We have not succeeded in answering all our problems. The answers we have found only serve to raise a whole set of new questions. In some ways we feel we are as confused as ever, but we believe we are confused on a higher level and about more important things.
Bernt Oksendal in Stochastic differential equations
CV
Research
Lab Code
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Beyond Science
Publications
If there is no link to the PDF, it means the article is not open-access, authors are not allowed to post PDFs on their personal websites, or I didn't create the pdf.
For those, you will need to email me for a copy.
- Ward, E., Parsons, K., Holmes, E., K. Balcomb, and J. Ford. 2009. The role of menopause and reproductive senescence in a long-lived social mammal. Frontiers in Zoology 6:4 Open Access PDF
- Hinrichsen, R. A. and E. E. Holmes. 2009. Using multivariate state-space models to study spatial structure and dynamics. In Spatial Ecology (editors Robert Stephen Cantrell, Chris Cosner, Shigui Ruan). CRC/Chapman Hall. Link to book PDF of text
- Ward, E. J., E. E. Holmes, and K. C. Balcomb. 2009. Quantifying the effects of prey abundance on killer whale reproduction. Journal of Applied Ecology 46:632-640 Abstract
- Ellner, S. P. and E. E. Holmes. 2008. Resolving the debate on when extinction risk is predictable. Ecology Letters 11: E1–E5. PDF
- Hauser, D. D. W., M. G. Logsdon, E. E. Holmes, G. R. VanBlaricom, R. W. Osborne. 2007. Summer distribution patterns of Southern Resident killer whales (Orcinus orca): core areas and spatial segregation of social groups. Marine Ecology Progress Series 351: 301-310. Link to abstract. Contact Donna Hauser for a reprint. Donna's MS Thesis
- Holmes, E. E., J. L. Sabo, S. V. Viscido, and W. Fagan. 2007. A statistical approach to quasi-extinction forecasting. Ecology Letters 10:1182–1198 Open Access PDF
- Holmes, E. E., L. Fritz, A. York and K. Sweeney. 2007. Age-structured modeling reveals long-term declines in the natality of western Steller sea lions. Ecological Applications 17:2214–2232. PDF Appendices In earlier versions of this paper, we had longer appendices which discussed why we feel that sightability and sex-ratios have not changed sufficiently to explain the dropping pup to nonpup ratio. This was cut during the 2nd revision process. Earlier appendices Code to get lambda and scaled Leslie matrices
- Hauser, D., G. VanBlaricom, E. Holmes, and R. Osbourne. 2006. Evaluating the use of whalewatch data in determining killer whale (Orcinus orca) distribution patterns. Journal of Cetacean Research and Management 8: 273-281. PDF
- Gustafson,R. G., J. Drake, M. J. Ford, J. M. Myers, E. E. Holmes, and R. S. Waples. 2006. Status Review of Cherry Point Pacific Herring (Clupea pallasii) and Update of the Status Review of the Georgia Basin Distinct Population Segment of Pacific Herring Under the U.S. Endangered Species Act. U.S. Dept. Commer., NOAA Tech. Memo.NMFS-NWFSC-76, 182pp.PDF
- Levin, P., E. E. Holmes, K. Piner and C. Harvey. 2006. Shifts in a Pacific Ocean fish assemblage: the potential influence of exploitation. Conservation Biology 20: 1181-1190. PDF
- Fagan, W. F and E. E. Holmes. 2006. Quantifying the extinction vortex. Ecology Letters 9:51-60.PDF
- Holmes, E.E., W.F. Fagan, J.J. Rango, A. Folarin, J.A., Sorensen, J.E. Lippe, and N.E. McIntyre. 2005. Cross validation of quasi-extinction risks from real time series: an examination of diffusion approximation methods. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-67, 37 p. PDF
- Holmes, E. E. 2004. Beyond theory to application and evaluation: diffusion approximations for population viability analysis. Ecological Applications 14: 1272-1293. PDF
- Holmes, E. E. and B. Semmens. 2004. Population viability analysis for metapopulations: a diffusion approximation approach. Pp. 565-598 in Ecology, Genetics, and Evolution of Metapopulations, editors Illka Hanski and Oscar E. Gaggiotti. Elsevier Press. [Galleys (has eqn typos)] [Text with corrections]
- Sabo, J. L., E. E. Holmes, and P. Kareiva. 2004. The efficacy of simple viability models in ecological risk assessment: Does density dependence matter? Ecology 85: 328-341. PDF
- Holmes, E. E. and A. E. York. 2003. Using age structure to detect impacts on threatened populations: a case study using Steller Sea Lions. Conservation Biology 17:1794-1806. PDF
- McClure, M. M., E. E. Holmes, B. L. Sanderson, and C. E. Jordan. 2003. A large-scale, multi-species risk assessment: anadromous salmonids in the Columbia River Basin. Ecological Applications 13(4):964-989. PDF
- Holmes, E. E. and W. F. Fagan. 2002. Validating population viability analysis for corrupted data sets. Ecology 83: 2379-2386. PDF
- Holmes, E. E. 2001. Estimating risks in declining populations with poor data. Proceedings of the National Academy of Science 98: 5072-5077. PDF
- Holmes, E. E. and P. M. Kareiva. 2000. Using single-species measurements to anticipate community level effects of environmental contaminants. In Environmental Contaminants and Terrestrial Vertebrates: Effects on Populations, Communities, and Ecosystems, P.H. Albers, G.H. Heinz, and H.M. Ohlendorf, editors. Published by the Society of Environmental Toxicology and Chemistry (SETAC), 315 pp.
- Holmes, E. E. and H.B. Wilson. 1998. Running from trouble: long distance dispersal and the competitive coexistence of inferior species. American Naturalist 151: 578-586. PDF
- Holmes, E. E. 1997. Basic epidemiological concepts in a spatial context. In Spatial Ecology (editors, D. Tilman and P. Kareiva). Princeton University Press.
- Holmes, E. E. 1995. Spatial models in ecology: explorations into the impact of spatial behavior on population dynamics. Dissertation. University of Washington.
- Holmes, E. E., M.A. Lewis, J. Banks, and R. Veit. 1994. Partial differential equation models in ecology. Ecology 75: 17-29. PDF
- Holmes, E. E. 1993. Is diffusion too simple? Comparisons with a telegraph model of dispersal. American Naturalist 142: 779-796. PDF