R Observatory: Metrics for biomes version 0.9.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

biomes

0.9.5Package record

Reproducible Occurrence-to-Biome Classification Using 31 Global Biome Schemes

0packages depend

729downloads / year

29.5%test coverage

13/13flavors OK

Overview

About

Maintained by Hans Christian GroßCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: Alexander Zizka

Reproducibly classifies occurrence records into biomes using 31 published global biome schemes compiled by Fischer and colleagues (2022) doi:10.1111/geb.13574, provided as harmonised raster layers at 10x10 km resolution globally. Includes functions to choose the most suitable biome scheme for a dataset by a data-driven ranking, to classify occurrence records, and to tabulate and visualise the result. Works with user-provided occurrences or a taxon name, in which case occurrences are downloaded from GBIF (https://www.gbif.org) and cleaned automatically.

Changes in 0.9.5

The example dataset is now bombacoideae_occurrences: 17,030 occurrence records of 185 Bombacoideae species (Zizka et al. 2020), the worked example of the companion paper. It is used in the README, the vignettes and all function examples; the previous dataset biomes_example has been removed.
biomes_information gains the column biome_definition (climate, vegetation, land_cover, ecoregion, integrative, anthropogenic); the definition argument of biomes_rank(), biomes_visualise() and biomes_full(scheme = ) ranks within one biome definition. Scheme 6 (Zhang et al. 2017, climate and NDVI clustering) is integrative.
biomes_rank(): the criterion is called effective_biomes (columns effective_biomes_raw / _scaled); tiebreaker = "biomes". The ranking uses exactly the three criteria of the companion paper (coverage, effective_biomes, granularity), min-max rescaled and averaged with equal weights; the experimental criteria evenness, informativeness and agreement and the scaling argument have been removed. A criterion without variation among the compared schemes is left out of the composite (attribute criteria_used), and a single compared scheme gets no composite score (NA) but is still returned as best_scheme.

Show all changes in 0.9.5Hide the rest of the changes in 0.9.5

biomes_visualise(): the rank panel labels schemes as 25 (Ramankutty & Foley, 1999), shows all compared schemes (or the top_n best) on one 0 to 1 axis (the rescaled criterion values that enter the composite score; axis titles carry the symbols of the paper, Coverage (C), Effective biomes (E), Granularity (G)) and outlines the best composite score and the best value of each criterion in red; panels carry left-aligned titles with the panel letter and the reference of the chosen scheme (titles); the map legend lists biome names only (legend_counts = FALSE); the barplot uses the map colours per biome, grey for off-map records, and thousands separators.
Maintainer e-mail updated.

From NEWS.md in the release

Install

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

install.packages("biomes", 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("azizka/biomes")

Development version from azizka/biomes. 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-biomes

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-biomes

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-biomes

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: 5.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK7 OK2026-09-01

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.9.5

READMEYes · 559 wordsVignettesYes · 4 · evaluation depends on the environmentNEWSYes · 100% structured · mentions 0.9.5Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 13 (1 internal)includes a package overview page
Examples that run: 50%5 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run
Exported functions with examples: 100%
Documented parameters: 95%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (4)

How these are measured

Downloads

729

CRAN downloads in the past year

Rank #17,788 · ~2/day · ~61/mo

Releases R versions

Daily download trend is not available in this view yet.

36030 days

72990 days

7291 year

Compare downloads with other packages →

Also on9 r2u45 autocran

How downloads are counted

Repository

azizka/biomes ↗Account: azizka

2Stars

0Forks

0Open issues

0Open PRs

1Releases

50Commits

3Commit identities

License file reads as CC-BY-4.0 · 50 commits · Last activity 2026-10-05 · +100% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 18
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2026-09-01 · 12026-10-06 · 2

How these are measured

PracticesBeta

8 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/azizka/biomes on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-05 · The repository has a site deploy workflow

pkgdown site last built 2026-10-05

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing biomes adds 55 packages (32 with compiled code, 60 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, ggplot2 6.0 MB.

Depends (2)

R >= 4.1.0terra

Imports (8)

readr checkmate rlang ggplot2 sf viridis tidyterrautils

LinkingTo (0)

none

Suggests (10)

knitr rmarkdown testthat dplyr tidyr rgbif CoordinateCleaner cowplot ggforce rstudioapi

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 (4)

Hans Christian Groß

Maintainer since 0.9.4 (2026), Author

Jan-Christopher Fischer

Author

Anna Walentowitz

Author

Alexander Zizka

Author, Funder

Releases (2)

Pick two releases to compare their code metrics.

0.9.5Latest
record
2026-10-05 · current release · diff ↗
0.9.4
record
2026-08-31
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-08-31
Total releases: 2 / 1 yrs
License: CC BY 4.0
Minimum R: ≥ 4.1.0
Bundled data: 152 KB / 3 files
Download size: 229 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("biomes")

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

It points to 10.64898/2026.09.25.754345, 10.1111/geb.13574.

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 biomes version 0.9.5 [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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