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warbleR: StreamlineBioacoustic Analysis

warbleR isintended to facilitate the analysis of the structure of animal acousticsignals in R. Users can collect open-access avian recordings or entertheir own data into a workflow that facilitates spectrographicvisualization and measurement of acoustic parameters.warbleR makes useof the fundamental sound analysis tools of the seewave package, andoffers new tools for acoustic structure analysis. These tools areavailable for batch analysis of acoustic signals.

The main features of the package are:

• Diverse tools for measuring acoustic structure
• The use of loops to apply tasks through acoustic signals referencedin a selection table
• The production of images in the working directory with spectrogramsto allow users organize data and verify acoustic analyses

The package offers functions to:

• Explore and downloadXeno‐Canto recordings
• Explore, organize and manipulate multiple sound files
• Detect signals automatically (in frequency and time) (but check theR packageohun for a morethorough and friendly implementation)
• Create spectrograms of complete recordings or individualsignals
• Run different measures of acoustic signal structure
• Evaluate the performance of measurement methods
• Catalog signals
• Characterize different structural levels in acoustic signals
• Statistical analysis of duet coordination
• Consolidate databases and annotation tables

Most of the functions allow the parallelization of tasks, whichdistributes the tasks among several processors to improve computationalefficiency. Tools to evaluate the performance of the analysis at eachstep are also available.

Installing

Install/load the package from CRAN as follows:

install.packages("warbleR")# load packagelibrary(warbleR)

To install the latest developmental version fromgithub you will need the R packageremotes:

remotes::install_github("maRce10/warbleR")# load packagelibrary(warbleR)

Usage

The package includes several vignettes explaining its main features.TheIntro towarbleR provides an overview of the package functionalities. ThevignetteAnnotationdata format gives a detailed description of the required format forinput annotations. There are also three additionalpackage vignetteswith examples on how to organize functions in an acoustic analysisworkflow.

A full description of the package (although a bit outdated) can befound in thisjournalarticle.

Other packages

The packagesseewave andtuneR provide ahuge variety of functions for acoustic analysis and manipulation. Theymoslty works on wave objects already imported into the R environment.The packagebaRulho focuses onquantifying habitat-induced degradation of acoustic signals with datainputs and ouputs similar to those ofwarbleR. ThepackageRravenfacilitates the exchange of data between R andRaven sound analysissoftware (Cornell Labof Ornithology) and can be very helpful for incorporating Raven asthe annotating tool into acoustic analysis workflow in R. The packageohun works on automateddetection of sound events, providing functions to diagnose and optimizedetection routines.dynaSpec is allowsto create dynamic spectrograms (i.e. spectrogram videos).

Citation

Please citewarbleR asfollows:

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

NOTE: please also cite thetuneR andseewave packagesif you use any spectrogram-creating or acoustic-measuring functions