R Observatory: Metrics for BioIndex version 0.6.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BioIndex

0.6.5Package record

Biological Indicators and Indices for MEDITS Survey Data

0packages depend

1.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Walter ZupaCRAN page ↗

Supports the standardized analysis of Mediterranean International Bottom Trawl Survey (MEDITS) data and the calculation of biological indicators for selected species and population components. The package provides functions to estimate abundance and biomass indices, analyse size structure and length frequency distributions, derive sex ratio and maturity related metrics, explore spatial patterns, and assess temporal trends across surveys. Developed for integration within the Regional Database for Fisheries (RDBFIS) framework, it is intended to work on quality checked input data and to produce reproducible outputs that can support monitoring, comparative analyses among Geographical Sub-Areas (GSAs) and countries, and fishery management.

Changes in 0.6.5

__Maintenance release__

Fixed species selection in merge_TATB(), merge_TATC(), and merge_TATBTC() when species = "all". The merge functions now retain all species records instead of incorrectly interpreting "all" as a MEDITS species code.
Added the rome_checks argument to merge_TATB(), merge_TATC(), and merge_TATBTC() to allow users to run or skip the internal syntactic checks based on RoME v0.2.3 logic.
Set rome_checks = FALSE as default in the updated merge functions, allowing users to bypass RoME-like syntactic checks unless explicitly requested with rome_checks = TRUE.
Updated roxygen2 documentation for merge_TATB(), merge_TATC(), and merge_TATBTC() to describe the use of species = "all" and the new rome_checks argument.

From NEWS.md in the release

Install

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

install.packages("BioIndex", 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-bioindex

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-BioIndex

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: 10.9 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK8 OK2026-05-30

Advisories

none known

How this is measured·How advisories are found

Documentation

Documentation signals are not tracked yet for this package.

Websitenot tracked

Vignettes (1)

BioIndex HTML

How these are measured

Downloads

1.8K

CRAN downloads in the past year

Rank #11,781 · ~5/day · ~154/mo

BioIndex Releases R versions

Daily download trend is not available in this view yet.

28530 days

92990 days

1.8K1 year

Compare downloads with other packages →

Also on52 r2u

How downloads are counted

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing BioIndex adds 83 packages (51 with compiled code, 97 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.1

Imports (15)

dplyr ggplot2 gridExtra hms magrittr marmapmethodsmgcvreshape2 shiny shinyjs stringr terra tidyterra zip

LinkingTo (0)

none

Suggests (4)

knitr mapproj maps rmarkdown

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 (5)

Walter Zupa

Author, Maintainer since 0.6.4 (2026)

Maria Teresa Spedicato

Author

Isabella Bitetto

Reviewer

Loredana Casciaro

Reviewer

Cosmidano Neglia

Reviewer

Releases (2)

0.6.5Latest
record
2026-07-23 · current release · diff ↗
0.6.4
record
2026-05-29
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-05-29
Total releases: 2 / 1 yrs
License: GPL-3 OSI
Download size: 3.9 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BioIndex")

Format

Zupa, W., Bitetto, I., Casciaro, L., Neglia, C., & Spedicato, M. T. (2026). BioIndex: Biological Indicators and Indices for MEDITS Survey Data (Version 0.6.5) [Computer software]. https://doi.org/10.32614/CRAN.package.BioIndex

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 BioIndex version 0.6.5 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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