R Observatory: Metrics for Ostats version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Ostats

0.2.0

O-Stats, or Pairwise Community-Level Niche Overlap Statistics

0packages depend

9.5Kdownloads / year

51.4%test coverage

13/13checks pass

Overview

About

Maintained by Quentin D. ReadFirst published 2021-07-263 releasesCRAN page ↗GitHub ↗

O-statistics, or overlap statistics, measure the degree of community-level trait overlap. They are estimated by fitting nonparametric kernel density functions to each species’ trait distribution and calculating their areas of overlap. For instance, the median pairwise overlap for a community is calculated by first determining the overlap of each species pair in trait space, and then taking the median overlap of each species pair in a community. This median overlap value is called the O-statistic (O for overlap). The Ostats() function calculates separate univariate overlap statistics for each trait, while the Ostats_multivariate() function calculates a single multivariate overlap statistic for all traits. O-statistics can be evaluated against null models to obtain standardized effect sizes. 'Ostats' is part of the collaborative Macrosystems Biodiversity Project "Local- to continental-scale drivers of biodiversity across the National Ecological Observatory Network (NEON)." For more information on this project, see the Macrosystems Biodiversity Website (https://neon-biodiversity.github.io/). Calculation of O-statistics is described in Read et al. (2018) doi:10.1111/ecog.03641, and a teaching module for introducing the underlying biological concepts at an undergraduate level is described in Grady et al. (2018) http://tiee.esa.org/vol/v14/issues/figure_sets/grady/abstract.html.

Install

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

install.packages("Ostats", 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("NEON-biodiversity/Ostats")

Development version from NEON-biodiversity/Ostats. 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-ostats

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-Ostats

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-Ostats

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 11.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.17

51.4%

Coverage · measured lines

100%

Documentation · exports

9

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 516 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 75%
Documented parameters: 100%
Return-value docs: 100%
References docs: 80%

Downloads

9.5K

CRAN downloads in the past year

Rank #5,152 · ~26/day · ~796/mo

Releases R versions

Daily download trend is not available in this view yet.

23330 days

1.5K90 days

9.5K1 year

Compare downloads with other packages →

Also on91 r2u18 autocran

Repository

GitHub ↗ neon-biodiversity/ostats

7Stars

2Forks

7Open issues

0Open PRs

3Releases

311Commits

7Contributors

ecologyr

311 commits · Last activity 2024-11-19

Stars over time

2022-01-20 · 72026-07-07 · 7

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/neon-biodiversity/ostats on 2026-08-16.

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (9)

sfsmisc matrixStats circular hypervolume ggplot2 gridExtra viridisgridMASS

LinkingTo (0)

none

Suggests (3)

testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (7)

Maintainer (1)

Quentin D. Read

Author, Maintainer

Authors (7)

Author, Maintainer

Author

Author

Author

Author

Author

Author

Listed in earlier versions (4)

Quentin D.

no longer listed · 0.1.0 to 0.2.0

Isadora E.

no longer listed · 0.1.0 to 0.2.0

Phoebe L.

no longer listed · 0.1.0 to 0.2.0

John M.

no longer listed · 0.1.0 to 0.2.0

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.2.0Latest
2022-09-12 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
0.1.1
2021-11-16 · diff ↗
0.1.0
2021-07-26
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-07-26
Total releases: 3 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 51 KB / 5 files
Download size: 525 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Ostats")

Format

Read, Q. D., Baiser, B., Fluck, I. E., Grady, J. M., Record, S., Yue, A., & Zarnetske, P. L. (2022). Ostats: O-Stats, or Pairwise Community-Level Niche Overlap Statistics (Version 0.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.Ostats

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 Ostats version 0.2.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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