babelmixr2

The goal of babelmixr2 is to interface nlmixr2 with other pharmacometric tools

https://github.com/nlmixr2/babelmixr2

Science Score: 26.0%

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Scientific vocabulary similarity
Low similarity (18.1%) to scientific vocabulary

Keywords

monolix nonmem pharmacometrics r

Last synced: 9 months ago · JSON representation

Repository

The goal of babelmixr2 is to interface nlmixr2 with other pharmacometric tools

Basic Info

Host: GitHub
Owner: nlmixr2
Language: R
Default Branch: main
Homepage: https://nlmixr2.github.io/babelmixr2/
Size: 22.6 MB

Statistics

Stars: 10
Watchers: 1
Forks: 2
Open Issues: 24
Releases: 9

Topics

monolix nonmem pharmacometrics r

Created over 4 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# babelmixr2


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![r-universe](https://nlmixr2.r-universe.dev/badges/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](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
. 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")
```

Owner

Name: nlmixr2
Login: nlmixr2
Kind: organization

Repositories: 21
Profile: https://github.com/nlmixr2

GitHub Events

Total

Create event: 24
Release event: 4
Issues event: 34
Watch event: 2
Delete event: 18
Issue comment event: 50
Push event: 139
Pull request event: 36
Fork event: 1

Last Year

Create event: 24
Release event: 4
Issues event: 34
Watch event: 2
Delete event: 18
Issue comment event: 50
Push event: 139
Pull request event: 36
Fork event: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time

Total issues: 102
Total pull requests: 92
Average time to close issues: 23 days
Average time to close pull requests: 4 days
Total issue authors: 9
Total pull request authors: 3
Average comments per issue: 1.62
Average comments per pull request: 0.51
Merged pull requests: 80
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 28
Pull requests: 50
Average time to close issues: 4 days
Average time to close pull requests: 3 days
Issue authors: 5
Pull request authors: 3
Average comments per issue: 0.96
Average comments per pull request: 0.22
Merged pull requests: 41
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

mattfidler (61)
billdenney (22)
TheoPapath (8)
john-harrold (5)
RichardHooijmaijers (2)
jeslo328 (1)
dzianismr (1)
bruc (1)
Grindelwarudo (1)

Pull Request Authors

mattfidler (68)
billdenney (22)
Enchufa2 (2)

Top Labels

Issue Labels

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Packages

Total packages: 1
Total downloads:
- cran 484 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 9
Total maintainers: 1

cran.r-project.org: babelmixr2

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

Homepage: https://nlmixr2.github.io/babelmixr2/
Documentation: http://cran.r-project.org/web/packages/babelmixr2/babelmixr2.pdf
License: GPL (≥ 3)
Latest release: 0.1.9
published 9 months ago

Versions: 9
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 484 Last month

Rankings

Dependent packages count: 29.8%

Dependent repos count: 35.5%

Average: 37.8%

Downloads: 48.1%

Maintainers (1)

matthew.fidler@gmail.com