The study of animal acoustic signals is a central tool for many fields in behavior, ecology and evolution. The growing availability of recordings in acoustic libraries provides an unprecedented opportunity to study animal acoustic signals at large temporal, geographic and taxonomic scales. However, the diversity of analytical methods and the multidimensionality of these signals posts significant challenges to conduct analyses that can quantify biologically meaningful variation. The recent development of acoustic analysis tools in the R programming environment provides a powerful means for overcoming these challenges, facilitating the gathering and organization of large acoustic data sets and the use of more elaborated analyses that better fit the studied acoustic signals.
The objective of this course, is to training biological sciences students and researchers in the detection and analysis of animal sounds in R. Specifically, it seeks to familiarize participants with computational tools in the R environment aiming at curating, detecting and analyzing animal acoustic signals, with an especial focus on quantifying fine-scale structural variation. The course will introduce the most relevant acoustics concepts to allow a detailed understanding of the metrics used for characterize acoustic signals. It will also guide participants through a variety of R packages for bioacoustics analysis, including seewave, tuneR, warbleR and baRulho.
General bioacoustics concepts
Bioacoustics as a scientific tool
History and development
Bioacoustics in other research fields
Analytical workflow in bioacoustics research
What is sound?
Sound as wave
Sound as a time series
Sound as a digital object
Graphical representations: oscillogram
Spectrograms and the Fourier transform
Raven / Sonic visualizer / audacity
Open and explore recordings
Modify-optimize visualization parameters
Acoustic signal annotation
Identifying structural units
Hierarchical structural levels
Acoustic data in R
Importing and manipulating sound in R
Read sound files as R objects
‘wave’ object structure
‘wave’ object manipulations
Explore, modify and measure ‘wave’ objects
Spectrograms and oscillograms
Filtering and re-sampling
Intro to warbleR
Extended selection tables
Selection table manipulation
warbleR functions and the bioacoustics analysis workflow
Quality control in recordings and annotation
Check and modify sound file format (check_wavs(), wav_info(), wav_dur(), mp32wav() y fix_wavs())
There will be a total 10 sessions, from 2-5 pm (CST), from March 15-26, 2021. Each session will consist of a theoretical introduction, demonstration of code and a self-learning practical.
Tuition, Room & Board
Tuition is $700. Additional scholarships may be available for students with demonstrated financial need. If you are interested in being considered for a partial scholarship, please make sure to include a request for a partial scholarship in your application. We will assess your situation individually and determine your eligibility for a scholarship if you are selected for the course.
Marcelo Araya Salas is an evolutionary behavioral ecologists deeply involved in the development of computational tools for bioacoustic analyses. He is the author of the R packages warbleR, baRulho and Rraven, which provide functions to streamline high-throughput acoustic analysis of animal sounds.