R Observatory: Metrics for pmxNODE version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pmxNODE

0.1.0

Application of NODEs in 'Monolix', 'NONMEM', and 'nlmixr2'

1packages depend

1.7Kdownloads / year

27.5%test coverage

13/13checks pass

Overview

About

Maintained by Dominic BrämFirst published 2025-11-261 releasesCRAN page ↗GitHub ↗

An easy-to-use tool for implementing Neural Ordinary Differential Equations (NODEs) in pharmacometric software such as 'Monolix', 'NONMEM', and 'nlmixr2', see Bräm et al. (2024) doi:10.1007/s10928-023-09886-4 and Bräm et al. (2025) doi:10.1002/psp4.13265. The main functionality is to automatically generate structural model code describing computations within a neural network. Additionally, parameters and software settings can be initialized automatically. For using these additional functionalities with 'Monolix', 'pmxNODE' interfaces with 'MonolixSuite' via the 'lixoftConnectors' package. The 'lixoftConnectors' package is distributed with 'MonolixSuite' (https://monolixsuite.slp-software.com/r-functions/2024R1/package-lixoftconnectors) and is not available from public repositories.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("pmxNODE", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("braemd/pmxNODE")

Development version from braemd/pmxNODE. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-pmxnode

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-pmxNODE

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-pmxNODE

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 4.5 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.71

27.5%

Coverage · measured lines

100%

Documentation · exports

3

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 686 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 46%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

1.7K

CRAN downloads in the past year

Rank #14,826 · ~5/day · ~145/mo

Releases R versions

Daily download trend is not available in this view yet.

25230 days

69190 days

1.7K1 year

Compare downloads with other packages →

Also on60 r2u10 autocran

Repository

GitHub ↗ braemd/pmxnode

4Stars

1Forks

0Open issues

0Open PRs

0Releases

87Commits

2Contributors

License GPL-3.0 · 87 commits · Last activity 2026-05-15

Stars over time

2025-06-12 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/braemd/pmxnode on 2026-08-03.

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (3)

tidyr ggplot2 checkmate

LinkingTo (0)

none

Suggests (7)

rxode2 nlmixr2 lixoftConnectors withr testthat (>= 3.0.0)knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

nlmixr2

Code & Tests

People & History

People (4)

Maintainer (1)

Dominic Bräm

Author, Maintainer

Authors (1)

Dominic Bräm

Author, Maintainer

Contributors (3)

Matthew Fidler

Contributor

Gilbert Koch

Contributor

Bernhard Steiert

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-11-26
Total releases: 1 / 1 yrs
License: GPL (>= 3) OSI
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pmxNODE")

Format

Bräm, D., Fidler, M., Koch, G., & Steiert, B. (2025). pmxNODE: Application of NODEs in 'Monolix', 'NONMEM', and 'nlmixr2' (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.pmxNODE

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for pmxNODE version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-08. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-08, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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