barulho
An R package to quantify habitat-induced degradation of (animal) acoustic signals
Science Score: 44.0%
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Keywords
acoustic-signals
animal
behavior
bioacoustics
cran
Keywords from Contributors
standardization
bayes-factors
Last synced: 7 months ago
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An R package to quantify habitat-induced degradation of (animal) acoustic signals
Basic Info
- Host: GitHub
- Owner: ropensci
- Language: HTML
- Default Branch: master
- Homepage: https://ropensci.github.io/baRulho/
- Size: 76.2 MB
Statistics
- Stars: 8
- Watchers: 3
- Forks: 2
- Open Issues: 3
- Releases: 0
Topics
acoustic-signals
animal
behavior
bioacoustics
cran
Created over 6 years ago
· Last pushed 8 months ago
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Readme
Changelog
Contributing
Citation
Codemeta
README.Rmd
---
title: "baRulho: quantifying degradation of (animal) sounds"
output: github_document
editor_options:
chunk_output_type: console
---
[](https://github.com/ropensci/software-review/issues/609)[](https://lifecycle.r-lib.org/articles/stages.html) [](https://cran.r-project.org/package=baRulho) [](https://www.repostatus.org/#active) [](https://www.gnu.org/licenses/gpl-3.0.en.html) [![minimal R version](https://img.shields.io/badge/R%3E%3D-`r strsplit(gsub("depends: R \\(|\\)", "", grep("^DEPENDS", ignore.case = TRUE, readLines(con = "./DESCRIPTION"), value = TRUE), ignore.case = TRUE), ",")[[1]][1]`-6666ff.svg)](https://cran.r-project.org/)
[](https://cran.r-project.org/package=baRulho)
[](https://cranlogs.r-pkg.org/badges/grand-total/baRulho)
[](https://app.codecov.io/gh/ropensci/baRulho?branch=master)
[](https://github.com/ropensci/baRulho/actions/workflows/R-CMD-check.yaml)
[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.
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/
# --------------------------------------------
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:
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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:
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given-names: Marcelo
email: marcelo.araya@ucr.ac.cr
orcid: https://orcid.org/0000-0003-3594-619X
keywords:
- acoustic-signals
- animal
- behavior
- bioacoustics
- cran
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}GitHub Events
Total
- Issues event: 3
- Watch event: 2
- Issue comment event: 1
- Push event: 230
Last Year
- Issues event: 3
- Watch event: 2
- Issue comment event: 1
- Push event: 230
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Marcelo Araya-Salas | m****a@u****r | 237 |
| maRce10 | m****7@g****m | 57 |
| Adam H. Sparks | a****s@i****m | 10 |
| github-actions[bot] | 4****] | 9 |
| gsvidaurre | g****i@g****m | 3 |
| Mike Mahoney | m****8@g****m | 1 |
Committer Domains (Top 20 + Academic)
ucr.ac.cr: 1
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 6
- Total pull requests: 0
- Average time to close issues: 19 days
- Average time to close pull requests: N/A
- Total issue authors: 4
- Total pull request authors: 0
- Average comments per issue: 0.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 0
- Average time to close issues: about 22 hours
- Average time to close pull requests: N/A
- Issue authors: 4
- Pull request authors: 0
- Average comments per issue: 0.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- maRce10 (3)
- LauraCBeck (1)
- maelle (1)
- auman-chan (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 506 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 11
- 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
- License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
- Status: removed
-
Latest release: 2.1.5
published 9 months ago
Rankings
Forks count: 17.8%
Stargazers count: 28.5%
Dependent packages count: 29.8%
Average: 30.1%
Dependent repos count: 35.5%
Downloads: 38.9%
Maintainers (1)
Last synced:
7 months ago
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
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- 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