nlmixr2 2.1.0/ rxode2 2.1.1
By Matthew Fidler in rxode2 nlmixr2
January 9, 2024
nlmixr2
2.1.0
was released 9 Jan 2024 which requires the newest
(and recently released) engine packages nlmixr2est
2.2.0
(released
12 Dec 2023) and rxode2
2.0.10
(released 13 Dec 2023).
I will be blogging about a few new features but want to mention a few now:
- More flexible mu referencing
- User defined functions can now be used with
nlmixr2
andrxode2
- Event handling changes
- Many new estimation methods for population only fitting
The truncated changelog for these packages are below:
nlmixr2 2.1.0
- Reexports
etExpand()
,model()<-
andini()<-
; Added required imports for newrxode2
/nlmixr2est
.
nlmixr2est 2.2.0
New Features
Algebraic mu referencing has been implemented in
nlme
andsaem
.New estimation method “nlm” has been added to estimate population only likelihoods using
stats::nlm
and possibly return a standardizednlmixr2
fit.New estimation method “nls” has been added to estimate population only problems. This uses
minpack.lm::nlsNM
by default if present, or thestats::nls
New estimation method “optim” has been added to estimate population only likelihoods. This uses
stats::optim
and returns a standardizednlmixr2
fit.New estimation method “nlminb” has been added to estimate population only likelihoods. This uses
stats::nlminb
and returns a standardizednlmixr2
fit.New estimation methods from the
minqa
package: “bobyqa”, “uobyqa” and “newuoa” have been added to estimate population only likelihoods. These methods returns a standardizednlmixr2
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 is10
. This also works-around a bug when there is only one subject simulated and thedata.frame
has a slightly different output.
Breaking changes
Removed
fit$saemTransformedData
since it isn’t actually used insaem
anymore (but will break anyone’s code who is using it)Now the internal function
.foceiPreProcessData()
requires the rxode2 controlrxControl()
because some of the new steady state lag features need to translate the data differently based onrxControl()
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)