Dr Len Thomas

Reader

tel: (44) (0) 1334 461801
fax: (44) (0) 1334 461800
email: lt5@st-andrews.ac.uk
room: 208  (The Observatory)
The Observatory
Buchanan Gardens
University of St Andrews
St Andrews
Fife
KY16 9LZ
UK


General Information



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.

 

Recent Publications

Warren, VE, Marques, TA, Harris, D, Thomas, L, Tyack, PL, Aguilar de Soto, N, Hickmott, LS & Johnson, MP 2017, 'Spatio-temporal variation in click production rates of beaked whales: implications for passive acoustic density estimation' Journal of the Acoustical Society of America, vol 141, no. 3, pp. 1962-1974. DOI: 10.1121/1.4978439
Jaramillo-Legorreta, A, Cardenas-Hinojosa, G, Nieto-Garcia, E, Rojas-Bracho, L, Hoef, JV, Moore, J, Tregenza, N, Barlow, J, Gerrodette, T, Thomas, L & Taylor, B 2017, 'Passive acoustic monitoring of the decline of Mexico's critically endangered vaquita' Conservation Biology, vol 31, no. 1, pp. 183-191. DOI: 10.1111/cobi.12789
Hohn, AA, Thomas, L, Carmichael, RH, Litz, J, Clemons-Chevis, C, Shippee, SF, Sinclair, C, Smith, S, Speakman, TR, Tumlin, MC & Zolman, ES 2017, 'Assigning stranded bottlenose dolphins to source stocks using stable isotope ratios following the Deepwater Horizon oil spill' Endangered Species Research, vol 33, pp. 235-252. DOI: 10.3354/esr00783
Schwacke, LH, Thomas, L, Wells, RS, McFee, WE, Hohn, AA, Mullin, KD, Zolman, ES, Quigley, BM, Rowles, TK & Schwacke, JH 2017, 'Quantifying injury to common bottlenose dolphins from the Deepwater Horizon oil spill using an age-, sex- and class-structured population model' Endangered Species Research, vol 33, pp. 265-279. DOI: 10.3354/esr00777
Thomas, L, Booth, CG, Rosel, PE, Hohn, A, Litz, J & Schwacke, LH 2017, 'Where were they from? Modelling the source stock of dolphins stranded after the Deepwater Horizon oil spill using genetic and stable isotope data' Endangered Species Research, vol 33, no. 1, pp. 253-264. DOI: 10.3354/esr00754
McDonald, TL, Hornsby, FE, Speakman, TR, Zolman, ES, Mullin, KD, Sinclair, C, Rosel, PE, Thomas, L & Schwacke, LH 2017, 'Survival, density, and abundance of common bottlenose dolphins in Barataria Bay (USA) following the Deepwater Horizon oil spill' Endangered Species Research, vol 33, pp. 193-209. DOI: 10.3354/esr00806
Savage, A, Thomas, L, Feilen, KL, Kidney, D, Soto, LH, Pearson, M, Medina, FS, Emeris, G & Guillen, RR 2016, 'An assessment of the population of cotton-top tamarins (Saguinus oedipus) and their habitat in Colombia' PLoS One, vol 11, no. 12, e0168324. DOI: 10.1371/journal.pone.0168324
Taylor, BL, Rojas-Bracho, L, Moore, J, Jaramillo-Legorreta, A, Ver Hoef, JM, Cardenas-Hinojosa, G, Nieto-Garcia, E, Barlow, J, Gerrodette, T, Tregenza, N, Thomas, L & Hammond, PS 2016, 'Extinction is imminent for Mexico’s endemic porpoise unless fishery bycatch is eliminated' Conservation Letters, vol Early View. DOI: 10.1111/conl.12331
Aguilar De Soto, N, Gkikopoulou, K, Hooker, S, Isojunno, S, Johnson, M, Miller, P, Tyack, P, Wensveen, P, Donovan, C, Harris, CM, Harris, D, Marshall, L, Oedekoven, C, Prieto, R & Thomas, L 2016, 'From physiology to policy: a review of physiological noise effects on marine fauna with implications for mitigation' Proceedings of Meetings on Acoustics, vol 27, no. 1, 040008. DOI: 10.1121/2.0000299
Tyack, PL, Bailey, H, Crocker, D, Estes, JE, Francis, CD, Harwood, J, Schwacke, L, Thomas, LJ & Wartzok, D 2016, Approaches to Understanding the Cumulative Effects of Stressors on Marine Mammals. National Academies Press, Washington DC. National Academies Press, Washington DC. DOI: 10.17226/23479
Frasier, KE, Wiggins, SM, Harris, D, Marques, TA, Thomas, L & Hildebrand, JA 2016, 'Delphinid echolocation click detection probability on near-seafloor sensors' Journal of the Acoustical Society of America, vol 140, no. 3, pp. 1918-1930. DOI: 10.1121/1.4962279
Williams, R, Thomas, L, Ashe, E, Clark, CW & Hammond, PS 2016, 'Gauging allowable harm limits to cumulative, sub-lethal effects of human activities on wildlife: a case-study approach using two whale populations' Marine Policy, vol 70, pp. 58-64. DOI: 10.1016/j.marpol.2016.04.023
Fleishman, E, Costa, DP, Harwood, J, Kraus, S, Moretti, D, New, LF, Schick, RS, Schwarz, LK, Simmons, SE, Thomas, L & Wells, RS 2016, 'Monitoring population-level responses of marine mammals to human activities' Marine Mammal Science, vol 32, no. 3, pp. 1004-1021. DOI: 10.1111/mms.12310
Northridge, SP, Kingston, AR & Thomas, LJ 2016, Annual Report on the Implementation of Council Regulation (EC) No 812/2004. defra.
Kidney, D, Rawson, BM, Borchers, DL, Stevenson, B, Marques, TA & Thomas, L 2016, 'An efficient acoustic density estimation method with human detectors applied to gibbons in Cambodia' PLoS One, vol 11, no. 5, e0155066, pp. 1-16. DOI: 10.1371/journal.pone.0155066
Ellison, WT, Racca, R, Clark, CW, Streever, B, Frankel, AS, Fleishman, E, Angliss, R, Berger, J, Ketten, D, Guerra, M, Leu, M, McKenna, M, Sformo, T, Southall, B, Suydam, R & Thomas, L 2016, 'Modeling the aggregated exposure and responses of bowhead whales Balaena mysticetus to multiple sources of anthropogenic underwater sound' Endangered Species Research, vol 30, pp. 95-108. DOI: 10.3354/esr00727
Potts, JM, Buckland, ST, Thomas, L & Savage, A 2016, 'Estimating Key Largo woodrat abundance using spatially explicit capture–recapture and trapping point transects' Wildlife Society Bulletin, vol Early View. DOI: 10.1002/wsb.651
Paxton, CGM, Scott-Hayward, LAS, MacKenzie, ML, Rexstad, E & Thomas, LJ 2016, Revised Phase III Data Analysis of Joint Cetacean Protocol Data Resources with Advisory Note: Report 517. vol. 517, Joint Nature Conservation Committee.
Russell, DJF, Hanson, NN & Thomas, LJ 2016, Marine Strategy Framework Directive. Estimating the European Grey Seal population: Special Committee on Seals. Briefing Paper 16/09. Sea Mammal Research Unit.
Harris, CM, Thomas, L, Sadykova, D, De Ruiter, SL, Tyack, PL, Southall, BL, Read, AJ & Miller, P 2016, The challenges of analyzing behavioral response study data: an overview of the MOCHA (Multi-study OCean acoustics Human effects Analysis) project. in AN Popper & A Hawkins (eds), Effects of Noise on Aquatic Life II. Advances in Experimental Medicine and Biology, vol. 875, Springer Science and Business Media, pp. 399-407, Third International Conference on the Effects of Noise on Aquatic Life, Budapest, Hungary, 11-16 August. DOI: 10.1007/978-1-4939-2981-8_47
Harris, CM, Sadykova, D, De Ruiter, SL, Tyack, PL, Miller, P, Kvadsheim, P, Lam, F-P & Thomas, L 2015, 'Dose response severity functions for acoustic disturbance in cetaceans using recurrent event survival analysis' Ecosphere, vol 6, no. 11, 236. DOI: 10.1890/ES15-00242.1
Hildebrand, J, Baumann-Pickering, S, Frasier, K, Trickey, J, Merkens, K, Wiggins, S, McDonald, M, Garrison, L, Harris, D, Marques, TA & Thomas, L 2015, 'Passive acoustic monitoring of beaked whale densities in the Gulf of Mexico' Scientific Reports, vol 5, 16343. DOI: 10.1038/srep16343
Marques, TA & Thomas, L 2015, A description of LATTE outputs. CREEM Technical Report, no. 2015-2, University of St Andrews.
King, SL, Schick, RS, Donovan, CR, Booth, CG, Burgman, M, Thomas, L & Harwood, J 2015, 'An interim framework for assessing the population consequences of disturbance' Methods in Ecology and Evolution, vol 6, no. 10, pp. 1150-1158. DOI: 10.1111/2041-210X.12411
Williams, R, Wright, AJ, Ashe, E, Blight, LK, Bruintjes, R, Canessa, R, Clark, CW, Cullis-Suzuki, S, Dakin, DT, Erbe, C, Hammond, PS, Merchant, MD, O'Hara, PD, Purser, J, Radford, AN, Simpson, SD, Thomas, L & Wale, MA 2015, 'Impacts of anthropogenic noise on marine life: publication patterns, new discoveries, and future directions in research and management' Ocean and Coastal Management, vol 115, pp. 17-24. DOI: 10.1016/j.ocecoaman.2015.05.021
Laplanche, C, Marques, TA & Thomas, L 2015, 'Tracking marine mammals in 3D using electronic tag data' Methods in Ecology and Evolution, vol 6, no. 9, pp. 987-996. DOI: 10.1111/2041-210X.12373
Northridge, S, Kingston, A & Thomas, L 2015, Annual report on the implementation of Council Regulation (EC) No 812/2004 during 2014. European Commission.
Glennie, R, Buckland, ST & Thomas, L 2015, 'The effect of animal movement on line transect estimates of abundance' PLoS One, vol 10, no. 3, e0121333. DOI: 10.1371/journal.pone.0121333
Miller, DL & Thomas, L 2015, 'Mixture models for distance sampling detection functions' PLoS One, vol 10, no. 3, e0118726. DOI: 10.1371/JOURNAL.PONE.0118726
Photopoulou, T, Lovell, P, Fedak, MA, Thomas, L & Matthiopoulos, J 2015, 'Efficient abstracting of dive profiles using a broken-stick model' Methods in Ecology and Evolution, vol 6, no. 3, pp. 278-288. DOI: 10.1111/2041-210X.12328
Campbell, GS, Thomas, L, Whitaker, K, Douglas, AB, Calambokidis, J & Hildebrand, JA 2015, 'Inter-annual and seasonal trends in cetacean distribution, density and abundance off southern California' Deep Sea Research Part II: Topical Studies in Oceanography, vol 112, pp. 143-157. DOI: 10.1016/j.dsr2.2014.10.008
Wensveen, PJ, Thomas, L & Miller, PJO 2015, 'A path reconstruction method integrating dead-reckoning and position fixes applied to humpback whales' Movement Ecology, vol 3, no. 1, pp. 31. DOI: 10.1186/s40462-015-0061-6
Laplanche, C, Marques, TALO & Thomas, LJ, Accompanying Marine Mammals into the Abyss: The Benefits of Electronic Tag Data for Undersea Tracking, 2015, Web publication/site, Blog post on the Official blog of Methods in Ecology and Evolution.
Harris, CM & Thomas, L 2015, Status and future of research on the behavioural responses of marine mammals to U.S. Navy sonar. CREEM Technical Report , no. 2015-3, University of St Andrews.
Marques, TA, Shaeffer, J, Moretti, D & Thomas, L 2015, Procedure description: using AUTEC’s hydrophones surrounding a DTAGed whale to obtain localizations. CREEM Technical Report, no. 2015-1, University of St Andrews.
Borchers, DL, Stevenson, BC, Kidney, D, Thomas, L & Marques, TA 2015, 'A unifying model for capture-recapture and distance sampling surveys of wildlife populations' Journal of the American Statistical Association, vol 110, no. 509, pp. 195-204. DOI: 10.1080/01621459.2014.893884
Gimenez, O, Buckland, ST, Morgan, BJT, Bez, N, Bertrand, S, Choquet, R, Dray, S, Etienne, M-P, Fewster, R, Gosselin, F, Merigot, B, Monestiez, P, Morales, JM, Mortier, F, Munoz, F, Ovaskainen, O, Pavoine, S, Pradel, R, Schurr, FM, Thomas, L, Thuiller, W, Trenkel, V, de Valpine, P & Rexstad, E 2014, 'Statistical ecology comes of age' Biology Letters, vol 10, 20140698. DOI: 10.1098/rsbl.2014.0698
Moretti, D, Thomas, L, Marques, T, Harwood, J & Dilley, A 2014, 'Errutum: A risk function for behavioral disruption of blainville's beaked whales mesoplodon densirostris from mid-frequency active sonar (PLoS ONE (2014) 9:12 (e85064) doi:10.1371/journal.pone.0085064)' PLoS One, vol 9, no. 12. DOI: 10.1371/journal.pone.0116555
Marques, TA, Buckland, ST, Borchers, DL, Rexstad, E & Thomas, L 2014, Distance Sampling. in M Lovric (ed.), International Encyclopedia of Statistical Science. Springer, pp. 398. DOI: 10.1007/978-3-642-04898-2_214
Photopoulou, T, Fedak, M, Thomas, L & Matthiopoulos, J 2014, 'Spatial variation in maximum dive depth in gray seals in relation to foraging.' Marine Mammal Science, vol 30, no. 3, pp. 923–938 . DOI: 10.1111/mms.12092
Antunes, R, Kvadsheim, PH, Lam, FPA, Tyack, PL, Thomas, L, Wensveen, PJ & Miller, PJO 2014, 'High thresholds for avoidance of sonar by free-ranging long-finned pilot whales (Globicephala melas)' Marine Pollution Bulletin, vol 83, no. 1, pp. 165-180. DOI: 10.1016/j.marpolbul.2014.03.056
Northridge, S, Kingston, A & Thomas, L 2014, Annual report on the implementation of Council Regulation (EC) No 812/2004 during 2013. defra.
Miller, P, Antunes, RN, Wensveen, PJ, Samarra, FIP, Alves, ACDC, Tyack, PL, Kvadsheim, PH, Kleivane, L, Lam, F-PA, Ainslie, MA & Thomas, L 2014, 'Dose-response relationships for the onset of avoidance of sonar by free-ranging killer whales' Journal of the Acoustical Society of America, vol 135, no. 2, pp. 975-993. DOI: 10.1121/1.4861346
New, LF, Clark, J, Costa, D, Fleishman, E, Hindell, M, Klanjšček, T, Lusseau, D, Kraus, S, McMahon, C, Robinson, P, Schick, RS, Schwartz, L, Simmons, S, Thomas, L, Tyack, PL & Harwood, J 2014, 'Using short-term measures of behaviour to estimate long-term fitness of southern elephant seals.' Marine Ecology Progress Series, vol 496, pp. 99-108. DOI: 10.3354/meps10547
Moretti, D, Thomas, L, Marques, TA, Harwood, J, Dilley, A, Neales, B, Shaffer, J, Mccarthy, E, New, LF, Jarvis, S & Morrissey, R 2014, 'A risk function for behavioral disruption of Blainville’s beaked whales (Mesoplodon densirostris) from mid-frequency active sonar' PLoS One, vol 9, no. 1, e85064. DOI: 10.1371/journal.pone.0085064
Newman, K, Buckland, ST, Morgan, B, King, R, Borchers, DL, Cole, D, Besbeas, P, Gimenez, O & Thomas, L 2014, Modelling population dynamics: Model formulation, fitting and assessment using state-space methods. Methods in Statistical Ecology, Springer, New York. DOI: 10.1007/978-1-4939-0977-3
Caillat, MA, Thomas, L & Gillespie, DM 2013, 'The effects of acoustic misclassification on cetacean species abundance estimation' Journal of the Acoustical Society of America, vol 134, no. 3, pp. 2469–2476. DOI: 10.1121/1.4816569
Harris, DV, Matias, L, Thomas, L, Harwood, J & Geissler, W 2013, 'Applying distance sampling to fin whale calls recorded by single seismic instruments in the northeast Atlantic.' Journal of the Acoustical Society of America, vol 134, no. 5, 3522. DOI: 10.1121/1.4821207
Miller, DL, Burt, ML, Rexstad, E & Thomas, L 2013, 'Spatial models for distance sampling data: recent developments and future directions' Methods in Ecology and Evolution, vol 4, no. 11, pp. 1001-1010. DOI: 10.1111/2041-210X.12105
Marques, TA, Thomas, L, Martin, S, Mellinger, D, Ward, J, Moretti, D, Harris, DV & Tyack, PL 2013, 'Estimating animal population density using passive acoustics' Biological Reviews of the Cambridge Philosophical Society, vol 88, no. 2, pp. 287–309. DOI: 10.1111/brv.12001
Williams, R, Vikingsson, GA, Gislason, A, Lockyer, C, New, L, Thomas, L & Hammond, PS 2013, 'Evidence for density-dependent changes in body condition and pregnancy rate of North Atlantic fin whales over four decades of varying environmental conditions' ICES Journal of Marine Science. DOI: 10.1093/icesjms/fst059
De Ruiter, SL, Southall, BL, Calambokidis, J, Zimmer, WMX, Sadykova, D, Falcone, EA, Friedlaender, AS, Joseph, JE, Moretti, D, Schorr, GS, Thomas, L & Tyack, PL 2013, 'First direct measurements of behavioural responses by Cuvier's beaked whales to mid-frequency active sonar' Biology Letters, vol 9, no. 4, pp. 1-5. DOI: 10.1098/rsbl.2013.0223
Northridge, S, Kingston, AR & Thomas, L 2013, Report to the European Commission on the Implementation of Regulation 812/2004 by the United Kingdom for the Calendar Year 2012. defra.
Lawrence, J, Gramacy, R, Thomas, L & Buckland, ST 2013, 'The importance of prior choice in model selection: a density dependence example.' Methods in Ecology and Evolution, vol 4, pp. 25-33. DOI: 10.1111/j.2041-210X.2012.00255.x
Schick, RS, New, L, Thomas, L, Costa, D, Hindell, M, McMahon, C, Robinson, P, Simmons, S, Thums, M, Harwood, J & Clark, J 2013, 'Estimating resource acquisition and at-sea body condition of a marine predator' Journal of Animal Ecology, vol 82, no. 6, pp. 1300-1315. DOI: 10.1111/1365-2656.12102
Langrock, R, Marques, TA, Baird, R & Thomas, L 2013, 'Modeling the diving behavior of whales: a latent-variable approach with feedback and semi-Markovian components' Journal of Agricultural, Biological and Environmental Statistics, vol 19, no. 1, pp. 82-100. DOI: 10.1007/s13253-013-0158-6
New, LF, Harwood, J, Thomas, L, Donovan, CR, Clark, J, Hastie, GD, Thompson, P, Cheney, B, Scott Hayward, LAS & Lusseau, D 2013, 'Modelling the biological significance of behavioural change in coastal bottlenose dolphins in response to disturbance' Functional Ecology, vol 27, pp. 314-322. DOI: 10.1111/1365-2435.12052
Martin, S, Marques, TA, Thomas, L, Morrissey, R, Jarvis, S, DiMarzio, N, Moretti, D & Mellinger, D 2013, 'Estimating minke whale (Balaenoptera acutorostrata) boing sound density using passive acoustic sensors' Marine Mammal Science, vol 29, pp. 142-158. DOI: 10.1111/j.1748-7692.2011.00561.x
McClintock, BT, King, R, Thomas, L, Matthiopoulos, J, McConnell, BJ & Morales, J 2012, 'A general discrete-time modeling framework for animal movement using multistate random walks' Ecological Monographs, vol 82, no. 3, pp. 335-349. DOI: 10.1890/11-0326.1
Jewell, RL, Thomas, L, Harris, CM, Kaschner, K, Wiff, RA, Hammond, PS & Quick, NJ 2012, 'Global analysis of cetacean line-transect surveys: detecting trends in cetacean density' Marine Ecology Progress Series, vol 453, pp. 227-240. DOI: 10.3354/meps09636
Marques, TALO, Thomas, L, Martin, S, Mellinger, D, Jarvis, S, Morrissey, R, Ciminello, C-A & DiMarzio, N 2012, 'Spatially explicit capture-recapture methods to estimate minke whale density from data collected at bottom-mounted hydrophones' Journal of Ornithology, vol 152, no. Supp 2, pp. 445-455. DOI: 10.1007/s10336-010-0535-7
Thomas, L & Marques, TA 2012, 'Passive acoustic monitoring for estimating animal density' Acoustics Today, vol 8, no. 3, pp. 35-44. DOI: 10.1121/1.4753915
Kyhn, L, Tougaard, J, Thomas, L, Duve, LR, Steinback, J, Amundin, M, Desportes, G & Teilmann, J 2012, 'From echolocation clicks to animal density - Acoustic sampling of harbour porpoises with static dataloggers' Journal of the Acoustical Society of America, vol 131, no. 1, pp. 550-560. DOI: 10.1121/1.3662070
Norris, T, Martin, S, Thomas, L, Yack, T, Oswald, J, Nosal, EM & Janik, VM 2012, 'Acoustic ecology and behavior of minke whales in the Hawaiian and Marianas islands: localization, abundance estimation, and characterization of minke whale "boings"' Advances in Experimental Medicine and Biology, vol 730, pp. 149-153.
Northridge, SP, Kingston, AR & Thomas, L 2012, Report to the European Commission on the Implementation of Regulation 812/2004 by the United Kingdom for the Calendar Year 2011. defra.
Ward, J, Thomas, L, Jarvis, S, DiMarzio, N, Moretti, D, Marques, TA, Dunn, CA, Claridge, D, Hartvig, EC & Tyack, PL 2012, 'Passive Acoustic Density Estimation of Sperm Whales in the Tongue of the Ocean, Bahamas' Marine Mammal Science. DOI: 10.1111/j.1748-7692.2011.00560.x
Potts, JM, Buckland, ST, Thomas, L & Savage, A 2012, 'Estimating abundance of cryptic but trappable animals using trapping point transects: a case study for Key Largo woodrats' Methods in Ecology and Evolution, vol 3, pp. 695-703. DOI: 10.1111/j.2041-210X.2012.00205.x
Langrock, R, King, R, Matthiopoulos, J, Thomas, L, Fortin, D & Morales, JM 2012, 'Flexible and practical modeling of animal telemetry data: hidden Markov models and extensions' Ecology, vol 93, no. 11, pp. 2336-2342. DOI: 10.1890/11-2241.1
Marques, TA, Munger, L, Thomas, L, Wiggins, S & Hildebrand, J 2012, An update to the methods in Endangered Species Research 2011 paper "Estimating North Pacific right whale Eubalaena japonica density using passive acoustic cue counting". CREEM Technical Report, no. 2012-1, University of St Andrews.
Mateos, M, Arroyo, G & Thomas, L 2012, 'The development and use of a method to fill time gaps in migration counts: seabird conservation applications.' Condor, vol 114, pp. 513-522. DOI: 10.1525/cond.2012.100053
Borkin, K, Summers, R & Thomas, L 2012, 'Distribution, density and stand-type preferences of wood ant Formica spp.nest mounts in a Scots pinewood.' European Journal of Entomology, vol 109, pp. 47-53.
Mellinger, DK, Martin, SW, Morrissey, RP, Thomas, L & Yosco, JJ 2011, 'A method for detecting whistles, moans, and other frequency contour sounds' Journal of the Acoustical Society of America, vol 129, no. 6, pp. 4055-4061. DOI: 10.1121/1.3531926
Kusel, E, Mellinger, D, Thomas, L, Marques, TALO, Moretti, D & Ward, J 2011, 'Cetacean population density from single fixed sensors using passive acoustics' Journal of the Acoustical Society of America, vol 129, no. 6, pp. 3610-3622. DOI: 10.1121/1.3583504
Marques, TALO, Munger, L, Thomas, L, Wiggins, S & Hildebrand, J 2011, 'Estimating North Pacific right whale (Eubalaena japonica) density using passive acoustic cue counting' Endangered Species Research, vol 13, no. 3, pp. 163-172. DOI: 10.3354/esr00325
Ward, J, Jarvis, S, Moretti, D, Morrissey, R, DiMarzio, N, Johnson, M, Tyack, P, Thomas, L & Marques, T 2011, 'Beaked whale (Mesoplodon densirostris) passive acoustic detection in increasing ambient noise' Journal of the Acoustical Society of America, vol 129, no. 2, pp. 662-669. DOI: 10.1121/1.3531844
Borchers, DL, Thomas, L, Buckland, ST, Skaug, H & Barlow, J 2011, Workshop on new developments in cetacean survey methods. CREEM Technical Report, no. 2011-3, University of St Andrews.
Northridge, SP, Kingston, AR & Thomas, L 2011, Report to the European Commission on the Implementation of Regulation 812/2004 by the United Kingdom for the Calendar Year 2010. defra.
Durant, S, Craft, M, Hilborn, R, Bashir, S, Hando, J & Thomas, L 2011, 'Long term trends in carnivore abundance using distance sampling in Serengeti national park, Tanzania' Journal of Applied Ecology, vol 48, pp. 1490-1500. DOI: 10.1111/j.1365-2664.2011.02042.x
Marques, TALO, Thomas, L & Royle, JA 2011, 'A hierarchical model for spatial capture-recapture data: comment' Ecology, vol 92, pp. 526-528.
Marques, TALO, Buckland, ST, Borchers, DL, Rexstad, E & Thomas, L 2011, Distance sampling. in M Lovric (ed.), International Encyclopedia of Statistical Science. Springer-Verlag, pp. 398-400. DOI: 10.1007/978-3-642-04898-2_214
McCarthy, E, Moretti, D, Thomas, L, DiMarzio, N, Morrissey, R, Jarvis, S, Izzy, A-M & Dilley, A 2011, 'Changes in spatial and temporal distribution and vocal behavior of Blainville's beaked whales (Mesoplodon densirostris) during multi-ship exercises with mid-frequency sonar' Marine Mammal Science, vol 27, pp. E206-E226. DOI: 10.1111/j.1748-7692.2010.00457.x
Lonergan, ME, Thompson, D, Thomas, LJ & Duck, CD 2011, 'An approximate Bayesian method applied to estimating the trajectories of four British grey seal (Halichoerus grypus) populations from pup counts.' Journal of Marine Biology. DOI: 10.1155/2011/597424
Moretti, D, Marques, TALO, Thomas, L, DiMarzio, N, Dilley, A, Morrissey, R, McCarthy, E, Ward, J & Jarvis, S 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 , vol 71, no. 11, pp. 1036-1042. DOI: 10.1016/j.apacoust.2010.04.011
Buckland, ST, Plumptre, AJ, Thomas, L & Rexstad, EA 2010, 'Design and analysis of line transect surveys for primates' International Journal of Primatology, vol 31, no. 5, pp. 833-847. DOI: 10.1007/s10764-010-9431-5
Savage, A, Thomas, L, Leighty, K, Soto, L & Medina, F 2010, 'Novel survey method finds dramatic decline of wild cotton-top tamarin population' Nature Communications, vol 1. DOI: 10.1038/ncomms1030
Buckland, ST, Plumptre, AJ, Thomas, L & Rexstad, E 2010, 'Line transect sampling of primates: can animal-to-observer distance methods work?' International Journal of Primatology, vol 31, no. 3, pp. 485-499. DOI: 10.1007/s10764-010-9408-4
Rexstad, E, Thomas, L, Borchers, D & Buckland, S 2010, 'Effect of unmodelled heterogeneity upon abundance estimation using line and point transects' Paper presented at International Statistical Ecology Conference 2010, Canterbury, United Kingdom, 6/07/10, .
Marques, TALO, Ward, J, Jarvis, S, Moretti, D, Morrissey, R, DiMarzio, N & Thomas, L 2010, Density estimation implications of increasing ambient noise on beaked whale click detection and classification. CREEM Technical Report, no. 2010-1, University of St Andrews.
Faustino, CES, Silva, MA, Marques, TALO & Thomas, L 2010, 'Designing a shipboard line transect survey to estimate cetacean abundance off the Azores archipelago' Arquipélago - Life and Marine Sciences, vol 27, pp. 49-58.
Thomas, L, Buckland, ST, Rexstad, EA, Laake, JL, Strindberg, S, Hedley, SL, Bishop, JRB, Marques, TA & Burnham, KP 2010, 'Distance software: design and analysis of distance sampling surveys for estimating population size' Journal of Applied Ecology, vol 47, no. 1, pp. 5-14. DOI: 10.1111/j.1365-2664.2009.01737.x
Williams, R & Thomas, L 2009, 'Cost-effective abundance estimation of rare marine animals: small-boat surveys for killer whales in British Colombia, Canada' Biological Conservation, vol 142, no. 7, pp. 1542-1547. DOI: 10.1016/j.biocon.2008.12.028
Newman, KB, Fernandez, C, Thomas, L & Buckland, ST 2009, 'Monte Carlo inference for state-space models of wild animal populations' Biometrics, vol 65, no. 2, pp. 572-583. DOI: 10.1111/j.1541-0420.2008.01073.x
Marques, TA, Thomas, L, Ward, J, Dimarzio, N & Tyack, PL 2009, 'Estimating cetacean population density using fixed passive acoustic sensors: An example with Blainville's beaked whales' Journal of the Acoustical Society of America, vol 125, no. 4, pp. 1982-1994. DOI: 10.1121/1.3089590
Fewster, RM, Buckland, ST, Burnham, KP, Borchers, DL, Jupp, PE, Laake, JL & Thomas, L 2009, 'Estimating the encounter rate variance in distance sampling' Biometrics, vol 65, no. 1, pp. 225-236. DOI: 10.1111/j.1541-0420.2008.01018.x
Cabrelli, A, Harwood, J, Matthiopoulos, J, New, LF & Thomas, L 2009, A critical review of the literature on population modelling. CREEM Technical Report, no. 2009-2, University of St Andrews.
Baillie, SR, Brooks, SP, King, R & Thomas, L 2009, Using a State-Space Model of the British Song Thrush Turdus philomelos population to diagnose the causes of a population decline. in DL Thomson, EG Cooch & MJ Conroy (eds), Modeling Demographic Processes in Marked Populations. Environmental and ecological statistics, vol. 3, Springer, pp. 541-561. DOI: 10.1007/978-0-387-78151-8_23
Nichols, JD, Thomas, L & Conn, PB 2009, Inferences about landbird abundance from count data: recent advances and future directions. in DL Thompson, EG Cooch & MJ Conroy (eds), Modeling Demographic Processes in Marked Populations. Springer Series: Environmental and Ecological Statistics, pp. 203-238.
Giminez, O, Bonner, SJ, King, R, Parker, RA, Brooks, SP, Jamieson, LE, Grosbois, V, Morgan, BJT & Thomas, L 2009, WinBUGS for population ecologists: Bayesian modeling using Markov Chain Monte Carlo methods. in DL Thomson, EG Cooch & MJ Conroy (eds), Modeling Demographic Processes in Marked Populations. Environmental and Ecological Statistics, vol. 3, Springer, pp. 883-915. DOI: 10.1007/978-0-387-78151-8_41
Patterson, TA, Thomas, L, Wilcox, C, Ovaskainen, O & Matthiopoulos, J 2008, 'State-space models of individual animal movement' Trends in Ecology and Evolution, vol 23, no. 2, pp. 87-94. DOI: doi:10.1016/j.tree.2007.10.009
Marques, TA, Thomas, L, Fancy, SG & Buckland, ST 2007, 'Improving estimates of bird density using multiple covariate distance sampling' The Auk, vol 124, no. 4, pp. 1229-1243. DOI: 10.1642/0004-8038(2007)124[1229:IEOBDU]2.0.CO;2


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