Project Outputs

Journal Articles

Review papers

Towards the end of the DECAF project, we wrote two review papers summarizing the state of the field at the time.  The first is short and fairly non-technical, aimed at an acoustical audience; the second is longer and more complete, aimed at biologists wishing to implement the methods.

• Thomas, L. and T.A. Marques. 2012. Passive acoustic monitoring for estimating animal density.  Acoustics Today 8(3): 35-44.
• Full text (pdf)
• Article at publisher's web site: doi:10.1121/1.4753915
• Marques, T.A., L. Thomas, S. Martin, D. Mellinger, J. Ward, D. Moretti, D. Harris and P. Tyack. 2013.  Estimating animal population density using passive acoustics. Biological Reviews 88: 287-309.
  
• Full text (pdf)
  
• Article at publisher's web site: doi: 10.1111/brv.12001
  

Primary research papers

These are the papers where we describe the novel research we undertook as part of the DECAF project.

• Martin, S. W., T. A. Marques, L. Thomas, R. P. Morrissey, S. Jarvis, N. DiMarzio, D. Moretti and D. K. Mellinger. 2013. Estimating minke whale (Balaenoptera acutorostrata) boing sound density using passive acoustic sensors. Marine Mammal Science 29: 142-158.

• Full text (pdf)
• Article at publisher's web site doi:10.1111/j.1748-7692.2011.00561.x
• Marques, T. A., Thomas, L., Martin, S. W., Mellinger, D. K., Jarvis, S., Morrissey, R. P., Ciminello, C., DiMarzio, N. 2012. Spatially explicit capture recapture methods to estimate minke whale abundance from data collected at bottom mounted hydrophones. Journal of Ornithology. 152 (Suppl 2):S445–S455
  
• Full text (pdf)
  
• Article at publisher's web site doi:10.1007/s10336-010-0535-7

• Ward, J., L. Thomas, S. Jarvis, N. DiMarzio, D. Moretti, T. A. Marques, C. Dunn, D. Claridge, E. Hartvig and P. Tyack. 2012. Passive Acoustic Density Estimation of Sperm Whales in the Tongue of the Ocean, Bahamas. Marine Mammal Science 28: E444-E455.
  
• Full text (pdf)
• Article at publisher's web site doi:10.1111/j.1748-7692.2011.00560.x
  

• Baggenstoss, P.M. 2011. An Algorithm for the Localization of Multiple Interfering Sperm Whales Using Multi-Sensor Time Difference of Arrival. Journal of the Acoustical Society of America. 130: 102-112.
  
• Full text (pdf)
• Article at publisher's web site doi:10.1121/1.3598454

• Baggenstoss, P.M. 2011. Separation of sperm whale click trains for multipath rejection. Journal of the Acoustical Society of America. 129: 3598-3609.
• Full text (pdf)
• Article at publisher's web site doi:10.1121/1.3578454

• Küsel, E.T., D.K. Mellinger, L. Thomas, T.A. Marques, D.J. Moretti, and J. Ward. 2011. Cetacean population density estimation from single fixed sensors using passive acoustics. Journal of the Acoustical Society of America 129: 3610-3622.
• Full text (pdf)
• Article at publisher's web site doi:10.1121/1.3583504
• Marques, T.A., L. Thomas and R.A. Royle. 2011. A hierarchical model for spatial capture-recapture data: comment.  Ecology. 92: 526-528.
  
• Full text (pdf)
• Electronic supplementary materials (zip).  Contains supplementary tables, WinBUGS and R code.
• Article at publisher's web site doi:10.1890/10-1440.1

• Mellinger, D.K., S.W. Martin, R.P. Morrissey, L. Thomas and J.J. Yosco.  2011.  A method for detecting whistles, moans and other frequency contour sounds.  Journal of the Acoustical Society of America 129: 4055-4061.

• Full text (pdf)
• Article at publisher's web site: 10.1121/1.3531926

• Ward, J., S. Jarvis, D. Moretti, N. DiMarzio, M. Johnson, P. Tyack, L. Thomas and T.A. Marques.  2011.  Beaked whale (Mesoplodon densirostris) passive acoustic detection in increasing ambient noise.  Journal of the Acoustical Society of America 129: 662-669.
  
• Full text (pdf)
  
• Article at publisher's web site: doi:10.1121/1.3531844
• Moretti, D., T.A. Marques, L. Thomas, N. DiMarzio, A. Dilley, R. Morrissey, E. McCarthy, J. Ward and S. Jarvis.  2010.  A dive counting density estimation method for Blainville's beaked whale (Mesoplodon densirostris) using a bottom-mounted hydrophone field as applied to a Mid-Frequency Active (MFA) sonar operation.  Applied Acoustics 71: 1036-2042.
  
• Full text (pdf)
  
• Article at publisher's web site doi:10.1016/j.apacoust.2010.04.011

• Marques, T.A., L. Thomas, J. Ward, N. DiMarzio, P. L. Tyack. 2009. Estimating cetacean population density using fixed passive acoustics sensors: an example with beaked whales. Journal of the Acoustical Society of America 125(4): 1982-1994.

• Abstract (pdf)
• Full text (pdf)
• Article at publisher's web site doi:10.1121/1.3089590
• DiMarzio, N., D. Moretti, J. Ward, R. Morrissey, S. Jarvis, A.M. Izzi, M. Johnson, P. Tyack and A. Hansen. 2008. Passive acoustic measurement of dive vocal behavior and group size of Blainville's beaked whale (Mesoplodon Densirostris) in the Tongue of the Ocean (TOTO). Canadian Acoustics 36(1): 166-173.
• Full text (pdf)
• Ward, J., R. Morrissey, D. Moretti, N. DiMarzio, S. Jarvis, M. Johnson, P. Tyack and C. White.  2008. Passive acoustic detection and localization of Mesoplodon Densirostris (Blainville's beaked whale) vocalizations using distributed bottom mounted hydrophones in conjunction with a digital tag (DTAG) recording. Canadian Acoustics 36(1): 60-66.
• Full text (pdf)

Related papers by project members

• Marques, T.A., L. Thomas, L. Munger, S. Wiggins and J.A. Hildebrand.  2011. Estimating North Pacific right whale (Eubalaena japonica) density using passive acoustic cue counting.  Endangered Species Research 13: 163-172.
  
• Full text. (pdf)
• Article at publisher's web site doi:10.3354/esr00325
• An End Sp Res Erratum was published on this. Open access here.  A complete explanation regarding the issue is presented in a CREEM report which can be found here.
  

Annual reports

Reports submitted to the National Oceanographic Partnership Program, covering project activities up until 30th September of each year.

• Final report  (pdf) Dated 26 May 2011
  

• 2010 Annual report.  (pdf)  Dated 20 November 2010; covering activities up to 30 September 2010. 
• 2009 Annual report.  (pdf)  Dated 1 December 2009; covering activities up to 30 September 2009. 
• 2008 Annual report.  (pdf)  Dated 1 December 2008; covering activities up to 30 September 2008. 
• 2007 Annual report.  (pdf) Dated 11 November 2007; covering activities up to 30 September 2007.

Technical reports and white papers

• Marques, T.A., J. Ward, S. Jarvis, D. Moretti, R. Morrissey, N. DiMarzio and L. Thomas. 2010. Density estimation implications of increasing ambient noise on beaked whale click detection and classification.  CREEM technical report 2010-1.
• Full text (pdf)
  
• Baggenstoss, P. 2010. Separation of sperm whale click trains fro multipath rejection and localization.  NUWC-NPT technical report 11,968. Dated 5 March 2010.
  
• Full text (pdf)
  
• Marques, T.A., L. Thomas, N. DiMarzio, R. Morrissey,  J. Ward, D. Moretti,  D. Mellinger, S. Martin and P. Tyack. 2009b. Estimating density of humpback whales using passive acoustic bottom-mounted detectors at PMRF – case study assessment and recommendations.  Working document dated 30 January 2009.
• Full text (pdf)
• Thomas, L. and S. Martin. 2006. Methods for estimating the density of cetaceans from fixed arrays of passive listening devices. Unpublished white paper, dated 7 June 2006.
  A technical white paper written by Len Thomas and Steve Martin as a discussion document to facilitate our discussions with potential collaborators about the proposed research. Some parts are now out of date, but it may be of use to others as an introduction to the issues.
• Full text (pdf)

Talks

• Thomas, 2012. DECAF: Density Estimation for Cetaceans from passive Acoustic Fixed sensors.  Joint Industry Program on Sound and Marine Life Program Review. 31 May 2012, Dulles, VA.  Talk.
• Thomas, L. 2011. Passive Acoustic Density Estimation. Workshop on new developments in cetacean survey methods, Society for Marine Mammology Biennial Conference. 27 November 2011, Tampa, FL.
  
• Thomas, L., T.A. Marques, S. Martin, D.J. Moretti, D. Mellinger, J. Ward, P. Tyack and D. Harris. 2011. DECAF (Density Estimation for Cetaceans from pasive Acoustic Fixed sensors) and beyond.  4th International Conference on the Effect of Sound on Marine Mammals.  5-9 September, Amsterdam.
  
• Marques, T.A., L. Thomas, S. Martin, D.K. Mellinger, J. Ward, P.L. Tyack, D.J. Moretti and D. Harris. 2011. Estimating cetacean density: if you can't see them then ... listen! Fifth International Workshop on Detection, Classification, Localization and Density Estimation of Marine Mammals using Passive Acoustics. August 25th, Mount Hood, Oregon.
  
• Thomas, L., and T. Marques. 2010. Estimating population density from fixed passive acoustic detectors.  International Statistical Ecology Conference 6 June 2010.  Talk.
  
• Talks at the special session on "Estimating Spatial Density of Animal Populations with Passive Acoustics" at the Acoustical Society of America conference, Apr. 19-23, 2010, Baltimore:  (These are just talks by DECAF team members; see Open Meetings page for abstracts for all talks given that day)
• Thomas, L., and T. Marques. 2010. Review of methods for estimating spatial density of animal populations with passive acoustics. Talk.
• Küsel, E.T., D.K. Mellinger, L. Thomas, T.A. Marques, D.J. Moretti, and J. Ward. 2010. Estimating density from single hydrophones by means of propagation modeling. Abstract.
  
• Mellinger, D.K., E.T. Küsel, L. Thomas, T. Marques, D. Moretti, P. Baggenstoss, J. Ward, N. DiMarzio, and R. Morrissey. 2010. Population density of sperm whales in the Bahamas estimated using propagation modeling. Abstract and talk.
• Martin, S.W., L. Thomas, T.A. Marques, R.P. Morrissey, S. Jarvis, N. DiMarzio and D.K. Mellinger.  2010.  Minke whale boing vocalization density estimation at the Pacific Missile Range Facility, Hawaii.  Abstract.
• Mellinger, D.K., E.T. Küsel, L. Thomas, T. Marques. 2009. Taming the Jez monster: Estimating fin whale spatial density using acoustic propagation modeling. Talk given at Fall 2009 meeting of the Acoustical Society of America, San Antonio, TX, USA, 28 October 2009. Abstract in J. Acoust. Soc. Am. 126(4):2229(A). PDF here.
  
• Marques, T.A., L. Thomas, S.W. Martin, D.K. Mellinger, S. Jarvis, N. DiMarzio and R.P. Morrissey.  2009. Spatially explicit capture-recapture methods to estimate minke whale abundance from data collected at bottom-mounted hydrophones.  Talk given at EURING 2009 technical meeting, Pescara, Italy, 15th September 2009.
  
• Talks given at one-day workshop: 1st International Workshop on Density Estimation of Marine Mammals Using Passive Acoustics, September 13th 2009: (These are just talks given by DECAF team members; see Open Meetings page for agenda and abstracts for all talks given that day)
• Thomas, L. and T. Marques. 2009. Review of methods for estimating cetacean density from passive acoustics.
• Marques, T.A., L. Thomas, J. Ward, N. DiMarzio, D. Moretti and P.L. Tyack. 2009.  Accounting for ambient noise in Blainville’s beaked whales density estimation.
• Küsel, E.T., D. K. Mellinger, L. Thomas, T. A. Marques, D. J. Moretti,  and J. Ward. 2009. Density estimation of Blainville’s beaked whales (Mesoplodon densirostris) from single hydrophones by means of propagation modeling.
  
• DiMarzio, N., D. Moretti, J. Ward, R. Morrissey, S. Jarvis, E. McCarthy, M. Johnson, P. Tyack, D. Claridge, C. Dunn, T. Marques and L. Thomas. 2009. Passive acoustic density estimation of Blainville’s beaked whales (Mesoplodon densirostris) using group localization combined with click counting.
  

• Talks given at 4th International Workshop on Detection, Localization and Classification of marine Mammals Using Passive Acoustics, September 10-12th 2009.
• Mellinger, D.K., S.W. Martin, J. Yosco, R. P. Morrissey, N. A. DiMarzio,  D. J. Moretti and L. Thomas. 2009. An algorithm for detection of whistles, moans, and other tonal sounds.
• Morrissey, R.P., N. A. DiMarzio, D.J. Moretti, S. W. Martin, D. K.  Mellinger, J. Yosco, C. Ciminello and Len Thoma. 2009. Passive acoustic detection of Minke whales (Balaenoptera acutorostrata) off the West Coast of Kauai, Hi.
  
• Talks given at one-day symposium on Estimating Cetacean Density from Passive Acoustics, Scripps Insitution of Oceanography, July 16th 2009 (see Open Meetings page for abstracts and other contributed talks):
  
• Thomas, L. and T. A. Marques. 2009.  Review of methods for estimating cetacean density from passive acoustics.
• Marques, T. A., J. Ward, L. Thomas, N. DiMarzio, P. Tyack, D. Moretti and S. W. Martin. 2009. Estimating beaked whale density at AUTEC using tagged whale data.
• Küsel, E., D. Mellinger, T. A. Marques, L. Thomas, D. Moretti and J. Ward.  2009. Estimating beaked whale density from single hydrophones by means of propagation modelling.
• Martin, S.W., T. A. Marques, L. Thomas, D. Moretti, R. Morrissey, N. DiMarzio, S. Jarvis, D. K. Mellinger and T. Norris. Estimating minke whale boing density at Pacific Missile Range Facility, Hawaii.
  

• Thomas, L. and T. Marques. 2009 Estimating whale densities from their calls.  Talk given at NCSE annual workshop, St Andrews, 22nd June 2009.
  
• Küsel, E., D. Mellinger, L. Thomas, T. Marques, D. Moretti and J. Ward.  2009.  Beaked whale density estimation from single hyrdophones by means of propagation modeling.  Talk given at 157th meeting of the Acoustical Society of America, May 18-22nd 2009.
  
• Thomas, L. 2008.  DECAF - Density Estimation for Cetaceans from passive Acoustic Fixed sensors (pdf).  Talk given at the Joint Industry Programme (JIP) on Exploration and Production, Sound and Marine Life, Programme Review Meeting, Houston, USA. 30 October 2008.
  
• Marques, T. A. and L. Thomas. 2008. Density estimation for cetaceans from passive acoustic sensors: an example with beaked whales.  Talk given at the XVI Congress of the Portuguese Statistical Society, Vila Real, Portugal.  3 October 2008.
  
• Presentations given at "Density Estimation from Passive Acoustics" Workshop held in Paris, 29th June 2008. List of presentations from Paris workshop (pdf)
  
• Marques, T. A. and L. Thomas. 2008. DECAF Overview and Initial Results.  CREEM Seminar Series, University of St Andrews. 27 February 2008.

Poster presentations

• Marques, T. A. and L. Thomas. 2008.  Estimating cetacean density from passive acoustic arrays (pdf).  Poster presentation given at International Statistical Ecology Conference, July 9-11th 2008, St Andrews, Scotland.
  

Data files

Files containing datasets generated during the DECAF project are in the Data Files directory and from the OBIS-SEAMAP web site.

Tutorial material

 Copies of tutorial lecture notes, datasets and computer code are available from the Open Meetings page of this web site.