ohun

Automatic detection of acoustic signals

https://github.com/ropensci/ohun

Science Score: 57.0%

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Low similarity (19.6%) to scientific vocabulary

Keywords

audio-processing bioacoustics sound-event-detection spectrogram streamline-analysis

Keywords from Contributors

animal interpretability standardization hack

Last synced: 4 months ago · JSON representation ·

Repository

Automatic detection of acoustic signals

Basic Info

Host: GitHub
Owner: ropensci
Language: HTML
Default Branch: master
Homepage: https://docs.ropensci.org/ohun/
Size: 175 MB

Statistics

Stars: 16
Watchers: 3
Forks: 2
Open Issues: 7
Releases: 0

Topics

audio-processing bioacoustics sound-event-detection spectrogram streamline-analysis

Created over 4 years ago · Last pushed 5 months ago

Metadata Files

Readme Changelog Contributing Citation Codemeta

README.Rmd

---
title: "ohun: optimizing sound event detection"
output: github_document
editor_options: 
  chunk_output_type: console
---




[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html)
[![Dependencies](https://tinyverse.netlify.com/badge/ohun)](https://cran.r-project.org/package=ohun)
[![Project Status: Active  The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![Licence](https://img.shields.io/badge/licence-GPL--2-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)
[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/ohun)](https://cran.r-project.org/package=ohun)
[![Total Downloads](https://cranlogs.r-pkg.org/badges/grand-total/ohun)](https://cranlogs.r-pkg.org/badges/grand-total/ohun)
[![Codecov test coverage](https://codecov.io/gh/maRce10/ohun/branch/master/graph/badge.svg)](https://app.codecov.io/gh/maRce10/ohun?branch=master)
[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/568_status.svg)](https://github.com/ropensci/software-review/issues/568)




[ohun](https://github.com/ropensci/ohun) is intended to facilitate the automated detection of sound events, providing functions to diagnose and optimize detection routines. It provides utilities for comparing detection and annotations of audio events described by frequency and time boxes.

The main features of the package are:
 
   - The use of reference annotations for detection diagnostic and optimization 
   - The use of signal detection theory indices to evaluate detection performance 

The package offers functions for:

   - Curate references and acoustic data sets
   - Diagnose detection performance
   - Optimize detection routines based on reference annotations
   - Energy-based detection
   - Template-based detection
  
The implementation of detection diagnostics that can be applied to both built in detection methods and to those obtained from other software packages makes the package [ohun](https://github.com/ropensci/ohun) an useful tool for conducting direct comparisons of the performance of different routines. In addition, the compatibility of [ohun](https://github.com/ropensci/ohun) with data formats already used by other sound analysis R packages (e.g. seewave, warbleR) enables the integration of [ohun](https://github.com/ropensci/ohun) into more complex acoustic analysis workflows in a popular programming environment within the research community. 
 
All functions allow the parallelization of tasks (using the packages parallel and [pbapply](https://CRAN.R-project.org/package=pbapply)), which distributes the tasks among several processors to improve computational efficiency. The package works on sound files in '.wav', '.mp3', '.flac' and '.wac' format.

Install/load the package from CRAN as follows:

```{r, eval = FALSE}

# From CRAN would be
install.packages("ohun")

#load package
library(ohun)

```


To install the latest developmental version from [github](https://github.com/) you will need the R package [remotes](https://cran.r-project.org/package=remotes):

```{r, eval = FALSE}
remotes::install_github("ropensci/ohun")

#load package
library(ohun)

```

Further system requirements due to the dependency [seewave](https://rug.mnhn.fr/seewave/) may be needed. Take a look a [this link]( https://rug.mnhn.fr/seewave/inst.html) for instruction on how to install/troubleshoot these external dependencies. 

Take a look at the vignettes for an overview of the main features of the packages:

- [Optimizing sound event detection](https://docs.ropensci.org/ohun/articles/intro_to_ohun.html)
- [Energy-based detection](https://docs.ropensci.org/ohun/articles/energy_based_detection.html)
- [Template-based detection](https://docs.ropensci.org/ohun/articles/template_based_detection.html)

This package has been [peer-reviewed by rOpenSci](https://github.com/ropensci/software-review/issues/568).

---

Please cite [ohun](https://github.com/ropensci/ohun) as follows:

 Araya-Salas, M., Smith-Vidaurre, G., Chaverri, G., Brenes, J. C., Chirino, F., Elizondo-Calvo, J., & Rico-Guevara, A. (2023). ohun: An R package for diagnosing and optimizing automatic sound event detection. Methods in Ecology and Evolution, 14, 2259–2271. https://doi.org/10.1111/2041-210X.14170

Owner

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
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title: 'ohun: Optimizing Acoustic Signal Detection'
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identifiers:
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abstract: Facilitates the automatic detection of acoustic signals, providing functions
  to diagnose and optimize the performance of detection routines. Detections from
  other software can also be explored and optimized. This package has been peer-reviewed
  by rOpenSci. Araya-Salas et al. (2022) <https://doi.org/10.1101/2022.12.13.520253>.
authors:
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repository: https://CRAN.R-project.org/package=ohun
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url: https://docs.ropensci.org/ohun/
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  email: marcelo.araya@ucr.ac.cr
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references:
- type: software
  title: tuneR
  abstract: 'tuneR: Analysis of Music and Speech'
  notes: Imports
  url: https://tuner.R-forge.R-project.org
  repository: https://CRAN.R-project.org/package=tuneR
  authors:
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  - family-names: Krey
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  - family-names: Mersmann
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  - family-names: Schnackenberg
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  - family-names: Guénard
    given-names: Guillaume
  - family-names: Ellis
    given-names: Daniel P. W.
  - name: Underbit Technologies
  year: '2025'
  doi: 10.32614/CRAN.package.tuneR
- type: software
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  abstract: 'warbleR: Streamline Bioacoustic Analysis'
  notes: Imports
  url: https://marce10.github.io/warbleR/
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  authors:
  - family-names: Araya-Salas
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  year: '2025'
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  authors:
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  authors:
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  year: '2025'
- type: software
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  notes: Imports
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  authors:
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  - family-names: Simonis
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  year: '2025'
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  authors:
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  notes: Suggests
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GitHub Events

Total

Issues event: 4
Watch event: 3
Issue comment event: 1
Push event: 30

Last Year

Issues event: 4
Watch event: 3
Issue comment event: 1
Push event: 30

Committers

Last synced: almost 2 years ago

All Time

Total Commits: 292
Total Committers: 3
Avg Commits per committer: 97.333
Development Distribution Score (DDS): 0.158

Past Year

Commits: 215
Committers: 3
Avg Commits per committer: 71.667
Development Distribution Score (DDS): 0.214

Top Committers

Name	Email	Commits
Marcelo Araya-Salas	m**a@u**r	246
Alec L. Robitaille	r**c@g**m	44
github-actions[bot]	4****]	2

Committer Domains (Top 20 + Academic)

ucr.ac.cr: 1

Issues and Pull Requests

Last synced: 5 months ago

All Time

Total issues: 14
Total pull requests: 10
Average time to close issues: 10 months
Average time to close pull requests: about 14 hours
Total issue authors: 5
Total pull request authors: 2
Average comments per issue: 1.07
Average comments per pull request: 0.6
Merged pull requests: 10
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

maRce10 (3)
bioGAMA (2)
athenasyarifa (1)

Pull Request Authors

maRce10 (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 370 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 5
Total maintainers: 1

cran.r-project.org: ohun

Optimizing Acoustic Signal Detection

Homepage: https://docs.ropensci.org/ohun/
Documentation: http://cran.r-project.org/web/packages/ohun/ohun.pdf
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Status: removed
Latest release: 1.0.3
published 5 months ago

Versions: 5
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 370 Last month

Rankings

Stargazers count: 15.1%

Forks count: 17.0%

Average: 22.7%

Dependent repos count: 23.8%

Dependent packages count: 28.6%

Downloads: 28.9%

Maintainers (1)

marcelo.araya@ucr.ac.cr

Last synced: 4 months ago

Dependencies

DESCRIPTION cran

R >= 3.2.1 depends
tuneR * depends
warbleR >= 1.1.27 depends
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fftw * imports
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methods * imports
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utils * imports
viridis * imports

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.github/workflows/update-citation-cff.yaml actions

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r-lib/actions/setup-r v2 composite
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ohun.Rcheck/00_pkg_src/ohun/DESCRIPTION cran

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vdiffr * suggests
viridis * suggests

ohun.Rcheck/ohun/DESCRIPTION cran

R >= 3.2.1 depends
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cli * imports
fftw * imports
ggplot2 * imports
igraph * imports
methods * imports
rlang * imports
seewave >= 2.0.1 imports
sf * imports
stats * imports
tuneR * imports
utils * imports
warbleR >= 1.1.29 imports
Sim.DiffProc * suggests
knitr * suggests
rmarkdown * suggests
testthat * suggests
vdiffr * suggests
viridis * suggests

.github/workflows/R-CMD-check.yaml actions

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r-lib/actions/setup-pandoc v2 composite
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.github/workflows/pkgdown.yaml actions

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