GIBBONR: An R package for the detection and classification of acoustic signals using machine learning

1. The recent improvements in recording technology, data storage and battery life have led to an increased interest in the use of passive acoustic monitoring for a variety of research questions. One of the main obstacles in implementing wide scale acoustic monitoring programs in terrestrial environments is the lack of user-friendly, open source programs for processing acoustic data. 2. Here we describe the new, open-source R package GIBBONR which has functions for classification, detection and visualization of acoustic signals using different readily available machine learning algorithms in the R programming environment. 3. We provide a case study showing how GIBBONR functions can be used in a workflow to classify and detect Bornean gibbon (Hylobates muelleri) calls in long-term recordings from Danum Valley Conservation Area, Sabah Malaysia. 4. Machine learning is currently one of the most rapidly growing fields-- with applications across many disciplines-- and our goal is to make commonly used signal processing techniques and machine learning algorithms readily available for ecologists who are interested in incorporating bioacoustics techniques into their research.

[1]  Peter H. Wrege,et al.  Acoustic monitoring for conservation in tropical forests: examples from forest elephants , 2017 .

[2]  Andreas M. Ali,et al.  Acoustic monitoring in terrestrial environments using microphone arrays: applications, technological considerations and prospectus , 2011 .

[3]  Patrick Mäder,et al.  Machine learning for image based species identification , 2018, Methods in Ecology and Evolution.

[4]  S. Malaivijitnond,et al.  Lar gibbon (Hylobates lar) great call reveals individual caller identity , 2015, American journal of primatology.

[5]  Simon J. Godsill,et al.  Detection of abrupt spectral changes using support vector machines an application to audio signal segmentation , 2002, 2002 IEEE International Conference on Acoustics, Speech, and Signal Processing.

[6]  Marcelo Araya-Salas,et al.  warbleR: an r package to streamline analysis of animal acoustic signals , 2017 .

[7]  Dena J. Clink,et al.  Application of a semi-automated vocal fingerprinting approach to monitor Bornean gibbon females in an experimentally fragmented landscape in Sabah, Malaysia , 2019 .

[8]  Edzer J. Pebesma,et al.  Multivariable geostatistics in S: the gstat package , 2004, Comput. Geosci..

[9]  Matthias Zeppelzauer,et al.  Towards an automated acoustic detection system for free-ranging elephants , 2015, Bioacoustics.

[10]  Adrian E. Raftery,et al.  mclust Version 4 for R : Normal Mixture Modeling for Model-Based Clustering , Classification , and Density Estimation , 2012 .

[11]  Lie Lu,et al.  Digital Object Identifier (DOI) 10.1007/s00530-002-0065-0 Multimedia Systems , 2003 .

[12]  Klaus Zuberbühler,et al.  Sequential information in a great ape utterance , 2016, Scientific Reports.

[13]  Hjalmar S. Kühl,et al.  Assessing the performance of a semi‐automated acoustic monitoring system for primates , 2015 .

[14]  Frank Kurth,et al.  Detecting bird sounds in a complex acoustic environment and application to bioacoustic monitoring , 2010, Pattern Recognit. Lett..

[15]  P. Tyack,et al.  Estimating animal population density using passive acoustics , 2012, Biological reviews of the Cambridge Philosophical Society.

[16]  Kate E. Jones,et al.  Emerging opportunities and challenges for passive acoustics in ecological assessment and monitoring , 2018, Methods in Ecology and Evolution.

[17]  Douglas A. Reynolds,et al.  A Tutorial on Text-Independent Speaker Verification , 2004, EURASIP J. Adv. Signal Process..

[18]  Sara C Keen,et al.  Automated detection of low-frequency rumbles of forest elephants: A critical tool for their conservation. , 2017, The Journal of the Acoustical Society of America.

[19]  Alex Rogers,et al.  AudioMoth: Evaluation of a smart open acoustic device for monitoring biodiversity and the environment , 2018 .

[20]  Therese M. Donovan,et al.  Tools for automated acoustic monitoring within the R package monitoR , 2016 .

[21]  Carel P van Schaik,et al.  Validation of an acoustic location system to monitor Bornean orangutan (Pongo pygmaeus wurmbii) long calls , 2015, American journal of primatology.

[22]  Dena J. Clink,et al.  Investigating Individual Vocal Signatures and Small-Scale Patterns of Geographic Variation in Female Bornean Gibbon (Hylobates muelleri) Great Calls , 2017, International Journal of Primatology.

[23]  Nick S. Jones,et al.  Robust, real-time and autonomous monitoring of ecosystems with an open, low-cost, networked device , 2017, bioRxiv.

[24]  Thierry Aubin,et al.  SEEWAVE, A FREE MODULAR TOOL FOR SOUND ANALYSIS AND SYNTHESIS , 2008 .

[25]  I. Elamvazuthi,et al.  Voice Recognition Algorithms using Mel Frequency Cepstral Coefficient (MFCC) and Dynamic Time Warping (DTW) Techniques , 2010, ArXiv.

[26]  Christian Wellekens,et al.  DISTBIC: A speaker-based segmentation for audio data indexing , 2000, Speech Commun..

[27]  Klaus Zuberbühler,et al.  A method for automated individual, species and call type recognition in free-ranging animals , 2013, Animal Behaviour.

[28]  Hjalmar S. Kühl,et al.  Towards the automated detection and occupancy estimation of primates using passive acoustic monitoring , 2015 .

[29]  P. Malathi,et al.  Speaker dependent speech emotion recognition using MFCC and Support Vector Machine , 2016, 2016 International Conference on Automatic Control and Dynamic Optimization Techniques (ICACDOT).

[30]  Ammie K. Kalan,et al.  It's time to listen: there is much to be learned from the sounds of tropical ecosystems , 2018, Biotropica.

[31]  Max Kuhn,et al.  The caret Package , 2007 .