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

spectrogram streamline-analysis file-upload weighted unitful parallel simulations report crop transform

Last synced: about 15 hours ago
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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 (over 5 years ago)
Default Branch: master
Last Pushed: 2025-04-19T04:20:24.000Z (8 days ago)
Last Synced: 2025-04-19T11:17:31.995Z (8 days ago)
Topics: acoustic-signals, animal, behavior, bioacoustics, cran
Language: HTML
Homepage: https://ropensci.github.io/baRulho/
Size: 73.9 MB
Stars: 6
Watchers: 3
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://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. 

## Other packages

The packages [seewave](https://cran.r-project.org/package=seewave) and  [tuneR](https://cran.r-project.org/package=seewave) 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: 2.1.5
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: [email protected]
  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: [email protected]
  orcid: https://orcid.org/0000-0003-3594-619X
keywords:
- acoustic-signals
- animal
- behavior
- bioacoustics
- cran
references:
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  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
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  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
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- type: software
  title: stats
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  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: seewave
  abstract: 'seewave: Sound Analysis and Synthesis'
  notes: Imports
  url: https://rug.mnhn.fr/seewave/
  repository: https://CRAN.R-project.org/package=seewave
  authors:
  - family-names: Sueur
    given-names: Jerome
    email: [email protected]
  - family-names: Aubin
    given-names: Thierry
  - family-names: Simonis
    given-names: Caroline
  year: '2025'
  doi: 10.32614/CRAN.package.seewave
- type: software
  title: tuneR
  abstract: 'tuneR: Analysis of Music and Speech'
  notes: Imports
  repository: https://CRAN.R-project.org/package=tuneR
  authors:
  - family-names: Ligges
    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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  abstract: 'cli: Helpers for Developing Command Line Interfaces'
  notes: Imports
  url: https://cli.r-lib.org
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  authors:
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    given-names: Gábor
    email: [email protected]
  year: '2025'
  doi: 10.32614/CRAN.package.cli
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  url: https://rlang.r-lib.org
  repository: https://CRAN.R-project.org/package=rlang
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  - family-names: Henry
    given-names: Lionel
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  year: '2025'
  doi: 10.32614/CRAN.package.rlang
- type: software
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  authors:
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    address: Vienna, Austria
  year: '2025'
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- type: software
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  abstract: 'warbleR: Streamline Bioacoustic Analysis'
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  repository: https://CRAN.R-project.org/package=warbleR
  authors:
  - family-names: Araya-Salas
    given-names: Marcelo
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    orcid: https://orcid.org/0000-0003-3594-619X
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  year: '2025'
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  authors:
  - family-names: Araya-Salas
    given-names: Marcelo
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  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
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  abstract: 'kableExtra: Construct Complex Table with ''kable'' and Pipe Syntax'
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  year: '2025'
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  abstract: 'testthat: Unit Testing for R'
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  authors:
  - family-names: Wickham
    given-names: Hadley
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  version: '>= 3.0.0'
- type: software
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  notes: Suggests
  url: https://covr.r-lib.org
  repository: https://CRAN.R-project.org/package=covr
  authors:
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    given-names: Jim
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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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- type: software
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  abstract: 'Rraven: Connecting R and ''Raven'' Sound Analysis Software'
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  url: https://github.com/maRce10/Rraven
  repository: https://CRAN.R-project.org/package=Rraven
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    given-names: Marcelo
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  abstract: 'monitoR: Acoustic Template Detection in R'
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  - family-names: Katz
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  - family-names: package
    given-names: with code for the Fourier transform from the seewave
  - family-names: direction
    given-names: code for the readMP3 function from the tuneR package. Therese Donovan
      provided creative
  - family-names: support.
    given-names: database design
  year: '2025'
  doi: 10.32614/CRAN.package.monitoR

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Package metadata

Total packages: 1
Total downloads:
- cran: 392 last-month
Total dependent packages: 0
Total dependent repositories: 0
Total versions: 10
Total maintainers: 1

cran.r-project.org: baRulho

Quantifying (Animal) Sound Degradation

Homepage: https://github.com/ropensci/baRulho
Documentation: http://cran.r-project.org/web/packages/baRulho/baRulho.pdf
Licenses: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Latest release: 2.1.3 (published 3 months ago)
Last Synced: 2025-04-25T10:31:13.098Z (1 day ago)
Versions: 10
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 392 Last month
Rankings:
- Forks count: 17.77%
- Stargazers count: 28.503%
- Dependent packages count: 29.797%
- Average: 30.075%
- Dependent repos count: 35.455%
- Downloads: 38.852%
Maintainers (1)
- [email protected]

Dependencies

DESCRIPTION cran

R >= 3.2.1 depends
warbleR >= 1.1.27 depends
fftw * imports
methods * imports
pbapply * imports
seewave * imports
stats * imports
tuneR * imports
utils * imports
viridis * imports
ggplot2 * suggests
kableExtra * suggests
knitr * suggests
png * suggests
rmarkdown * suggests
testthat * suggests

.github/workflows/pkgdown.yaml actions

JamesIves/github-pages-deploy-action v4.4.1 composite
actions/checkout v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/readme.yml actions

actions/checkout v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/tic.yml actions

actions/checkout v3 composite
actions/upload-artifact v2 composite
pat-s/always-upload-cache v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-tinytex v2 composite

Score: 9.845010622777153

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