Submitted

1. Lawrence, J.D., R.B. Gramacy, L. Thomas and S.T. Buckland. The importance of prior choice in model selection: a density dependence example.
   • [abstract (pdf)]
2. Langrock, R., R. King, J. Matthiopoulos, L. Thomas, D. Fortin and J.M. Morales. Flexible and practical modeling of animal telemetry data: hidden Markov models and extensions.
   • [abstract (pdf)]
3. New, L.F., J. Harwood, L. Thomas, C. Donovan, J.S. Clark, G. Hastie, P.M. Thompson, B. Cheney, L. Scott-Hayward and D. Lusseau. Modelling the biological significance of behavioural change in coastal bottlenose dolphins in response to disturbance.
   • [abstract (pdf)]
4. Schick, R.S., L.F. New, L. Thomas, D.P. Costa, M.A. Hindell, C.R. McMahon, P.W. Robinson, S.E. Simmons, M. Thums, J. Harwood and J.S. Clark. Estimating resource acquisition and at-sea body condition of a marine predator with implications for population health.
   • [abstract (pdf)]

In press

1. Martin, S.W., T.A. Marques, L. Thomas, R.P. Morrissey, S. Jarvis, N. DiMarzio, D. Moretti and D. Mellinger. Estimating minke whale (Balenoptera acutorostrata) boing sound density using passive acoustic sensors. Marine Mammal Science.
   • [preprint (pdf)]
   • [doi:10.1111/j.1748-7692.2011.00561.x preprint at publisher's web site (pdf)]
2. Mateos, M., G.M. Arroyo and L. Thomas. The development and use of a method to fill time gaps in migration counts: seabird conservation applications. The Condor.
   • [preprint (pdf)]
3. McClintock, B.T., R. King, L. Thomas, J. Matthiopoulos, B.J. McConnell, J.M. Morales. A general modeling framework for animal movement and migration using multi-state random walks. Ecological Monographs.
   • [preprint, with Supplemental Material at the end (pdf)]
   • [doi:10.1890/11-0326.1 preprint at publisher's web site (pdf)]
4. Potts, J.M., S.T. Buckland, L. Thomas and A. Savage. Trapping point transects: cost-effective monitoring of the abundance of cryptic but trappable animals. Methods in Ecology and Evolution.
   • [preprint (pdf)]
5. Ward, J.A., L. Thomas, S. Jarvis, N. DiMarzio, D. Moretti, T.A. Marques, C. Dunn, D. Claridge, E. Hartvig and P. Tyack. Passive acoustic density estimation of sperm whales in the Tongue of the Ocean, Bahamas. Marine Mammal Science.
   • [preprint (pdf)]
   • [doi:10.1111/j.1748-7692.2011.00560.x preprint at publisher's web site (pdf)]

1. Borkin, K.M., R.W. Summers and L. Thomas. 2012. Distribution, density and stand-type preferences of wood ant Formica spp.nest mounts in a Scots pinewood. European Journal of Entomology.109: 47-53.
   • [full text (pdf)]
   • [article at publishers' web site (html abstract, pdf paper)]
2. Jewell, R., L. Thomas, C.M. Harris, K. Kaschner, R. Wiff, P.S. Hammond, N.J. Quick. Global analysis of cetacean line-transect surveys: detecting trends in cetacean density. Marine Ecology Progress Series.453: 227-240.
   • [full text (pdf)]
   • [doi:10.3354/meps09636 article at publisher's web site (pdf). Open Access.]
3. Kyhn L.A., J. Tougaard, L. Thomas, L.R. Duve, J. Steinback, M. Amundin, G. Desportes and J. Teilmann. 2012. From echolocation clicks to animal density - Acoustic sampling of harbour porpoises with static dataloggers. Journal of the Acoustical Society of America 131: 550-560.
   • [full text (pdf)]
   • [doi:10.1121/1.3662070 article at publishers' web site (pdf and html)]
4. 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)]
   • [doi:10.1007/s10336-010-0535-7 - article at publishers' web site (pdf)]
5. Durant, S., M. Craft, R. Hilborn, S. Bashir, J. Hando and L. Thomas. 2011. Long term trends in carnivore abundance using distance sampling in Serengeti national park, Tanzania. Journal of Applied Ecology 48: 1490-1500.
   • [full text (pdf)]
   • [doi:10.1111/j.1365-2664.2011.02042.x - article at publishers' web site (pdf and html)]
6. Küsel, E.T., D.K. Mellinger, L. Thomas, T.A. Marques, D.J. Moretti, and J. Ward. 2011. Cetacean population density from single fixed sensors using passive acoustics. Journal of the Acoustical Society of America 129: 3610-3622.
   • [full text (pdf)]
   • [doi:10.1121/1.3583504 article at publishers' web site (pdf and html)]
7. Lonergan, M., D. Thompson, L. Thomas and C. Duck. 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, Article ID 597424. doi: 10.1155/2011/597424
   • [full text (pdf)]
   • [doi:10.1155/2011/597424 article at publishers' web site (pdf and html). Open Access.]
8. 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)]
   • [doi:10.3354/esr00325 article at publishers' web site (pdf and html). Open Access.]
   • [short erratum (pdf)]
   • [explanation of the erratum (pdf); also available in in our research repository.]
9. Marques, T. A., Thomas, L., and J. A. Royle. 2011. A hierarchical model for spatial capture-recapture data: comment. Ecology 92: 526-528.
   • [full text (pdf)]
   • [supplementary material (zip)]
   • [doi:10.1890/10-1440.1 article at publishers' web site (pdf and html).]
   • [supplementary material at publishers' web site (html)]
10. McCarthy, E., D. Moretti, L. Thomas, N. DiMarzio, R. Morrissey, S. Jarvis, J. Ward, A. Izzi, A. Dilley. 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 27(3): E206-E226.
    • [full text (pdf)]
    • [doi:10.1111/j.1748-7692.2010.00457.x article at publishers' web site (pdf and html)]
11. 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)]
    • [doi:10.1121/1.3531926 article at publishers' web site (pdf and html)]
12. Ward, J., Jarvis, S., Moretti, D., Morrissey, R., DiMarzio, N., Thomas, L. and Marques, T.  2011. Beaked whale (Mesoplodon densirostris) passive acoustic detection with increasing ambient noise. Journal of the Aocustical Society of America 129: 662-669.
    • [full text (pdf)]
    • [doi:10.1121/1.3531844 article at publishers' web site (pdf and html).]
13. Buckland, S.T., A.J. Plumptre, L. Thomas and E.A. Rexstad. 2010. Line transect sampling of primates: Can animal-to-observer distance methods work? International Journal of Primatology 31: 485-499.
    • [full text (pdf)]
    • [doi:10.1007/s10764-010-9408-4 article at publishers' web site (pdf and html)]
14. Buckland, S.T., A.J. Plumptre, L. Thomas and E.A. Rexstad. 2010. Design and analysis of line transect surveys for primates. International Journal of Primatology 31: 833-847.
    • [full text (pdf)]
    • [doi:10.1007/s10764-010-9431-5 article at publishers' web site (pdf and html)]
15. Faustino, C.E.S., M.A. Silva, T.A. Marques & L. Thomas. 2010. Designing a shipboard line transect survey to estimate cetacean abundance off the Azores archipelago. Arquipélago. Life and Marine Sciences 27: 49-58.
    • [full text (pdf)]
    • [full text at publishers' web site (pdf)]
16. 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: 1036-1042.
    • [full text (pdf)]
    • [full text on DECAF web site (pdf)]
    • [doi:10.1016/j.apacoust.2010.04.011 article at publishers' web site (pdf and html)]
17. Savage, A., L. Thomas, K.A. Leighty, L.H. Soto and Felix S. Medina. 2010. Novel survey method finds dramatic decline of wild cotton-top tamarin population. Nature communications 1:30. doi: 10.1038/ncomms1030.
    • [doi:10.1038/ncomms1030 article at publisher's web site (pdf and html). Open Access.]
    • [Short video (7 minutes) describing the work. (Same video, in different formats, at local site.)]
18. Thomas, L., S.T. Buckland, E.A. Rexstad, J.L. Laake, S. Strindberg, S.L. Hedley, J.R.B. Bishop, T.A. Marques and K.P. Burnham. 2010. Distance software: design and analysis of distance sampling surveys for estimating population size. Journal of Applied Ecology 47:5-14.
    • [doi:110.1111/j.1365-2664.2009.01737.x article at publishers web site (pdf and html). Open Access.]
    • [abstract and preprint (St Andrews Digital Research Repository)]
    • [local copy (pdf)]
19. Fewster, R.M., S.T. Buckland, K.P. Burnham, D.L. Borchers, P.E. Jupp, J.L. Laake and L. Thomas. 2009. Estimating the encounter rate variance in distance sampling. Biometrics 65: 225-236.
    • [full text of paper, with supplementary materials appended (pdf)]
    • [doi:10.1111/j.1541-0420.2008.01018.x article at publishers web site (pdf and html).]
    • [Supplementary materials at Biometrics journal web site (pdf).]
20. Marques, T.A., L. Thomas, J. Ward, N. DiMarzio, P. L. Tyack. 2009. Estimating cetacean population density using fixed passive acoustic sensors: an example with beaked whales. Journal of the Acoustical Society of America 125: 1982-1994.
    • [abstract (pdf)]
    • [full text - on DECAF project web site (pdf)]
    • [doi:10.1121/1.3089590 article at publishers web site (pdf and html).]
21. Newman, K.B., C. Fernández, S.T. Buckland and L. Thomas. 2009. Monte Carlo inference for state-space models of wild animal populations. Biometrics 65: 572-583.
    • [full text of paper and supplementary materials (pdf)]
    • [doi:10.1111/j.1541-0420.2008.01073.x article at publishers web site (pdf and html).]
    • [Supplementary materials at Biometrics journal web site (pdf).]
22. Williams, R. and L. Thomas. 2009. Cost-effective abundance estimation of rare marine animals: small-boat surveys for killer whales in British Columbia, Canada. Biological Conservation 142: 1542-1547.
    • [full text (pdf)]
    • [10.1016/j.biocon.2008.12.028 article at publishers web site (pdf and html).]
23. Patterson, T.A., L. Thomas, C. Wilcox, O. Ovaskainen and J. Matthiopoulos. 2008. State-space models of individual animal movement. Trends in Ecology and Evolution 23: 87-94.
    • [full text (pdf)]
    • [doi:10.1016/j.tree.2007.10.009 article at publishers web site (pdf and html).]
24. Buckland, S.T., K.B. Newman, C. Fernández, L. Thomas and J. Harwood. 2007. Embedding population dynamics models in inference. Statistical Science 22: 44-58.
    • [full text - local copy (pdf)]
    • [full text on arXiv (links to various formats)]
    • [doi:10.1214/088342306000000673 article on Euclid (various formats)]
25. Marques, T.A., L. Thomas, S.G. Fancy and S.T. Buckland. 2007. Improving estimates of bird density using multiple covariate distance sampling. The Auk 127: 1229-1243.
    • [full text (pdf)]
    • [doi:10.1642/0004-8038(2007)124[1229:IEOBDU]2.0.CO;2 article at publishers web site (pdf and html)]
26. Thomas, L., R. Williams and D. Sandilands. 2007. Designing line transect surveys for complex survey regions. Journal of Cetacean Research and Management 9: 1-13.
    • [full text (pdf)]
    • [Supplimentary materials (zip) - demonstration Distance projects]
27. Williams, R. and L. Thomas. 2007. Distribution and abundance of marine mammals in the coastal waters of British Columbia, Canada. Journal of Cetacean Research and Management 9: 15-28.
    [full text (pdf)]
28. Harrison, P.J., S.T. Buckland, L. Thomas, R. Harris, P. Pomeroy and J. Harwood. 2006. Incorporating movement into models of grey seal population dynamics. Journal of Animal Ecology 75: 634-645.
    • [full text (pdf)]
    • [Appendix S1 (pdf) - full description of algorithm]
    • [Appendix S2 (zip) - R code]
    • [doi:10.1111/j.1365-2656.2006.01084.x article at publishers web site (pdf and html)]
29. Buckland, S.T., R.W. Summers, D.L. Borchers and L. Thomas. 2006. Point transect sampling with traps or lures. Journal of Applied Ecology 43: 377-384.
    • [full text (pdf)]
    • [doi:10.1111/j.1365-2664.2006.01135.x article at publishers web site (pdf and html)]
30. Newman, K.B., S.T. Buckland, S.T. Lindley, L. Thomas & C Fernández. 2006. Hidden process models for animal population dynamics. Ecological Applications 16: 74-86.
    • [full text (pdf)]
    • [doi:10.1890/04-0592 article at publishers web site (pdf and html)]
31. Matthiopoulos, J., J. Harwood & L. Thomas. 2005. Metapopulation consequences of site fidelity for colonially breeding mammals and birds. Journal of Animal Ecology 74: 716-727.
    • [full text (pdf)]
    • [doi:10.1111/j.1365-2656.2005.00970.x article at publishers web site (pdf and html)]
32. Thomas, L., S.T. Buckland, K.B. Newman & J. Harwood. 2005. A unified framework for modelling wildlife population dynamics. Australian and New Zealand Journal of Statistics 47: 19-34.
    • [abstract, reprint and SPlus code (Eprints archive)]
    • [doi:10.1111/j.1467-842X.2005.00369.x article at publishers web site (pdf and html)]
33. Buckland, S.T., K.B. Newman, L. Thomas & N.B. Koesters. 2004. State-space models for the dynamics of wild animal populations. Ecological modelling 171: 157-175.
    • [full text (pdf)]
    • [doi:10.1016/j.ecolmodel.2003.08.002 article at publishers web site (pdf and html)]
34. Anderson, D.R., K.P. Burnham, B.C. Lubow, L. Thomas, P.S. Corn, P.A. Medica, & R.W. Marlow. 2001. Field testing line transect estimation of desert tortoise abundance. Journal of Wildlife Management 65: 583-597.
    • [article on JSTOR (html and pdf)]
35. Thomas, L. 1997. Retrospective power analysis. Conservation Biology 11: 276-280.
    • [abstract, reprint and SAS macros (Eprints archive)]
    • [doi:10.1046/j.1523-1739.1997.96102.x article at publishers web site (pdf and html)]
36. Thomas, L. & J. Proctor. 1997. Invertebrates in the litter and soil on the ultramafic Mount Giting-Giting, Republic of the Philippines. Journal of Tropical Ecology 13: 125-131.
    • [article on JSTOR (html and pdf)]
37. Thomas, L. 1996. Monitoring long-term population change: why are there so many analysis methods? Ecology 77: 49-58.
    • [full text (pdf)]
    • [article on JSTOR (html and pdf)]
38. Thomas, L. & F. Juanes. 1996. The importance of statistical power analysis: an example from Animal Behaviour. Animal Behaviour 52: 856-859.
    • [full text (pdf)]
    • [SAS macros (zip)]
    • [doi:10.1006/anbe.1996.0232 article at publishers web site (pdf and html)]
39. Thomas, L. & K. Martin. 1996. The importance of analysis method for Breeding Bird Survey population trend estimates. Conservation Biology 10: 479-490.
    • [abstract and reprint (Eprints archive)]
    • [article on JSTOR (html and pdf)]
40. Hannon, S., K. Martin, L. Thomas & J. Scheik. 1993. Investigator disturbance and clutch predation in Willow Ptarmigan: methods for evaluating impact. Journal of Field Ornithology 64: 575-586.
    • [full text (pdf)]

Other publications

1. Marques, T.A., S.T. Buckland, D.L. Borchers, E. Rexstad and L. Thomas. 2011. Conventional distance sampling.(version 1). StatProb: The Encyclopedia Sponsored by Statistics and Probability Societies.
   • [full text (html) at publisher's web site]
2. Marques, T.A., S.T. Buckland, D.L. Borchers, E. Rexstad and L. Thomas. 2011. Distance sampling. Pp 398-400 in Lovric, M. (Ed), International Encyclopedia of Statistical Sciences. Springer-Verlag, Berlin.
   • [full text (pdf)]
   • [doi:10.1007/978-3-642-04898-2_214 article at publisher's web site (pdf and html).]
   • [direct link to html version of article at publisher's web site (html).]
   • [web site for whole book (html).]
3. Thomas, L. 2009. Grey seals red in tooth and claw: how Darwin helps model their population. Significance 6(3):108-112
   • [full text (pdf)]
   • [doi:10.1111/j.1740-9713.2009.00372.x article at publishers web site (pdf and html).]
4. Baillie, S.R., S.P. Brooks, R. King and L. Thomas. 2008. Using a state-space model of the UK Song Thrush Turdus philomelos population to diagnose the causes of a population decline. Pp 543-564 in Thomson, D.L., E.G. Cooch and M.J. Conroy (Eds.) Modeling Demographic Processes in Marked Populations. Environmental and Ecological Statistics Vol 3. Springer. ISBN: 978-0-387-78150-1.
   • [full text (pdf)]
   • [doi:10.1007/978-0-387-78151-8_23 chapter at publishers web site (pdf and html).]
5. Giminez, O., S. Bonner, R. King, R.A. Parker, S. Brooks, L.E. Jamieson, V. Grosbois, B.J.T. Morgan and L. Thomas. 2008. WinBUGS for population ecologists: Bayesian modeling using Markov Chain Monte Carlo methods. Pp 885-918 in Thomson, D.L., E.G. Cooch and M.J. Conroy (Eds.) Modeling Demographic Processes in Marked Populations. Environmental and Ecological Statistics Vol 3. Springer. ISBN: 978-0-387-78150-1.
   • [full text (pdf)]
   • [abstract, manuscript and WinBUGS code (Eprints archive)]
   • [doi:10.1007/978-0-387-78151-8_41 chapter at publishers web site (pdf and html).]
6. Nichols, J.D., L. Thomas and P.B. Conn. 2008. Inferences about landbird abundance from count data: recent advances and future directions. Pp 203-238 in Thomson, D.L., E.G. Cooch and M.J. Conroy (Eds.) Modeling Demographic Processes in Marked Populations. Environmental and Ecological Statistics Vol 3. Springer. ISBN: 978-0-387-78150-1.
   • [full text (pdf)]
   • [doi:10.1007/978-0-387-78151-8_9 chapter at publishers web site (pdf and html).]
7. Buckland, S.T., K.B. Newman, C. Fernández, L. Thomas and J. Harwood. 2006. Defining matrix population models and fitting them to data. Actos do XIII Congresso Annual da SPE, pp.15-27.
8. Buckland, S.T., D.R. Anderson, K.P. Burnham, J.L. Laake, D.L. Borchers & L. Thomas (editors). 2004. Advanced Distance Sampling. Oxford University Press.
   • [local book web site]
   • [online preview from Google books (approx 80% of book)]
   • [publisher's web site]
   • [Distance software]
9. Thomas, L., K.P. Burnham & S.T Buckland. 2004. Temporal inferences from distance sampling surveys. Chapter 5 in Buckland, S.T., D.R. Anderson, K.P. Burnham, J.L. Laake, D.L. Borchers & L. Thomas (Eds.), Advanced Distance Sampling. Oxford University Press.
   • See above for book links.
   • [R code for figure 5.6 (zip)]
10. Strindberg, S., S.T Buckland & L. Thomas. 2004. Design of distance sampling surveys and Geographic Information Systems. Chapter 7 in Buckland, S.T., D.R. Anderson, K.P. Burnham, J.L. Laake, D.L. Borchers & L. Thomas (Eds.), Advanced Distance Sampling. Oxford University Press.
    • See above for book links.
11. Thomas, L., G. Geupel, N. Nur & G. Ballard. 2004. Optimizing the allocation of count days in a migration monitoring program. Pp. 97-111 in Ralph, C.J. & E.H. Dunn (Eds.), Monitoring Bird Populations Using Mist Nets, Studies in Avian Biology 29, Cooper Ornithological Society.
    • [full text (pdf)]
    • [volume front matter (index, etc) (pdf)]
    • [literature cited in whole volume (pdf)]
12. Thomas, L., S.T. Buckland, K.P. Burnham, D.R. Anderson, J.L. Laake, D.L. Borchers & S. Strindberg. 2002. Distance sampling. Pp 544-552 in Encyclopedia of Environmetrics. A.H. El-Shaarawi & W. W. Piegorsch. John Wiley & Sons, Chichester.
    • [full text (pdf)]
13. Thomas, L. and K.U. Karanth. 2002. Statistical concepts: Estimating absolute densities of prey species using line transect sampling. Pp 87-110 in Monitoring Tigers and Their Prey. K.U. Karanth & J.D. Nichols, editors. Centre for Wildlife Studies, India.
14. Karanth, K.U., L. Thomas & N.S. Kumar. 2002. Field surveys: estimating absolute densities of prey species using line transect sampling. Pp 111-120 in Monitoring Tigers and Their Prey. K.U. Karanth & J.D. Nichols, editors. Centre for Wildlife Studies, India.
15. Buckland, S.T., L. Thomas, F.F.C. Marques, S. Strindberg, S.L. Hedley, J.H. Pollard, D.L. Borchers & M.L. Burt. 2002. Distance sampling: recent advances and future directions. P79-97 in Quantitative Methods for Current Environmental Issues. V. Barnett, A. El.Shaarawi, C. Anderson and P. Chatwin, editors. Springer-Verlag.
16. Buckland, S.T., D.R. Anderson, K.P. Burnham, J.L. Laake, D.L. Borchers & L. Thomas. 2001. Introduction to Distance Sampling. Oxford University Press.
    • [local book web site]
    • [online preview from Google books (approx 80% of book)]
    • [publisher's web site]
    • [Distance software]
17. Steidl, R.J. & L. Thomas. 2001. Power analysis and experimental design. Pp 14-36 in Design and Analysis of Ecological Experiments, 2nd edition. S. Scheiner and J. Gurevitch, editors. Oxford University Press.
    • [full text (minus references) (pdf)]
18. Thomas, L. 1999. Distance 3.5. Bulletin of the Ecological Society of America 80(2): 114-115.
    • [full text (pdf)]
19. Thomas, L. & C. Krebs. 1997. A review of power analysis software. Bulletin of the Ecological Society of America 78(2): 128-139.
    • [full text (pdf)]

Unpublished and technical reports

1. Paxton, C.G.M., M. Mackenzie, M.L. Burth, E. Rexstad and L. Thomas. 2011. Phase II Data Analysis of Joint Cetacean Protocol Data. Report to Joint Nature Conservation Committee. JNCC Contract No. C09-0207-0216. Dated August 2011
   • [Link to JNCC JCP web pages giving more background on this project]
2. Thomas, L., M.O. Hammill and W.D. Bowen. 2011. Estimated size of the Northwest Atlantic grey seal population 1977-2007. Canadian Science Advisory Secretariat Research Document 2007/082.
   • [full text (pdf)]
3. Thomas, L., M.O. Hammill and W.D. Bowen. 2011. Assessment of Population Consequences of Harvest Strategies for the Northwest Atlantic grey seal population. Canadian Science Advisory Secretariat Research Document 2011/007.
   • [full text (pdf)]
4. Thomas, L., T. Marques, D. Borchers, C. Stephenson, D. Moretti, R. Morrissey, N. DiMarzio, J. Ward, D. Mellinger, S. Martin and P. Tyack. 2011. DECAF - Density Estimation for Cetaceans from passive Acoustic Fixed sensors. Final Programmatic Report to National Fish and Wildlife Foundation. Dated 26th May 2011.
   • [full text (pdf) from DECAF project web site]
5. 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) from DECAF project web site]
6. Paxton, C.G.M. and L. Thomas. 2010. Phase one Data Analysis of Joint Cetacean Protocol Data. Report to Joint Nature Conservation Committee. JNCC Contract No. C09-0207-0216. Dated March 2010
   • [full text (pdf)]
   • [Link to JNCC JCP web pages giving more background on this project]
7. Thomas, L. 2010. Estimating the size of the UK grey seal population between 1984 and 2009. NERC Special Committee on Seals Briefing Paper 10/2. Updated 16 March 2011.
   • [full text (pdf)]
8. Thomas, L., T. Marques, D. Borchers, C. Stephenson, D. Moretti, R. Morrissey, N. DiMarzio, J. Ward, D. Mellinger, S. Martin and P. Tyack. 2010. DECAF - Density Estimation for Cetaceans from passive Acoustic Fixed sensors. Annual Report to National Oceanographic Partnership Program for period 1 Oct 2009 - 30 Sept 2010.
   • [full text (pdf) from DECAF project web site]
9. Cabrelli, A., J. Harwood, J. Matthiopoulos, L. New and L. Thomas. 2009. A critical review of the literature on population modelling. Final report to the Joint Industry Project of the International Association of Oil and Gas Producers on contract JIP22 07_20. July 2009. CREEM Technical Report 2009-2.
   • [abstract and table of contents (pdf)]
   • [full text (pdf) at university research repository]
10. Thomas, L. and J. Harwood. 2009. Estimating the size of the UK grey seal population between 1984 and 2008. NERC Special Committee on Seals Briefing Paper 09/2.
    • [full text (pdf)]
11. Thomas, L., T. Marques, D. Borchers, C. Stephenson, D. Moretti, R. Morrissey, N. DiMarzio, J. Ward, D. Mellinger, S. Martin and P. Tyack. 2009. DECAF - Density Estimation for Cetaceans from passive Acoustic Fixed sensors. Annual Report to National Oceanographic Partnership Program for period 1 Oct 2008 - 30 Sept 2009.
    • [full text (pdf) from DECAF project web site]
12. Thomas, L. 2008. Potential use of Joint Cetacean Protocol data for determining changes in species' range and abundance: exploratory analysis of southern Irish Sea data. Report to Joint Nature Conservation Committee, National Parks and Wildlife Service, and Countryside Council for Wales. JNCC Contract No. F90-01-1208. Dated June 2008, revised January 2009.
    • [full text (pdf)]
    • [Link to JNCC JCP web pages giving more background on this project]
13. Thomas, L. and J. Harwood. 2008. Estimating the size of the UK grey seal population between 1984 and 2007. NERC Special Committee on Seals Briefing Paper 08/3.
    • [full text (pdf)]
14. Thomas, L., T. Marques, D. Borchers, C. Stephenson, D. Moretti, R. Morrissey, N. DiMarzio, J. Ward, D. Mellinger, S. Martin and P. Tyack. 2008. DECAF - Density Estimation for Cetaceans from passive Acoustic Fixed sensors. Annual Report to National Oceanographic Partnership Program for period 1 Oct 2007 - 30 Sept 2008.
    • [full text (pdf) from DECAF project web site]
15. Thomas, L., M.O. Hammill and W.D. Bowen. 2007. Estimated size of the Northwest Atlantic grey seal population 1977-2007. Canadian Science Advisory Secretariat Research Document 2007/082.
    • [full text (pdf)]
16. Thomas, L. and J. Harwood. 2007. Estimating the size of the UK grey seal population between 1984 and 2006. NERC Special Committee on Seals Briefing Paper 07/3.
    • [full text (pdf)]
17. Thomas, L., T. Marques, D. Borchers, C. Stephenson, D. Moretti, R. Morrissey, N. DiMarzio, J. Ward, D. Mellinger, S. Martin and P. Tyack. 2007. DECAF - Density Estimation for Cetaceans from passive Acoustic Fixed sensors. Annual Report to National Oceanographic Partnership Program for period 1 Oct 2006 - 30 Sept 2007.
    • [full text (pdf) from DECAF project web site]
18. Lynam, C. R. King, L. Thomas, S.T. Buckland. 2007. Incorporating Model Uncertainty into the Sequential Importance Sampling Framework using a Model Averaging Approach, or Trans-Dimensional Sequential Importance Sampling. CREEM Technical Report 2007-6.
    • [abstract and full text (Eprints archive)]
19. Matthiopoulos, J., L. Thomas, B. McConnell, C.D. Duck, D. Thompson, P. Pomeroy, J. Harwood, E.J. Milner-Gulland, N. Wolf and M. Mangel. 2006. Putting long-term, population monitoring data to good use: the causes of density dependence in UK grey seals. NERC Special Committee on Seals Briefing Paper 06/8.
    • [full text (pdf)]
20. Thomas, L. and J. Harwood. 2006. Estimating the size of the UK grey seal population between 1984 and 2005, and related research. NERC Special Committee on Seals Briefing Paper 06/3.
    • [full text (pdf)]
21. Thomas, L. and J. Harwood. 2005. Estimating the size of the UK grey seal population between 1984 and 2004: model selection, survey effort and sensitivity to priors. NERC Special Committee on Seals Briefing Paper 05/3.
    • [full text (pdf)]
22. Thomas, L., T. van Lamsweerde and J. Harwood. 2004. The nature of density dependence in British grey seal populations. NERC Special Committee on Seals Briefing Paper 04/4.
    • [full text (pdf)]
23. Thomas, L. and J. Harwood. 2004. A comparison of grey seal population models incorporating density dependent pup survival and fecundity. NERC Special Committee on Seals Briefing paper 04/6.
    • [full text (pdf)]
24. Thomas, L. and J. Harwood. 2004. Possible impacts on the Brisith grey seal population of deliberate killing related to salmon farming. NERC Special Committee on Seals Briefing paper 04/7.
    • [full text (pdf)]
25. Matthiopoulos, J. J. Harwood and L. Thomas. 2003. Modelling the short-term movements of grey seals between breeding colonies and their long-term population consequences. NERC Special Committee on Seals Briefing paper 03/12.
    [full text (pdf)]
26. Thomas, L. and J. Harwood. 2003. Estimating grey seal population size using a Bayesian state-space model. NERC Special Committee on Seals Briefing paper 03/3.
    • [full text (pdf)]
27. Northridge, S. and L. Thomas 2003. Monitoring levels required in European Fisheries to assess cetacean bycatch, with particular reference to UK fisheries. Report to DEFRA.
    • [full text (pdf)]
28. D.L. Borchers and L. Thomas. 2003. Incorporating dual-observer methods into software Distance: preliminary work. DFO project 41207-110-178-4802-90618.
29. Thomas, L., R. Beyers, J. Hart and S.T. Buckland. 2001. Recommendations for a survey design for the Central African forest region. Monitoring Illegal Killing of Elephants Central African Pilot Project, Technical Report 1.
    • [external link to full text (html)]
    • [local copy of report, annex 1-4, and annex 5-7
30. Beyers, R., L. Thomas, J. Hart and S.T. Buckland. 2001. Recommendations for ground-based survey methods for elephants in the Central African forest region. Monitoring Illegal Killing of Elephants Central African Pilot Project, Technical Report 2.
    • [external link to full text (html)]
    • [local copy of report (html) and annexes (pdf)]
31. Thomas, L. 2001. Consultancy Report. WCS-India Ungulate Density Project.
32. Thomas, L. 2001. Development of statistical procedures and software for long-term monitoring of birds in National Parks. U.S. National Parks Service P2370000005.
33. Thomas, L. 1997. Evaluation of statistical methods for estimating long term population change from extensive wildlife surveys. PhD Thesis, University of British Columbia.
    • [abstract and index (pdf)]

PhD Theses (co-)supervised

1. Potts J.M. 2011. Estimating abundance of rare, small mammals: A cast study of the Key Largo woodrat (Neotoma floridana small). PhD Thesis, University of St Andrews.
   • [abstract and full text (DRR archive)]
   • [Local coverage and newspaper report of close encounter with python during fieldwork!]
2. Bishop, J.R.B. 2009. Embedding population dynamics in mark-recapture models. PhD in Statistics, PhD Thesis, University of St Andrews.
   • [abstract and full text (DRR archive)]
   • [Jon displaying his baking skills]

MSc/MRes Theses (co-)supervised

1. Hogg, A. Measures of Market Systematic Risk. MSc Applied Statistics and Datamining, University of St Andrews.
2. Mi, Xiuting. State-space models for the analysis of animal movement. MSc Applied Statistics and Datamining, University of St Andrews.
3. Bal, P. 2010. Estimating gopher tortoise abundance through design-based and model-based methods. MRes in Environmental Biology, University of St Andrews.
   • [abstract and full text (DRR archive)]
4. Harries, O. 2010. A critical assessment of data collected from whale watching operations: A case study on Scottish harbour porpoises and potential applications towards management and conservation. MRes Marine Mammal Science, University of St Andrews.
5. Brady, I.J. 2009. Increasing the efficiency of Insights discovery questionnaires. MSc Applied Statistics and Datamining, University of St Andrews.
6. Kidney, D. 2009. Line transect sampling using triangulation: investigating the effect of bearing error on density estimation. MSc in Statistics, University of St Andrews.
7. Faustino, C.E.S. 2008. Designing a shipboard line transect survey to estimate cetacean abundance off the Azores Archipelago, Portugal. MRes Marine Mammal Science, University of St Andrews.
   • [abstract, full text, and Distance project (Eprints archive)]
8. DiTraglia, F.J. 2007. Models of Random Wildlife Movement with an Application to Distance Sampling. MMaths Statistics, University of St Andrews.
   • [abstract and full text (Eprints archive)]
9. Photopoulos, T. 2007. Behavioural changes of a long-ranging diver in response to oceanographic conditions. MRes Environmental Biology, University of St Andrews.
   • [abstract and full text (Eprints archive)]
10. Gangadharan, A. 2005. Density Estimation and Time Trend Analysis of Large Herbivores in Nagarhole, India. MRes Environmental Biology, University of St Andrews.
    • [abstract and full text (Eprints archive)]