R Observatory: Metrics for dynafluxr version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

dynafluxr

1.0.1Package record

Retrieve Reaction Rate Dynamics from Metabolite Concentration Time Courses

0packages depend

2.2Kdownloads / year

37.3%test coverage

13/13flavors OK

Overview

About

Maintained by Serguei SokolCRAN 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().

Changes in 1.0.1

corrections for public release on CRAN

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

CRAN check page ↗

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

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMEYes · 109 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 4
Examples that run: 100%1 run in a plain check
Exported functions with examples: 25%
Documented parameters: 83%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

glyco HTML

How these are measured

Downloads

2.2K

CRAN downloads in the past year

Rank #19,426 · ~6/day · ~183/mo

Releases R versions

Daily download trend is not available in this view yet.

19230 days

68390 days

2.2K1 year

Compare downloads with other packages →

Also on55 r2u

How downloads are counted

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing dynafluxr adds 50 packages (31 with compiled code, 31 MB of source tarballs). Heaviest: bslib 5.6 MB, promises 3.1 MB, sass 2.9 MB.

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.

How these are counted

Code & Tests

People & History

People (1)

Serguei Sokol

Author, Maintainer since 1.0.1 (2025)

Releases (1)

R
R 4.6.0 released · 2026-04-24
1.0.1Latest
record
2025-07-10 · 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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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