R Observatory: Metrics for dynafluxr version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

dynafluxr

1.0.1

Retrieve Reaction Rate Dynamics from Metabolite Concentration Time Courses

0packages depend

2Kdownloads / year

37.3%test coverage

13/13checks pass

Overview

About

Maintained by Serguei SokolFirst published 2025-07-101 releasesCRAN page ↗

Reaction rate dynamics can be retrieved from metabolite concentration time courses. User has to provide corresponding stoichiometric matrix but not a regulation model (Michaelis-Menten or similar). Instead of solving an ordinary differential equation (ODE) system describing the evolution of concentrations, we use B-splines to catch the concentration and rate dynamics then solve a least square problem on their coefficients with non-negativity (and optionally monotonicity) constraints. Constraints can be also set on initial values of concentration. The package 'dynafluxr' can be used as a library but also as an application with command line interface dynafluxr::cli("-h") or graphical user interface dynafluxr::gui().

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)

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

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

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-dynafluxr

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-dynafluxr

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

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

Health

CRAN checks

13OK

Slowest check: 1.9 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.01

37.3%

Coverage · measured lines

100%

Documentation · exports

10

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 109 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 83%
Return-value docs: 100%
References docs: 0%

Downloads

2K

CRAN downloads in the past year

Rank #19,657 · ~5/day · ~167/mo

Releases R versions

Daily download trend is not available in this view yet.

16030 days

56090 days

2K1 year

Compare downloads with other packages →

Also on80 r2u

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (2)

bspline nlsic

Imports (8)

optparse qpdf arrApply slam gmresls shiny shinyjs shinyFiles

LinkingTo (0)

none

Suggests (2)

RUnit knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Serguei Sokol

Author, Maintainer

Authors (1)

Serguei Sokol

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.1Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-07-10
Total releases: 1 / 1 yrs
License: GPL-2 OSI
Download size: 190 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("dynafluxr")

Format

Sokol, S. (2025). dynafluxr: Retrieve Reaction Rate Dynamics from Metabolite Concentration Time Courses (Version 1.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.dynafluxr

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 dynafluxr version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-08-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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