In nlmixr2/babelmixr: Use 'nlmixr2' to Interact with Open Source and Commercial Software

knitr::opts_chunk$set(
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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)

• Calculate scaling factors and automatically add initial conditions based on non-compartmental analysis (using PKNCA)

Monolix Setup

While not required, you can get/install the R 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url https://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/. When 'lixoftConnectors' is available, R can run 'Monolix' directly instead of using a command line.

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")
  )

or, you can convert to Monolix with

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

or, you can convert to NONMEM with

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

nlmixr2/babelmixr documentation built on Sept. 8, 2024, 1:21 a.m.