Profile

Prof Len Thomas

Prof Len Thomas
Professor of Statistics


 

My main research areas are: (1) Development of methods and software for estimating the size, density and distribution of wild animal and plant populations. I mostly work on a group of related methods called distance sampling. (2) Use of computer intensive methods to fit and compare stochastic models of wildlife population dynamics. Here, I mostly work on algorithms called particle filters. For more details about my work, including links to my publications, please see my personal home page.

source: symbiosis

 

Recent publications


50  (of 73 published available) for lt5 with keyword Marine clear keyword filter. (source: University of St Andrews PURE)
Please click title of any item for full details.

2018 (10)
Biological Conservation
vol.226 pp.42-53
(Article)
Basin-scale distribution of harbour porpoises in the Baltic Sea provides basis for effective conservation actions
Ida Carlén, Len Thomas, Julia Carlström, Mats Amundin, Jonas Teilmann, Nick Tregenza, Jakob Tougaard, Jens C. Koblitz, Signe Sveegaard, Daniel Wennerberg, Olli Loisa, Michael Dähne, Katharina Brundiers, Monika Kosecka, Line Anker Kyhn, Cinthia Tiberi Ljungqvist, Iwona Pawliczka, Radomil Koza, Bartlomiej Arciszewski, Anders Galatius, Martin Jabbusch, Jussi Laaksonlaita, Jussi Niemi, Sami Lyytinen, Anja Gallus, Harald Benke, Penina Blankett, Krzysztof E. Skóra, Alejandro Acevedo-Gutiérrez 
Keywords: Spatial distribution, Passive acoustic monitoring, Population structure, Harbour porpoise, Marine protected areas, Biodiversity conservation
2018 (1)
Marine Pollution Bulletin
vol.126 pp.1-18
(Review article)
Comparing methods suitable for monitoring marine mammals in low visibility conditions during seismic surveys
Ursula K. Verfuss, Douglas Michael Gillespie, Jonathan Charles David Gordon, Tiago A. Marques, Brianne Miller, Rachael Plunkett, James A. Theriault, Dominic John Tollit, Daniel P. Zitterbart, Philippe Hubert, Len Thomas 
Keywords: Marine mammals, Monitoring methods, Underwater noise, Seismic survey, Detection performance, Low visibility
2018 (12)
Methods in Ecology and Evolution
vol.9 pp.2362-2371
(Article)
Estimating effective detection area of static passive acoustic data loggers from playback experiments with cetacean vocalisations
Hanna K. Nuuttila, Katharina Brundiers, Michael Dähne, Jens C. Koblitz, Len Thomas, Winnie Courtene-Jones, Peter G. H. Evans, John R. Turner, Jim D. Bennell, Jan G. Hiddink 
Keywords: Abundance, C-POD, Density estimation, Detection function, Effective detection radius, Static passive acoustic monitoring
2018 (27/3)

(Other report)
Evaluating the effect of measurement error in pairs of 3D bearings in point transect sampling estimates of density
Tiago A. Marques, Pedro Duarte, Telmo Peixe, Len Thomas 

Journal of the Acoustical Society of America
vol.143 pp.2980-2993
(Article)
Fin whale density and distribution estimation using acoustic bearings derived from sparse arrays
Danielle Harris, Jennifer L. Miksis-Olds, Julia A. Vernon, Len Thomas 
Keywords: Arts and Humanities (miscellaneous), Acoustics and Ultrasonics
2018 (1)
Journal of Applied Ecology
vol.55 pp.396-404
(Review article)
Marine mammals and sonar
Catriona M Harris, Len Thomas, Erin Falcone, John Hildebrand, Dorian Houser, Petter Kvadsheim, Frans-Peter A. Lam, Patrick Miller, David J. Moretti, Andrew Read, Hans Slabbekoorn, Brandon L. Southall, Peter Lloyd Tyack, Douglas Wartzok, Vincent Janik 
Keywords: Sonar, Cetaceans, Human disturbance, Impact assessment, Anti-predator response, Anthropogenic noise, Behavioural response, Marine mammals, Dose response
2018 (2)
Journal of the Acoustical Society of America
vol.143 pp.954-967
(Article)
Modelling the broadband propagation of marine mammal echolocation clicks for click-based population density estimates
Alexander von Benda-Beckmann, Len Thomas, Peter Lloyd Tyack, Michael Ainslie 

Ecology and Evolution
vol.Early View 
(Review article)
Understanding the population consequences of disturbance
Enrico Pirotta, Daniel P. Costa, Erica Fleishman, Scott D. Kraus, David Lusseau, David Moretti, Leslie Frances New, Robert Schilling Schick, Lisa K. Schwarz, Samantha E. Simmons, Len Thomas, Peter Lloyd Tyack, Michael J. Weise, Randall S. Wells, John Harwood 
Keywords: Anthropogenic disturbance, Environmental impact assessments, Marine mammals, Nonconsumptive effects, Population consequences, Trait-mediated indirect interactions, Uncertainty
2017 (5/5)

(Commissioned report)
Annual report on the implementation of Council Regulation (EC) No 812/2004 during 2016
Simon Northridge, Al Kingston, Len Thomas 
Keywords: DEFRA
2017 (31/1)
Endangered Species Research
vol.33 pp.235-252
(Article)
Assigning stranded bottlenose dolphins to source stocks using stable isotope ratios following the Deepwater Horizon oil spill
A A Hohn, Len Thomas, R. H. Carmichael, J. Litz, C. Clemons-Chevis, S. F. Shippee, C. Sinclair, S. Smith, T. R. Speakman, M. C. Tumlin, E. S. Zolman 
Keywords: Carbon, Gulf of Mexico, Nitrogen, Stock structure, Sulfur, Tursiops truncatusEcology, Nature and Landscape Conservation
2017 (9)
Environmental and Ecological Statistics
vol.24 pp.399-414
(Article)
Estimation bias under model selection for distance sampling detection functions
Len Thomas, Tiago A. Marques 
Keywords: Detection models, Line transect, Model selection, Point transect, Wildlife abundance estimation
2017 (12/10)
Conservation Letters
vol.10 pp.588-595
(Letter)
Extinction is imminent for Mexico’s endemic porpoise unless fishery bycatch is eliminated
Barbara L Taylor, Lorenzo Rojas-Bracho, Jeffrey Moore, Armando Jaramillo-Legorreta, Jay M Ver Hoef, Gustavo Cardenas-Hinojosa, Edwyna Nieto-Garcia, Jay Barlow, Tim Gerrodette, Nicholas Tregenza, Len Thomas, Philip Steven Hammond 
Keywords: Extinction, Illegal fishing, Line transect, Phocoena sinus, Totoaba macdonaldi, Vaquita abundance , Passive acoustic monitoring , C-POD
2017 (12)
Ecosphere
vol.8 
(Article)
Individual, ecological, and anthropogenic influences on activity budgets of long-finned pilot whales
Saana Isojunno, Dinara Sadykova, Stacy Lynn De Ruiter, Charlotte Curé, Fleur Visser, Len Thomas, Patrick Miller, Catriona M Harris 
Keywords: Anthropogenic noise, Activity synchrony, Benthic habitat, Deep diving mammal, DTAG, Ethogram, Globicephala melas, Hidden Markov model, Naval sonar
2017 (11)
Journal of the Acoustical Society of America
vol.142 pp.EL512-EL517
(Article)
Last call: Passive acoustic monitoring shows continued rapid decline of critically endangered vaquita
Len Thomas, Armando Jaramillo-legorreta, Gustavo Cardenas-hinojosa, Edwyna Nieto-garcia, Lorenzo Rojas-bracho, Jay M. Ver Hoef, Jeffrey Moore, Barbara Taylor, Jay Barlow, Nicholas Tregenza 
2017 (7)
Ecological Applications
vol.27 pp.1694-1698
(Letter)
Model-based approaches to deal with detectability
Tiago A. Marques, Len Thomas, Marc Kery, Stephen Terrence Buckland, David Louis Borchers, Eric Rexstad, Rachel M. Fewster, Darryl I. Mackenzie, J. Andrew Royle, Gurutzeta Guillera-Arroita, Colleen M. Handel, David C. Pavlacky, Richard Joseph Camp 
Keywords: Relative-abundance, Distance, Occupancy
2017 (2)
Conservation Biology
vol.31 pp.183-191
(Article)
Passive acoustic monitoring of the decline of Mexico's critically endangered vaquita
Armando Jaramillo-Legorreta, Gustavo Cardenas-Hinojosa, Edwyna Nieto-Garcia, Lorenzo Rojas-Bracho, Jay Ver Hoef, Jeffrey Moore, Nicholas Tregenza, Jay Barlow, Tim Gerrodette, Len Thomas, Barbara Taylor 
Keywords: Extinction, Phocoena sinus, Population decline, Statistical modeling
2017 (31/1)
Endangered Species Research
vol.33 pp.265-279
(Article)
Quantifying injury to common bottlenose dolphins from the Deepwater Horizon oil spill using an age-, sex- and class-structured population model
Lori H. Schwacke, Len Thomas, Randall S Wells, Wayne E. McFee, Aleta A. Hohn, Keith D. Mullin, Eric S. Zolman, Brian M. Quigley, Teri K. Rowles, John H. Schwacke 
Keywords: Bayesian model, Cetacean, Deepwater Horizon, Density dependence, Impact assessment, Monte Carlo analysis, Population model, SurvivalEcology, Nature and Landscape Conservation
2017 (3)
Journal of the Acoustical Society of America
vol.141 pp.1962-1974
(Article)
Spatio-temporal variation in click production rates of beaked whales
Victoria E. Warren, Tiago A. Marques, Danielle Harris, Len Thomas, Peter Lloyd Tyack, Natacha Aguilar de Soto, Mark Johnson 
Keywords: Arts and Humanities (miscellaneous), Acoustics and Ultrasonics
2017 (10)
Advances in Statistical Analysis
vol.101 pp.399-438
(Article)
Statistical modelling of individual animal movement
Toby A Patterson, Alison Parton, Roland Langrock, Paul G. Blackwell, Len Thomas, Ruth King 
Keywords: Hidden Markov model, Measurement error, Ornstein–Uhlenbeck process, State-space model, Stochastic differential equation, Time seriesEconomics and Econometrics, Analysis, Applied Mathematics, Modelling and Simulation, Statistics and Probability, Social Sciences (miscellaneous)
2017 (31/1)
Endangered Species Research
vol.33 pp.193-209
(Article)
Survival, density, and abundance of common bottlenose dolphins in Barataria Bay (USA) following the Deepwater Horizon oil spill
Trent L. McDonald, Fawn E. Hornsby, Todd R. Speakman, Eric S. Zolman, Keith D. Mullin, Carrie Sinclair, Patricia E. Rosel, Len Thomas, Lori H. Schwacke 
Keywords: Capture-recapture, Photo-identification, Robust design, Spatial-capture model, Tursiops truncatusEcology, Nature and Landscape Conservation
2017 (1/12)
Journal of Fish and Wildlife Management
vol.8 pp.377-386
(Article)
Techniques for estimating the size of low-density gopher tortoise populations
Jonathan M. Stober, Lora L. Smith, Tiago A. Marques, Len Thomas 
Keywords: Abundance, Burrows, Cluster size analysis, Gopher tortoise, Line transect distance sampling, Population density, Systematic samplingAnimal Science and Zoology, Ecology, Evolution, Behavior and Systematics, Ecology, Nature and Landscape Conservation
2017 (27/12)
Marine Ecology Progress Series
vol.585 pp.213-227
(Article)
Whale distribution in a breeding area
Daniel Danilewicz, Philip Steven Hammond, Len Thomas, Alexandre N Zerbini 
Keywords: Shelter, Conservation, Density surface model, Cetacean, Line transect, Reproduction
2017 (31/1)
Endangered Species Research
vol.33 pp.253-264
(Article)
Where were they from? Modelling the source stock of dolphins stranded after the Deepwater Horizon oil spill using genetic and stable isotope data
Len Thomas, P E Rosel, A. Hohn, J. Litz, L H Schwacke 
Keywords: Bayesian hierarchical model, Data integration, Deepwater Horizon, Genetic assignment, Stable isotope ratios, StrandingEcology, Nature and Landscape Conservation
2016 (28/12)
PLoS One
vol.11 
(Article)
An assessment of the population of cotton-top tamarins (Saguinus oedipus) and their habitat in Colombia
Anne Savage, Len Thomas, Katie L. Feilen, Luis H. Soto, Mackenzie Pearson, Felix S. Medina, German Emeris, Rosamira R. Guillen 
Keywords: Medicine(all), Biochemistry, Genetics and Molecular Biology(all), Agricultural and Biological Sciences(all)
2016 (19/5)
PLoS One
vol.11 pp.1-16
(Article)
An efficient acoustic density estimation method with human detectors applied to gibbons in Cambodia
Benjamin M. Rawson, David Louis Borchers, Ben Stevenson, Tiago A. Marques, Len Thomas 
2016 (1/6)

(Commissioned report)
Annual Report on the Implementation of Council Regulation (EC) No 812/2004
Simon Northridge, Al Kingston, Len Thomas 
Keywords: Bycatch, 812/2004DEFRA
2016 (9)
Journal of the Acoustical Society of America
vol.140 pp.1918-1930
(Article)
Delphinid echolocation click detection probability on near-seafloor sensors
Kaitlin E. Frasier, Sean M. Wiggins, Danielle Harris, Tiago A. Marques, Len Thomas, John A. Hildebrand 
Keywords: Arts and Humanities (miscellaneous), Acoustics and Ultrasonics
2016 (6)
Wildlife Society Bulletin
vol.40 pp.331-338
(Article)
Estimating Key Largo woodrat abundance using spatially explicit capture–recapture and trapping point transects
Stephen Terrence Buckland, Len Thomas, Anne Savage 
Keywords: Abundance, Distance sampling, Key Largo woodrat, Neotoma floridana smalli, Small mammals, Spatially explicit capture–recapture, Trapping point transects
2016 (12)
Proceedings of Meetings on Acoustics
vol.27 
(Review article)
From physiology to policy
Natacha Aguilar de Soto, Sascha Kate Hooker, Saana Isojunno, Mark Johnson, Patrick Miller, Peter Lloyd Tyack, Paul Wensveen, Carl Robert Donovan, Catriona M Harris, Danielle Harris, Laura Helen Marshall, Cornelia Sabrina Oedekoven, Rocio Prieto, Len Thomas 
2016 (8)
Marine Policy
vol.70 pp.58-64
(Article)
Gauging allowable harm limits to cumulative, sub-lethal effects of human activities on wildlife
Rob Williams, Len Thomas, Christopher W. Clark, Philip Steven Hammond 
Keywords: Allowable harm limits, Cumulative impact, Industrialization, Marine mammal, Ocean, Population dynamics, Whale
2016

(Other report)
Marine Strategy Framework Directive. Estimating the European Grey Seal population
Debbie JF Russell, Nora Nell Hanson, Len Thomas 
Keywords: SCOS
2016 (2/5)
Endangered Species Research
vol.30 pp.95-108
(Article)
Modeling the aggregated exposure and responses of bowhead whales Balaena mysticetus to multiple sources of anthropogenic underwater sound
William T. Ellison, Roberto Racca, Christopher W. Clark, Bill Streever, Adam S. Frankel, Erica Fleishman, Robyn Angliss, Joel Berger, Darlene Ketten, Melania Guerra, Matthias Leu, Megan McKenna, Todd Sformo, Brandon Southall, Robert Suydam, Len Thomas 
Keywords: Arctic, Cumulative effects, Harassment, Incidental take, Marine mammals, Negligible impact
2016
pp.399-407
(Conference contribution)
The challenges of analyzing behavioral response study data
Catriona M Harris, Len Thomas, Dinara Sadykova, Stacy Lynn De Ruiter, Peter Lloyd Tyack, Brandon L. Southall, Andrew J. Read, Patrick Miller 
Keywords: Sonar, Cetaceans, Change-point, Dose-response, State-space modelling
2015 (30/10)

(Other report)
A description of LATTE outputs
Tiago A. Marques, Len Thomas 
2015 (21/9)
Movement Ecology
vol.3 
(Article)
A path reconstruction method integrating dead-reckoning and position fixes applied to humpback whales
Paul Wensveen, Len Thomas, Patrick Miller 
Keywords: Megaptera novaeangliae, Marine mammal, Positioning, Fine-scale movement, State-space model, Bio-logging, Track reconstruction, Archival tag, Focal follow
2015
Journal of the American Statistical Association
vol.110 pp.195-204
(Article)
A unifying model for capture-recapture and distance sampling surveys of wildlife populations
David Louis Borchers, Ben Stevenson, Len Thomas, Tiago A. Marques 
Keywords: Abundance estimation, Acoustic survey, Closed population, Measurement error, Visual survey
2015 (1/6)

(Commissioned report)
Annual report on the implementation of Council Regulation (EC) No 812/2004 during 2014
Simon Northridge, Al Kingston, Len Thomas 
Keywords: Bycatch observer programmesDEFRA
2015 (20/11)
Ecosphere
vol.6 
(Article)
Dose response severity functions for acoustic disturbance in cetaceans using recurrent event survival analysis
Catriona M Harris, Dinara Sadykova, Stacy Lynn De Ruiter, Peter Lloyd Tyack, Patrick Miller, Petter Kvadsheim, Frans-Peter Lam, Len Thomas 
Keywords: behavioral response, Cetaceans, Controlled exposure experiment, Cox proportional hazards model, Globicephala melas, Orcinus orca, Physeter macrocephalus, Response intensity, Sonar
2015 (3)
Methods in Ecology and Evolution
vol.6 pp.278-288
(Article)
Efficient abstracting of dive profiles using a broken-stick model
Theoni Photopoulou, Philip Lovell, Mike Fedak, Len Thomas, Jason Matthiopoulos 
Keywords: Animal telemetry, Broken-stick model, CTD-SRDL, Dive profile, Dive type, Dive zone index, Elephant seal, Data abstractionEnvironmental Science (miscellaneous)
2015 (10)
Ocean and Coastal Management
vol.115 pp.17-24
(Article)
Impacts of anthropogenic noise on marine life
Andrew J Wright, LK Blight, R Bruintjes, R Canessa, CW Clark, S Cullis-Suzuki, DT Dakin, C Erbe, Philip Steven Hammond, MD Merchant, PD O'Hara, J Purser, AN Radford, SD Simpson, Len Thomas, MA Wale 
Keywords: Anthropogenic, Conservation, Ecology, Marine, Ocean noise, Policy, Shipping
2015 (2)
Deep Sea Research Part II: Topical Studies in Oceanography
vol.112 pp.143-157
(Article)
Inter-annual and seasonal trends in cetacean distribution, density and abundance off southern California
G.S. Campbell, Len Thomas, K. Whitaker, A.B. Douglas, J. Calambokidis, J.A. Hildebrand 
Keywords: Cetaceans, Line transect, Density, Abundance, Distribution, Trends, Southern California, CalCOFI
2015 (20/3)
PLoS One
vol.10 
(Article)
Mixture models for distance sampling detection functions
David Lawrence Miller, Len Thomas 
2015 (12/11)
Scientific Reports
vol.5 
(Article)
Passive acoustic monitoring of beaked whale densities in the Gulf of Mexico
John Hildebrand, Simone Baumann-Pickering, Kaitlin Frasier, Jennifer Trickey, Karlina Merkens, Sean Wiggins, Mark McDonald, Lance Garrison, Danielle Harris, Tiago A. Marques, Len Thomas 
2015

(Other report)
Procedure description
Tiago A. Marques, Jessica Shaeffer, Len Thomas 
2015

(Other report)
Status and future of research on the behavioural responses of marine mammals to U.S. Navy sonar
Catriona M Harris, Len Thomas 
2015 (23/3)
PLoS One
vol.10 
(Article)
The effect of animal movement on line transect estimates of abundance
Richard Glennie, Stephen Terrence Buckland, Len Thomas 
2015 (9)
Methods in Ecology and Evolution
vol.6 pp.987-996
(Article)
Tracking marine mammals in 3D using electronic tag data
C. Laplanche, Tiago A. Marques, Len Thomas 
Keywords: Animal movement modelling, Dead reckoning, Electronic tag, Flow noise, Hierarchical Bayesian modelling, Track reconstruction, Triaxial magnetometer and accelerometer
2014 (2)
Journal of the Acoustical Society of America
vol.135 pp.975-993
(Article)
Dose-response relationships for the onset of avoidance of sonar by free-ranging killer whales
Patrick Miller, Ricardo Nuno Antunes, Paul Wensveen, Filipa Isabel Pereira Samarra, Ana Catarina De Carvalho Alves, Peter Lloyd Tyack, Petter H. Kvadsheim, Lars Kleivane, Frans-Peter A. Lam, Michael A. Ainslie, Len Thomas 
2014

(Book)
Modelling population dynamics
Ken Newman, Stephen Terrence Buckland, Byron Morgan, Ruth King, David Louis Borchers, Diana Cole, Panagiotis Besbeas, Olivier Gimenez, Len Thomas 
2014 (7)
Marine Mammal Science
vol.30 pp.923–938
(Article)
Spatial variation in maximum dive depth in gray seals in relation to foraging.
Theoni Photopoulou, Mike Fedak, Len Thomas, Jason Matthiopoulos 
Keywords: Maximum dive depth, Spatial variation, Generalized additive mixed model, Halichoerus grypus, Space use, Habitat preferenceEnvironmental Science(all)

Contact Details:

Prof Len Thomas
The Observatory
Buchanan Gardens
University of St Andrews
St Andrews
KY16 9LZ
Fife
UK

tel: (44) (0) 1334 461801
fax: (44) (0) 1334 461800
room: 208
email: lt5@st-andrews.ac.uk

Related:

research@st-andrews
Personal Homepage
Centre for Research into Ecological & Environmental Modelling
School of Mathematics & Statistics
National Centre for Statistical Ecology
Scottish Oceans Institute

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Contact

The Secretary
Scottish Oceans Institute
Institiud Chuantan na h-Alba
Gatty Marine Laboratory
East Sands St Andrews
KY16 8LB
Scotland
UK

tel: +44 (0) 1334 463472
fax: +44 (0) 1334 463443
email: soi@st-andrews.ac.uk

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