R Observatory: Metrics for ecocbo version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ecocbo

1.0.0Package record

Calculating Optimum Sampling Effort in Community Ecology

0packages depend

3.1Kdownloads / year

39.6%test coverage

13/13flavors OK

Overview

About

Maintained by Arturo Sanchez-PorrasCRAN page ↗GitHub ↗Issues ↗

A system for calculating the optimal sampling effort, based on the ideas of "Ecological cost-benefit optimization" as developed by A. Underwood (1997, ISBN 0 521 55696 1). Data is obtained from simulated ecological communities with prep_data() which formats and arranges the initial data, and then the optimization follows the following procedure of four functions: (1) prep_data() takes the original dataset and creates simulated sets that can be used as a basis for estimating statistical power and type II error. (2) sim_beta() is used to estimate the statistical power for the different sampling efforts specified by the user. (3) sim_cbo() calculates then the optimal sampling effort, based on the statistical power and the sampling costs. Additionally, (4) scompvar() calculates the variation components necessary for (5) Underwood_cbo() to calculate the optimal combination of number of sites and samples depending on either an economic budget or on a desired statistical accuracy. Lastly, (6) plot_power() helps the user visualize the results of sim_beta().

Changes in 1.0.0

Major update

PERMANOVA refactor: The implementation used by prep_data() now uses a distance-based MANOVA (dbManova...()) pipeline using Gower-centered distance matrices. This replaces the previous SS calculations based on Huygens' theorem
The new approach is numerically more stable, especially with non-Euclidean distances (e.g., Bray–Curtis), where negative eigenvalues can invalidate naive SS partitions.
Sums of squares are obtained from projection matrices in the PCoA space (SSCP traces), with correct handling of negative eigenvalues (sign weighting), avoiding drift due to rounding/centering errors.
Results are therefore more robust and interpretable across a wider range of ecological distances.

Notes on compatibility

The user API of prep_data() remains the same. Small numerical differences may occur due to more correct SS partitioning.

From NEWS.md in the release

Install

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

install.packages("ecocbo", 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("arturoSP/ecocbo")

Development version from arturoSP/ecocbo. 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-ecocbo

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-ecocbo

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-ecocbo

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: 3.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMEYes · 272 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 19 (5 internal)includes a package overview page
Examples that run: 100%7 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 53%

Vignettes (1)

ecocbo-guide HTML

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #15,659 · ~9/day · ~262/mo

Releases R versions

Daily download trend is not available in this view yet.

32930 days

77390 days

3.1K1 year

Compare downloads with other packages →

Also on92 r2u10 autocran

How downloads are counted

Repository

arturosp/ecocbo ↗Account: arturoSP

0Stars

1Forks

0Open issues

0Open PRs

0Releases

99Commits

2Commit identities

License file reads as GPL-3.0 · 99 commits · Last activity 2026-03-28

Responsiveness

How these are sampled

PRs merged (all time): 89%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Forks over time

2024-01-31 · 12026-07-07 · 1

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/arturosp/ecocbo on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (1)

README.Rmd

Reproducibility and dev environment (1)

data-raw/

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing ecocbo adds 117 packages (59 with compiled code, 102 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.1.0

Imports (13)

ggplot2 ggpubrstatsrlang tibble dplyr tidyr tidyselect parabar parallelly vegan SSP plotly

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

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 (2)

Arturo Sanchez-Porras

Author, Maintainer since 0.10.2 (2023)

Edlin Guerra-Castro

Author, Copyright holder

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
record
2025-11-22 · current release · diff ↗
0.13.0
record
2025-08-23 · diff ↗ ·
removed 7 exports
SS, balanced_sampling, balanced_sampling2, permanova_oneway, permanova_twoway, prep_data_nestedsymmetric, prep_data_single

added 1 export
Underwood_cbo
R
R 4.5.0 released · 2025-04-11
0.12.0
record
2024-08-21 · diff ↗ ·
added 6 exports
SS, balanced_sampling2, permanova_twoway, prep_data, prep_data_nestedsymmetric, prep_data_single
R
R 4.4.0 released · 2024-04-24
0.10.2
record
2023-08-18
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-08-18
Total releases: 4 / 3 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Bundled data: 1.6 MB / 7 files
Download size: 1.9 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ecocbo")

Format

Sanchez-Porras, A., & Guerra-Castro, E. (2025). ecocbo: Calculating Optimum Sampling Effort in Community Ecology (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.ecocbo

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 ecocbo version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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