R Observatory: Metrics for bioinactivation version 1.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bioinactivation

1.3.1Package record

Mathematical Modelling of (Dynamic) Microbial Inactivation

0packages depend

4.3Kdownloads / year

22.2%test coverage

13/13flavors OK

Overview

About

Maintained by Alberto GarreCRAN page ↗

Functions for modelling microbial inactivation under isothermal or dynamic conditions. The calculations are based on several mathematical models broadly used by the scientific community and industry. Functions enable to make predictions for cases where the kinetic parameters are known. It also implements functions for parameter estimation for isothermal and dynamic conditions. The model fitting capabilities include an Adaptive Monte Carlo method for a Bayesian approach to parameter estimation.

Changes in 1.3.1

Bug fix in time_to_logreduction that caused the function to give an error when the survivor curve had NAs.

From NEWS.md in the release

Install

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

install.packages("bioinactivation", 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-bioinactivation

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-bioinactivation

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-bioinactivation

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.6 min · r-oldrel-windows-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 1.3.1

READMEYes · 126 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.3.1Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 47
Examples that run: 100%4 run in a plain check
Exported functions with examples: 29%
Documented parameters: 100%
Return-value docs: 86%
Help pages citing references: 0%

Vignettes (1)

bioinactivation: Software for modelling microbial inactivation HTML

How these are measured

Downloads

4.3K

CRAN downloads in the past year

Rank #7,169 · ~12/day · ~360/mo

Releases R versions

Daily download trend is not available in this view yet.

56630 days

1.2K90 days

4.3K1 year

Compare downloads with other packages →

Also on503 r2u23 autocran77 c2d4u

How downloads are counted

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing bioinactivation adds 34 packages (20 with compiled code, 24 MB of source tarballs). Heaviest: ggplot2 6.0 MB, FME 3.7 MB, deSolve 1.9 MB.

Depends (1)

R >= 2.10

Imports (10)

dplyr deSolve FME lazyeval ggplot2MASSgraphics (>= 3.1.3)statsrlang purrr

LinkingTo (0)

none

Suggests (4)

knitr testthat rmarkdown tidyr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Alberto Garre

Author, Maintainer · added in 1.1.1

Jose A. Egea

Author · added in 1.1.1

Pablo S. Fernandez

Author · added in 1.1.1

Maintainer since 1.0.1 (2015)

Listed in earlier versions (3)

Show 3 peopleHide 3 people

Jose A. Egea Larrosa

no longer listed · 1.0.1

Pablo S. Fernandez Egea

no longer listed · 1.0.1

Alberto Garre Perez

no longer listed · 1.0.1

Releases (11)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.3.1Latest
record
2025-11-03 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.3.0
record
2025-04-06 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.2.3
record
2019-08-01 · diff ↗ ·
added 2 exports
goodness_of_fit, time_to_logreduction
1.2.2
record
2019-06-05 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.2.1
record
2017-12-15 · diff ↗
1.2.0
record
2017-11-23 · diff ↗
R
R 3.4.0 released · 2017-04-21

Show 7 earlier eventsHide 7 earlier events

1.1.5
record
2017-01-29 · diff ↗
1.1.3
record
2016-09-18 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.1.2
record
2016-03-21 · diff ↗
1.1.1
record
2016-02-04 · diff ↗ ·
added 5 exports
is.FitInactivation, is.FitInactivationMCMC, is.IsoFitInactivation, is.PredInactivationMCMC, predict_inactivation_MCMC
1.0.1
record
2015-12-11
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-12-11
Total releases: 11 / 11 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10
Bundled data: 2.5 KB / 4 files
Download size: 190 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("bioinactivation")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1016/j.foodres.2017.01.012.

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 bioinactivation version 1.3.1 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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