by CRAN)

• gcc USBAN fix (as requested by CRAN)

What's Changed

• Lin cmt b fixed by @mattfidler in #646
• Fallback to archive by @mattfidler in #648
• 661 make sure the UI is uncompressed before checking for meta information by @mattfidler in #662
• Update events-classic by @mattfidler in #652
• Poped check free by @mattfidler in #664
• 670 a different model with est = rxsolve crashes r by @mattfidler in #671
• Add rxFPixPGop by @mattfidler in #673
• Update random tests and readme by @mattfidler in #676
• increase tol by @mattfidler in #678
• pedantic-no-remap by @mattfidler in #680
• 681 gcc usban fixes by @mattfidler in #682

Full Changelog: v2.1.2...v2.1.3

v2.1.2

rxode2 2.1.2

Other changes

• rxUi compression now defaults to fast compression

• Fixes String literal formatting issues as identified by CRAN (#643)

• Removes linear compartment solutions with gradients for intel c++
  compiler (since they crash the compiler).

What's Changed

• Move Rinternals inclusion order down by @mattfidler in #635
• Add fast compression by @mattfidler in #641
• Add forder and rxInv string fixes as requested by CRAN by @mattfidler in #644

Full Changelog: v2.1.0...v2.1.2

v2.1.0

rxode2 2.1.0

Breaking changes

• Steady state with lag times are no longer shifted by the lag time
  and then solved to steady state by default. In addition the steady
  state at the original time of dosing is also back-calculated. If you
  want the old behavior you can bring back the option with
  ssAtDoseTime=FALSE.

• "dop853" now uses the hmax/h0 values from the rxControl() or
  rxSolve(). This may change some ODE solving using "dop853"

• When not specified (and xgxr is available), the x axis is no longer
  assumed to be in hours

New features

• User defined functions can now be R functions. For many of these R
  functions they can be converted to C with rxFun() (you can see the
  C code afterwards with rxC("funName"))

• Parallel solving of models that require sorting (like modeled lag
  times, modeled duration etc) now solve in parallel instead of downgrading
  to single threaded solving

• Steady state infusions with a duration of infusions greater than the
  inter-dose interval are now supported.

• Added $symengineModelNoPrune and $symengineModelPrune for
  loading models into rxode2 with rxS()

• When plotting and creating confidence intervals for multiple
  endpoint models simulated from a rxode2 ui model, you can
  plot/summarize each endpoint with sim. (ie. confint(model, "sim") or plot(model, sim)).

  If you only want to summarize a subset of endpoints, you can focus
  on the endpoint by pre-pending the endpoint with sim. For example
  if you wanted to plot/summarize only the endpoint eff you would
  use sim.eff. (ie confint(model, "sim.eff") or plot(model, sim.eff))

• Added model$simulationIniModel which prepend the initial
  conditions in the ini({}) block to the classic rxode2({}) model.

• Now model$simulationModel and model$simulationIniModel will save
  and use the initialization values from the compiled model, and will
  solve as if it was the original ui model.

• Allow ini(model) <- NULL to drop ini block and as.ini(NULL)
  gives ini({}) (Issue #523)

• Add a function modelExtract() to extract model lines to allow
  modifying them and then changing the model by piping or simply
  assigning the modified lines with model(ui) <- newModifiedLines

• Add Algebraic mu-referencing detection (mu2) that allows you to
  express mu-referenced covariates as:

cl <- exp(tcl + eta.cl + wt_cl * log(WT/70.5))

Instead of the

cl <- exp(tcl + eta.cl + wt_cl * log.WT.div.70.5)

That was previously required (where log.WT.div.70.5 was calculated
in the data) for mu expressions. The ui now has more information to
allow transformation of data internally and transformation to the old
mu-referencing style to run the optimization.

• Allow steady state infusions with a duration of infusion greater than
  the inter-dose interval to be solved.

• Solves will now possibly print more information when issuing a
  "could not solve the system" error

• The function rxSetPipingAuto() is now exported to change the way you
  affect piping in your individual setup

• Allow covariates to be specified in the model piping, that is mod %>% model(a=var+3, cov="var") will add "var" as a covariate.

• When calculating confidence intervals for rxode2 simulated objects
  you can now use by to stratify the simulation summary. For
  example you can now stratify by gender and race by: confint(sim, "sim", by=c("race", "gender"))

• When calculating the intervals for rxode2 simulated objects you
  can now use ci=FALSE so that it only calculates the default
  intervals without bands on each of the percentiles; You can also
  choose not to match the secondary bands limits with levels but use
  your own ci=0.99 for instance

• A new function was introduced meanProbs() which calculates the
  mean and expected confidence bands under either the normal or t
  distribution

• A related new function was introduced that calculates the mean and
  confidence bands under the Bernoulli/Binomial distribution
  (binomProbs())

• When calculating the intervals for rxode2 simulated objects you
  can also use mean=TRUE to use the mean for the first level of
  confidence using meanProbs(). For this confidence interval you can
  override the n used in the confidence interval by using n=#. You
  can also change this to a prediction interval instead using
  pred=TRUE.

• Also when calculating the intervals for rxode2 simulated object
  you can also use mean="binom" to use the binomial distributional
  information (and ci) for the first level of confidence using
  binomProbs(). For this confidence interval you can override the
  n used in the confidence interval by using n=#. You can also
  change this to a prediction interval instead using pred=TRUE. With
  pred=TRUE you can override the number of predicted samples with
  m=#

• When plotting the confint derived intervals from an rxode2
  simulation, you can now subset based on a simulated value like
  plot(ci, Cc) which will only plot the variable Cc that you
  summarized even if you also summarized eff (for instance).

• When the rxode2 ui is a compressed ui object, you can modify the ini
  block with $ini <- or modify the model block with $model <-.
  These are equivalent to ini(model) <- and model(model) <-,
  respectively. Otherwise, the object is added to the user defined
  components in the function (ie $meta). When the object is
  uncompressed, it simply assigns it to the environment instead (just
  like before).

• When printing meta information that happens to be a lotri
  compatible matrix, use lotri to express it instead of the default
  R expression.

• Allow character vectors to be converted to expressions for piping
  (#552)

• rxAppendModel() will now take an arbitrary number of models and
  append them together; It also has better handling of models with
  duplicate parameters and models without ini() blocks (#617 / #573
  / #575).

• keep will now also keep attributes of the input data (with special
  handling for levels); This means a broader variety of classes will
  be kept carrying more information with it (for example ordered
  factors, data frame columns with unit information, etc)

• Piping arguments append for ini() and model() have been
  aligned to perform similarly. Therefore ini(append=) now can take
  expressions instead of simply strings and model(append=) can also
  take strings. Also model piping now can specify the integer line
  number to be modified just like the ini() could. Also
  model(append=FALSE) has been changed to model(append=NULL).
  While the behavior is the same when you don't specify the argument,
  the behavior has changed to align with ini() when piping. Hence
  model(append=TRUE) will append and model(append=FALSE) will now
  pre-pend to the model. model(append=NULL) will modify lines like
  the behavior of ini(append=NULL). The default of model(line)
  modifying a line in-place still applies. While this is a breaking
  change, most code will perform the same.

• Labels can now be dropped by ini(param=label(NULL)). Also
  parameters can be dropped with the idiom model(param=NULL) or
  ini(param=NULL) changes the parameter to a covariate to align with
  this idiom of dropping parameters

• rxRename has been refactored to run faster

Internal new features

• Add as.model() for list expressions, which implies model(ui) <- ui$lstExpr will assign model components. It will also more
  robustly work with character vectors

• Simulated objects from rxSolve now can access the model variables
  with $rxModelVars

• Simulation models from the UI now use rxerr.endpoint instead of
  err.endpoint for the sigma residual error. This is to align
  with the convention that internally generated variables start with
  rx or nlmixr

• Sorting only uses timsort now, and was upgraded to the latest
  version from Morwenn

Bug fixes

• Simulating/solving from functions/ui now prefers params over omega
  and sigma in the model (#632)

• Piping does not add constants to the initial estimates

• When constants are specified in the model({}) block (like k <- 1), they will not
  be to the ini block

• Bug fix for geom_amt() when the aes transformation has x

• Bug fix for some covariate updates that may affect multiple compartment
  models (like issue #581)

Maintenance fixes

• Modify plot code to work with development xgxr

What's Changed

• Update pkgdown by @billdenney in #508
• export .matchesLangTemplate() by @billdenney in #516
• Add mu2 detection by @mattfidler in #524
• Add as.ini(NULL) which fixes ini(model) <- NULL by @mattfidler in #525
• Remove duplicate by @mattfidler in #529
• 531 when time is na a backdoor debugging is needed by @mattfidler in #532
• Extract model lines initial function by @mattfidler in #534
• S0521 patch 2 by @mattfidler in #540
• Create RxODEchs.po by @s0521 in #539
• Create R-RxODEchs.po by @s0521 in #538
• Link to info on symengine installation; spelling fixes by @billdenney in #541
• Fix and test for nse by @mattfidler in #545
• Fix/test $ by @mattfidler in https://github.com/nlmixr2/rxode2/pull/...

v2.0.14

rxode2 2.0.14

• CRAN requested that FORTRAN kind be changed as it was not portable;
  This was commented code, and simply removed the comment.

• Bug-fix for geom_amt(); also now uses linewidth and at least ggplot2 3.4.0

• Some documentation was cleaned up from rxode2 2.0.13

Full Changelog: v2.0.13...v2.0.14

v2.0.13

• A bug was fixed so that the zeroRe() function works with correlated omega
  values.

• A bug was fixed so that the rename() function works with initial
  conditions for compartments (cmt(0))

What's Changed

• zeroRe() works with correlated omega matrices by @billdenney in #482
• Allow append to work with parameter promotion by @billdenney in #478
• Single thetas by @mattfidler in #489
• 495 solve function by @mattfidler in #497
• Add test and fix for #495 by @mattfidler in #496
• 487 piping bug rename doesnt work with initial conditions by @mattfidler in #498
• Simplify zeroRe to use ini(); Fix #490 by @billdenney in #501

Full Changelog: v2.0.12...v2.0.13