Use 'nlmixr2' to Interact with Open Source and Commercial Software

Run other estimation and simulation software via the 'nlmixr2' (Fidler et al (2019) ) interface including 'PKNCA', 'NONMEM' and 'Monolix'. While not required, you can get/install the '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, 'Monolix' can be run directly instead of setting up command line usage.

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")