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.

Holmes, E. E. 2018. Fish Catch Forecasting with R. Online text for short course (see teaching tab). (Online)
Ward, E. J., K. Oken, K. A. Rose, S. Sable, K. Watkins, E. E. Holmes, and M. D. Scheuerell. 2018. Applying spatiotemporal models to monitoring data to quantify fish responses to the Deepwater Horizon oil spill in the Gulf of Mexico. Environmental Monitoring and Assessment 190-530. (PDF)
Holmes, E. E., E. J. Ward and M. D. Scheuerell. 2018. Analysis of multivariate time series using the MARSS package. (PDF). User Guide for the MARSS R package
Holmes, E. E., M. D. Scheuerell, and E. J. Ward. 2017. Applied Time Series Analysis for Fisheries and Environmental Sciences. Online text for our course at University of Washington. (Online)
Ferguson, L., M. Srinivasan, E. Oleson, S. Hayes, S.K. Brown, R. Angliss, J. Carretta, E. Holmes, E. Ward, J. Kocik, K. Mullin, R. Dean, and J. Davis (eds.). 2017. Proceedings of the First National Protected Species Assessment Workshop. U.S. Dept. of Commer., NOAA. NOAA Technical Memorandum NMFS-F/SPO-172, 92 p. (PDF)
Tolimieri, N., E. E. Holmes, G. D. Williams, R. Pacunski, and D. Lowry. 2017. Population assessment using multivariate time-series analysis: A case study of rockfishes in Puget Sound. Ecology and Evolution 7(8): 2045-7758. (PDF)
Ford, M. J., K. Barnas, T. Cooney, L. G. Crozier, M. Diaz, J. J. Hard, E. E. Holmes, D. M. Holzer, R. G. Kope, P. W. Lawson, M. Liermann, J. M. Myers, M. Rowse, D. J. Teel, D. M. Van Doornik, T. C. Wainwright, L. A. Weitkamp, M. Williams. 2015. Status Review Update for Pacific Salmon and Steelhead Listed under the Endangered Species Act: Pacific Northwest. National Marine Fisheries Service, Northwest Fisheries Science Center. (PDF)
Keith, D.M., H.R. Akcakaya, S.H.M. Butchart, B. Collen, N. K. Dulvy, E. E. Holmes, J. A. Hutchings, D. Keinath, M. K. Schwartz, A. O. Shelton, and R. S. Waples. 2015. Temporal correlations in population trends: conservation implications from time-series analysis of diverse animal taxa. Biological Conservation 192:247-257. (Link to Paper)
See, K. E. and E. E. Holmes. 2015. Reducing bias and improving precision in species extinction forecasts. Ecological Applications 25: 1157-1165. (Abstract) (PDF)
Ruhi, A., E. E. Holmes, J. N. Rinne, and J. L. Sabo. 2015. Anomalous droughts, not invasion, decrease persistence of native fishes in a desert river. Global Change Biology 21:1482-1496. (PDF)
Holmes, E. E. 2014. Computation of standardized residuals for (MARSS) models. Technical Report. arXiv:1411.0045 [stat.ME] PDF
Francis, T. B., E. M. Wolkovich, M. D. Scheuerell, S. L. Katz, E. E. Holmes, and S. E. Hampton. 2014. Shifting Regimes and Changing Interactions in the Lake Washington, USA, Plankton Community from 1962-1994." PlosOne: e110363. (PDF)
Ward, E.J., E.E. Holmes, J.T. Thorson, and B. Collen. 2014. Complexity is costly: comparing parametric and non-parametric methods for short-term population forecasting. Oikos 123:652-661. (PDF)
Hampton, S.E., E.E. Holmes, D.E. Pendleton, L.P. Scheef, M.D. Scheuerell, and E.J. Ward. 2013. Quantifying effects of abiotic and biotic drivers on community dynamics with multivariate autoregressive (MAR) models. Ecology 94:2663-2669 (PDF) (Supplement) (MAR1 R Package)(Annotabled table of MAR papers)
Holmes, E. E. 2013. Derivation of the EM algorithm for constrained and unconstrained multivariate autoregressive state-space (MARSS) models. Technical Report. arXiv:1302.3919 [stat.ME] PDF Multivariate autoregressive state-space models go by different names in different fields. Dynamic linear models, vector autoregressive models, dynamic factor analysis models, multivariate discrete time Gompertz models and multivariate regression models with ARMA errors, are some of the many types of discrete time multivariate time-series models that can be written in MARSS form.
Mongillo, T. M., E. E. Holmes, D. P. Noren, G. R. VanBlaricom, A. E. Punt, S. M. O'Neill, G. M. Ylitalo, M. B. Hanson, P. S. Ross. 2012. Predicted polybrominated diphenyl ether (PBDE) and polychlorinated biphenyl (PCB) accumulation in southern resident killer whales. Marine Ecology Progress Series 453:263-277. (Abstract)
Holmes, E. E., E. J. Ward and K. Wills. 2012. MARSS: Multivariate autoregressive state-space models for analyzing time-series data. R Journal 4: 11-19. (PDF)
Scheef, L. P., D. E. Pendleton, S. E. Hampton, S. L. Katz, E. E. Holmes, M. D. Scheuerell, and D.G. Johns. 2012. Assessing marine plankton community structure from long-term monitoring data with multivariate autoregressive (MAR) models: a comparison of fixed station vs. spatially distributed sampling data. Limnology & Oceanography: Methods 10: 54-64. (Abstract)
Drake, J., E. A. Berntson, J. M. Cope, R. G. Gustafson, E. E. Holmes, P. S. Levin, N. Tolimieri, R. S. Waples, S. Sogard, G. D. Williams. 2010. Status review of five rockfish species in Puget Sound, Washington: Bocaccio (Sebastes paucispinis), canary rockfish (S. pinniger), yelloweye rockfish (S. ruberrimus), greenstriped rockfish (S. elongatus), and redstripe rockfish (S. proriger). U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-108. (PDF)
Ward, E., Semmens, B., Holmes, E., and K. Balcomb. 2010. Effects of multiple levels of social organization on survival and abundance. Conservation Biology 25:350-355. (PDF)
Holmes, E. E. and E. J. Ward. 2010. Analysis of multivariate time series using the MARSS package (PDF). User Guide for the MARSS package.
Viscido, S. V. and E. E. Holmes. 2010. LAMBDA: A software tool for statistical modeling of communities and ecosystems. Environmental Modelling and Software 25(12): 1905-1908
Ward, E. J., Chirakkal, H., Gonz?lez-Su?rez, M., Aurioles-Gamboa, D., Holmes, E. E. and Gerber, L. 2009. Inferring spatial structure from time-series data: using multivariate state-space models to detect metapopulation structure of California sea lions in the Gulf of California, Mexico. Journal of Applied Ecology 47:47-56. (Abstract)
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 (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. (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. (Abstract). Contact Dr. Hauser for a reprint. (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 (PDF) (List of datasets used)
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) (Salmon Data Used)
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. (Link to book)
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. (Link to book)
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)

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