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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# babelmixr2
<!-- badges: start -->
[](https://github.com/nlmixr2/babelmixr2/actions/workflows/R-CMD-check.yaml)
[](https://cran.r-project.org/package=babelmixr2)
[](https://cran.r-project.org/package=babelmixr2)
[](https://cran.r-project.org/package=babelmixr2)
[](https://app.codecov.io/gh/nlmixr2/babelmixr2?branch=main)
[](https://www.codefactor.io/repository/github/nlmixr2/babelmixr2)
<!-- badges: end -->
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](https://CRAN.R-project.org) with:
``` r
install.packages("babelmixr2")
```
You can install from r-universe by:
``` r
# 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`](https://nlmixr2.github.io/babelmixr2/articles/running-nonmem.html) or `Monolix`
- Convert your [`NONMEM` model to a nlmixr2
model](https://nlmixr2.github.io/nonmem2rx/articles/convert-nlmixr2.html)
(in conjunction with `nonmem2rx`)
- Convert you [`Monolix` model to a nlmixr2
model](https://nlmixr2.github.io/monolix2rx/articles/convert-nlmixr2.html)
(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:
```r
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:
```r
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:
```r
mod <- nlmixr(nlmixrFun, nlmmixrData, est="nonmem")
```