The goal of babelmixr2 is to convert nlmixr2 syntax to other commonly used tools.
You can install the released version of babelmixr2 from CRAN with:
install.packages("babelmixr2")
You can install from r-universe by:
# Download and install babelmixr2 in R
install.packages('babelmixr2',
repos = c(
nlmixr2 = 'https://nlmixr2.r-universe.dev',
CRAN = 'https://cloud.r-project.org'))
Otherwise you can always install from GitHub:
babelmixr2
Babelmixr2 can help you by:
Running your nlmixr2 model in a commercial nonlinear mixed
effects modeling tool like NONMEM
or Monolix
Convert your NONMEM
model to a nlmixr2 model (in conjunction with
nonmem2rx
)
Convert you Monolix
model to a nlmixr2 model (in conjunction with
monolix2rx
)
Calculate scaling factors and automatically add initial
conditions based on non-compartmental analysis (using
PKNCA
)
Perform Optimal design using nlmixr2 as an interface to
PopED
While not required, you can get/install the R ‘lixoftConnectors’ package in the ‘Monolix’ installation, as described at the following url https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization. When ‘lixoftConnectors’ is available, R can run ‘Monolix’ directly instead of using a command line.
After installed, if you use the standard interface, you can obtain new initial estimates with PKNCA:
<-
mod nlmixr2(
est = "pknca",
nlmixrFun, nlmmixrData, control = pkncaControl(concu = "ng/mL", doseu = "mg", timeu = "hr", volumeu = "L")
)
With babelmixr2 loaded, you can use nlmixr2
to convert a
nlmixr2 model to Monolix, run with monolix, and import back to nlmixr2
with the following:
<- nlmixr(nlmixrFun, nlmmixrData, est="monolix") mod
With babelmixr2 loaded you can use nlmixr2
to convert a
nlmixr2 model to NONMEM, run NONMEM and import back to nlmixr2 with the
following:
<- nlmixr(nlmixrFun, nlmmixrData, est="nonmem") mod