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babelmixr2

The goal of babelmixr2 is to convert nlmixr2 syntax to other commonly used tools.

Installation

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:

What you can do with 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

Monolix Setup

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.

PKNCA Example

After installed, if you use the standard interface, you can obtain new initial estimates with PKNCA:

mod <-
  nlmixr2(
    nlmixrFun, nlmmixrData, est = "pknca",
    control = pkncaControl(concu = "ng/mL", doseu = "mg", timeu = "hr", volumeu = "L")
  )

Monolix example

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:

mod <- nlmixr(nlmixrFun, nlmmixrData, est="monolix")

NONMEM example

With babelmixr2 loaded you can use nlmixr2 to convert a nlmixr2 model to NONMEM, run NONMEM and import back to nlmixr2 with the following:

mod <- nlmixr(nlmixrFun, nlmmixrData, est="nonmem")