v2.0.12
rxode2 2.0.12
New features
-
A new function
zeroRe()
allows simple setting of omega and/or sigma values
to zero for a model (#456) -
Diagonal zeros in the
omega
andsigma
matrices are treated as
zeros in the model. The correspondingomega
andsigma
matrices
drop columns/rows where the diagonals are zero to create a new
omega
andsigma
matrix for simulation. This is the same idiom
that NONMEM uses for simulation from these matrices. -
Add the ability to pipe model estimates from another model by
parentModel %>% ini(modelWithNewEsts)
-
Add the ability to append model statements with piping using
%>% model(x=3, append=d/dt(depot))
, still supports appending with
append=TRUE
and pre-pending withappend=NA
(the default is to
replace lines withappend=FALSE
) -
rxSolve's keep argument will now maintain character and factor classes from
input data with the same class (#190) -
Parameter labels may now be modified via
ini(param = label("text"))
(#351). -
Parameter order may be modified via the
append
argument toini()
when piping a model. For example,ini(param = 1, append = 0)
or
ini(param = label("text"), append = "param2")
(#352).
Internal changes
-
If lower/upper bounds are outside the required bounds, the
adjustment is displayed. -
When initial values are piped that break the model's boundary
condition reset the boundary to unbounded and message which boundary
was reset. -
Added
as.rxUi()
function to convert the following objects to
rxUi
objects:rxode2
,rxModelVars
,function
. Converting
nlmixr2 fits torxUi
will be placed in thes3
method in the
corresponding package. -
assertRxUi(x)
now usesas.rxUi()
so that it can be extended
outside ofrxode2
/nlmixr2
. -
rxode2
now supportsaddl
withss
doses -
Moved
rxDerived
torxode2parse
(and re-exported it here). -
Added test for transit compartment solving in absence of dosing to the
transit compartment (fixed inrxode2parse
but solving tested
here) -
Using
ini()
without any arguments on arxode2
type function will
return theini()
block. Also added a methodini(mod) <- iniBlock
to modify theini
block is you wish.iniBlock
should
be an expression. -
Using
model()
without any arguments on arxode2
type function
will return themodel()
block. Also added a new method
model(mod) <- modelBlock
-
Added a new method
rxode2(mod) <- modFunction
which allows
replacing the function with a new function while maintaining the
meta information about the ui (like information that comes from
nonmem2rx
models). ThemodFunction
should be the body of the
new function, the new function, or a newrxode2
ui. -
rxode2
ui objects now have a$sticky
item inside the internal
(compressed) environment. This$sticky
tells what variables to
keep if there is a "significant" change in the ui during piping or
other sort of model change. This is respected during model piping,
or modifying the model withini(mod)<-
,model(mod)<-
,
rxode2(mod)<-
. A significant change is a change in the model
block, a change in the number of estimates, or a change to the value
of the estimates. Estimate bounds, weather an estimate is fixed or
estimate label changes are not considered significant. -
Added
as.ini()
method to convert various formats to an ini
expression. It is used internally withini(mod)<-
. If you want to
assign something new that you can convert to an ini expression, add
a method foras.ini()
. -
Added
as.model()
method to convert various formats to a model
expression. It is used internally withmodel(mod)<-
. If you want to
assign something new that you can convert to a model expression, add
a method foras.model()
.
What's Changed
- Allow removal of linCmt() endpoints by @billdenney in #356
- Remove loadNamespace() wherever possible by @billdenney in #362
- Update CI by @billdenney in #353
- Minor code changes by @billdenney in #365
- Don't show warnings for directory creation by @billdenney in #368
- Start using already exported rxode2random fns by @mattfidler in #374
- Move linCmt() checks to rxode2parse, fix #361 by @mattfidler in #381
- Make testing quieter by @billdenney in #380
- Remove extra files by @billdenney in #383
- Correct default option for append in documentation (no code changes) by @billdenney in #390
- Issue 387 by @mattfidler in #391
- Issue 378 by @mattfidler in #392
- 366 currently this is not possible but perhaps in the future something like model append=lhs variable and it will append after the first occurrence of lhs variable by @mattfidler in #393
- Add eta association by @mattfidler in #397
- 403 assignment of null into an rxsolve object fails when it should remove the column by @mattfidler in #404
- Add failing tests for #190 by @mattfidler in #405
- Switch to arma_cerr_stream by @eddelbuettel in #406
- Remove cerr_stream by @mattfidler in #408
- Be a bit more paranoid by @mattfidler in #411
- Allow reordering parameters by @billdenney in #385
- Correct append mention by @billdenney in #418
- 414 allow models to be piped by @mattfidler in #415
- Fix typo by @billdenney in #419
- Complete testing for .nearPD() by @billdenney in #426
- Simplify and add testing for .amtTrans() by @billdenney in #425
- 427 error removing parameter by @mattfidler in #429
- Complete testing for assert.R by @billdenney in #430
- Add failing test for #433 by @mattfidler in #434
- add as.formula suppport by @mattfidler in #445
- Change rename to s3 method by @mattfidler in #446
- Expand documentation of ini() to show more examples by @billdenney in #447
- Add some test cases and fix the case where the rate column is dropped by @mattfidler in #449
- 450 from UI simulate zero diagonals as zero thetas by @mattfidler in #451
- ui piping for ini(eta1~fix) fix/test by @mattfidler in #452
- Add items from multiexp experiment by @mattfidler in #453
- Add zeroRe() by @billdenney in #457
- Add support for steady state addl by @mattfidler in #455
- 459 it is possible to set an estimate outside of the parameter boundaries by @mattfidler in #462
- 460 a negative lower bound for residual error is silently set to zero by @mattfidler in #463
- 458 when using transit by @mattfidler in #465
- Rm et trans by @mattfidler in #466
- Modify news to be separated out by features. Bump version by @mattfidler in #468
- Add a body assignment method for rxUi objects by @billdenney in #470
- 473 not done yet by @mattfidler in #474
New Contributors
- @eddelbuettel made their first contribution in #406
Full Changelog: v2.0.11...v2.0.12