baRulho

An R package to quantify habitat-induced degradation of (animal) acoustic signals.
https://github.com/ropensci/baRulho

Category: Biosphere
Sub Category: Bioacoustics and Acoustic Data Analysis

Keywords

acoustic-signals animal behavior bioacoustics cran

Keywords from Contributors

animal-acoustic-signals spectrogram streamline-analysis

Last synced: about 17 hours ago
JSON representation

Repository metadata

An R package to quantify habitat-induced degradation of (animal) acoustic signals

• Host: GitHub
• URL: https://github.com/ropensci/baRulho
• Owner: ropensci
• Created: 2019-10-23T12:57:16.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2025-10-31T18:07:46.000Z (about 2 months ago)
• Last Synced: 2025-12-09T13:51:08.853Z (16 days ago)
• Topics: acoustic-signals, animal, behavior, bioacoustics, cran
• Language: HTML
• Homepage: https://ropensci.github.io/baRulho/
• Size: 77.5 MB
• Stars: 9
• Watchers: 2
• Forks: 2
• Open Issues: 2
• Releases: 0
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • Contributing: CONTRIBUTING.md
  • Citation: CITATION.cff
  • Codemeta: codemeta.json

README.Rmd

          ---
title: "baRulho: quantifying degradation of (animal) sounds"
output: github_document
editor_options: 
  chunk_output_type: console
---




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[baRulho](https://cran.r-project.org/package=baRulho) is intended to facilitate the implementation of (animal) sound propagation experiments, which typically aim to quantify changes in signal structure when transmitted in a given habitat by broadcasting and re-recording animal sounds at increasing distances. 

These experiments aim to answer research questions such as: 

- How habitat structure has shaped the propagation properties of animal acoustic signals? 
- Which acoustic features are shaped by selection for improving propagation? 
- Which features are more degraded in different habitats? 
- How far a acoustic signals can be detected? 

A common sequence of steps to experimentally test hypotheses related to sound propagation is depicted in the following diagram:

```{r, echo=FALSE, out.width="100%", fig.align='center'}

knitr::include_graphics("man/figures/analysis_workflow.png")

```

_Diagram depicting a typical workflow for a experiment working on signal propagation and degradation. Nodes with black font indicate steps that can be conducted using baRulho functions. Blue nodes denote the functions that can be used at those steps._

 

[baRulho](https://docs.ropensci.org/baRulho//) offers functions for critical steps in this workflow (those in black, including 'checks') that required acoustic data manipulation and analysis.

The main features of the package are:

 - The use of loops to apply tasks through sounds referenced in a selection table (sensu [warbleR](https://cran.r-project.org/package=warbleR))
 - The production of image files with graphic representations of sound in time and/or frequency that let users verify acoustic analyses 
 - The use of annotation tables as the object format to input acoustic data and annotations and to output results 
 - The use of parallelization to distribute tasks among several cores to improve computational efficiency


[baRulho](https://docs.ropensci.org/baRulho//) builds upon functions and data formats from the [warbleR](https://cran.r-project.org/package=warbleR) and [seewave](https://cran.r-project.org/package=seewave) packages, so some experience with these packages is advised.

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

- [Align test sounds](https://docs.ropensci.org/baRulho//articles/align_test_sounds.html)
- [Quantify degradation](https://docs.ropensci.org/baRulho//articles/quantify_degradation.html)

## Installing baRulho

Install/load the package from CRAN as follows:

```{r, eval = FALSE}

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

# load package
library(baRulho)
```

It can also be install from [R-Universe](https://ropensci.org/blog/2021/06/22/setup-runiverse/) in this way:

```{r}
install.packages("baRulho", repos = "https://ropensci.r-universe.dev")
```


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}

# install remotes if not installed
if (!requireNamespace("remotes")) {
  install.packages("remotes")
}

# From github
remotes::install_github("ropensci/baRulho")

# load package
library(baRulho)
```

Further system requirements due to the dependency [seewave](https://cran.r-project.org/package=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. 

## Other packages

The packages [seewave](https://cran.r-project.org/package=seewave) and  [tuneR](https://cran.r-project.org/package=tuneR) provide a huge variety of functions for acoustic analysis and manipulation. They mostly work on wave objects already imported into the R environment. The package [warbleR](https://cran.r-project.org/package=warbleR) provides functions to visualize and measure sounds already referenced in annotation tables, similar to [baRulho](https://docs.ropensci.org/baRulho//). The package [Rraven](https://cran.r-project.org/package=Rraven) facilitates the exchange of data between R and [Raven sound analysis software](https://www.ravensoundsoftware.com/) ([Cornell Lab of Ornithology](https://www.birds.cornell.edu/home)) and can be very helpful for incorporating Raven as the annotating tool into acoustic analysis workflow in R. The package [ohun](https://github.com/ropensci/ohun) works on automated detection of sound events, providing functions to diagnose and optimize detection routines.


## Citation

Please cite [baRulho](https://docs.ropensci.org/baRulho//) as follows:

Araya-Salas M., E. Grabarczyk, M. Quiroz-Oliva, A. Garcia-Rodriguez, A. Rico-Guevara. (2023), *baRulho: an R package to quantify degradation in animal acoustic signals*. bioRxiv 2023.11.22.568305.

## References

1.  Dabelsteen, T., Larsen, O. N., & Pedersen, S. B. (1993). *Habitat-induced degradation of sound signals: Quantifying the effects of communication sounds and bird location on blur ratio, excess attenuation, and signal-to-noise ratio in blackbird song*. The Journal of the Acoustical Society of America, 93(4), 2206.

2.  Marten, K., & Marler, P. (1977). *Sound transmission and its significance for animal vocalization*. Behavioral Ecology and Sociobiology, 2(3), 271-290.

3.  Morton, E. S. (1975). *Ecological sources of selection on avian sounds*. The American Naturalist, 109(965), 17-34.

        

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "baRulho" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'baRulho: Quantifying (Animal) Sound Degradation'
version: 2.1.7
doi: 10.1111/2041-210X.14481
identifiers:
- type: doi
  value: 10.32614/CRAN.package.baRulho
abstract: Intended to facilitate acoustic analysis of (animal) sound propagation experiments,
  which typically aim to quantify changes in signal structure when transmitted in
  a given habitat by broadcasting and re-recording animal sounds at increasing distances.
  The package offers a workflow with functions to prepare the data set for analysis
  as well as to calculate and visualize several degradation metrics, including blur
  ratio, signal-to-noise ratio, excess attenuation and envelope correlation among
  others (Dabelsteen et al 1993 <https://doi.org/10.1121/1.406682>).
authors:
- family-names: Araya-Salas
  given-names: Marcelo
  email: marcelo.araya@ucr.ac.cr
  orcid: https://orcid.org/0000-0003-3594-619X
preferred-citation:
  type: article
  title: Quantifying degradation in animal acoustic signals with the R package baRulho.
  authors:
  - family-names: Araya-Salas
    given-names: M.
  - family-names: Grabarczyk
    given-names: Erin E.
  - family-names: Quiroz-Oliva
    given-names: Marcos
  - family-names: Garcia-Rodriguez
    given-names: Adrian
  - family-names: Rico-Guevara
    given-names: Alejandro
  journal: Methods in Ecology and Evolution
  year: '2025'
  doi: 10.1111/2041-210X.14481
repository: https://CRAN.R-project.org/package=baRulho
repository-code: https://github.com/ropensci/baRulho
url: https://docs.ropensci.org/baRulho/
contact:
- family-names: Araya-Salas
  given-names: Marcelo
  email: marcelo.araya@ucr.ac.cr
  orcid: https://orcid.org/0000-0003-3594-619X
keywords:
- acoustic-signals
- animal
- behavior
- bioacoustics
- cran
references:
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  notes: Imports
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  authors:
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    address: Vienna, Austria
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- type: software
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  abstract: 'seewave: Sound Analysis and Synthesis'
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  url: https://rug.mnhn.fr/seewave/
  repository: https://CRAN.R-project.org/package=seewave
  authors:
  - family-names: Sueur
    given-names: Jerome
    email: sueur@mnhn.fr
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    given-names: Thierry
  - family-names: Simonis
    given-names: Caroline
  year: '2025'
  doi: 10.32614/CRAN.package.seewave
- type: software
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  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
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    given-names: Uwe
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    orcid: https://orcid.org/0000-0001-5875-6167
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  notes: Imports
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  year: '2025'
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  notes: Imports
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    email: gabor@posit.co
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  authors:
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- type: software
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  url: https://www.R-project.org/
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  abstract: 'warbleR: Streamline Bioacoustic Analysis'
  notes: Depends
  url: https://marce10.github.io/warbleR/
  repository: https://CRAN.R-project.org/package=warbleR
  authors:
  - family-names: Araya-Salas
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  notes: Suggests
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  repository: https://CRAN.R-project.org/package=ggplot2
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  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
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    given-names: Yihui
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  abstract: 'kableExtra: Construct Complex Table with ''kable'' and Pipe Syntax'
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  repository: https://CRAN.R-project.org/package=kableExtra
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    given-names: Hao
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  year: '2025'
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  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
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    email: hadley@posit.co
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  abstract: 'covr: Test Coverage for Packages'
  notes: Suggests
  url: https://covr.r-lib.org
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  authors:
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  year: '2025'
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  abstract: 'formatR: Format R Code Automatically'
  notes: Suggests
  url: https://github.com/yihui/formatR
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  authors:
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    given-names: Yihui
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  abstract: 'Rraven: Connecting R and ''Raven'' Sound Analysis Software'
  notes: Suggests
  url: https://github.com/maRce10/Rraven
  repository: https://CRAN.R-project.org/package=Rraven
  authors:
  - family-names: Araya-Salas
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  url: https://github.com/jonkatz2/monitor
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  - family-names: Aubin
    given-names: Thierry
  - family-names: Simonis
    given-names: Caroline
  - family-names: Ligges
    given-names: Uwe
  year: '2025'
  doi: 10.32614/CRAN.package.monitoR

---

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Name	Email	Commits
Marcelo Araya-Salas	m****a@u****r	241
maRce10	m****7@g****m	57
github-actions[bot]	4****]	11
Adam H. Sparks	a****s@i****m	10
gsvidaurre	g****i@g****m	3
Mike Mahoney	m****8@g****m	1

Committer domains:

• ucr.ac.cr: 1

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Issue and Pull Request metadata

Last synced: 27 days ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/ropensci/baRulho

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Package metadata

• Total packages: 1
• Total downloads:
  • cran: 349 last-month
• Total dependent packages: 0
• Total dependent repositories: 0
• Total versions: 12
• Total maintainers: 1

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Dependencies

Score: 10.047587896509885