warbleR: Streamline Bioacoustic Analysis

lifecycle Dependencies Project Status: Active The project has reached a stable, usable state and is being actively developed. Licence CRAN_Status_Badge Total Downloads Codecov test coverage R-CMD-check

warbleR logo

warbleR is intended to facilitate the analysis of the structure of animal acoustic signals in R. Users can collect open-access avian recordings or enter their own data into a workflow that facilitates spectrographic visualization and measurement of acoustic parameters. warbleR makes use of the fundamental sound analysis tools of the seewave package, and offers new tools for acoustic structure analysis. These tools are available for batch analysis of acoustic signals.

The main features of the package are:

The package offers functions to:

Most of the functions allow the parallelization of tasks, which distributes the tasks among several processors to improve computational efficiency. Tools to evaluate the performance of the analysis at each step are also available.

Installing

Install/load the package from CRAN as follows:

install.packages("warbleR")

# load package
library(warbleR)

To install the latest developmental version from github you will need the R package remotes:

remotes::install_github("maRce10/warbleR")

# load package
library(warbleR)

Usage

Take a look at the package vignettes with detailed examples on how to organize functions in an acoustic analysis workflow.

A full description of the package (although a bit outdated) can be found in this journal article.

Other packages

The packages seewave and tuneR provide a huge variety of functions for acoustic analysis and manipulation. They moslty works on wave objects already imported into the R environment. The package baRulho focuses on quantifying habitat-induced degradatio of acoustic signals with data inputs and ouputs similar to those of warbleR. The package Rraven facilitates the exchange of data between R and Raven sound analysis software (Cornell Lab of Ornithology) and can be very helpful for incorporating Raven as the annotating tool into acoustic analysis workflow in R. The package ohun works on automated detection of sound events, providing functions to diagnose and optimize detection routines. dynaSpec is allows to create dynamic spectrograms (i.e. spectrogram videos).

Citation

Please cite warbleR as follows:

Araya-Salas, M. and Smith-Vidaurre, G. (2017), warbleR: an r package to streamline analysis of animal acoustic signals. Methods Ecol Evol. 8, 184-191.

NOTE: please also cite the tuneR and seewave packages if you use any spectrogram-creating or acoustic-measuring functions