List of common mistakes in population modeling
Aiello-Lammens, M.A. and H.R. Akçakaya. 2016. Using global sensitivity analysis of demographic models for ecological impact assessment. Conservation Biology (in press). [Methods and data available at https://github.com/mlammens/demgsa.]
Akçakaya, H. R. 1991. A method for simulating demographic stochasticity. Ecological Modelling 54:133-136.
Akçakaya, H. R. 2000a. Population viability analyses with demographically and spatially structured models. Ecological Bulletins 48:23-38.
Akçakaya, H. R. 2000b. Viability analyses with habitat-based metapopulation models. Population Ecology 42:45-53. (The original publication is available at http://www.springerlink.com)
Akçakaya, H. R. 2002. Estimating the variance of survival rates and fecundities. Animal Conservation 5:333-336.
Akçakaya, H. R. and J. L. Atwood. 1997. A habitat-based metapopulation model of the California Gnatcatcher. Conservation Biology 11:422-434.
Akçakaya, H. R. and L. R. Ginzburg. 1991. Ecological risk analysis for single and multiple populations. Pages 73-87 in: Species Conservation: A Population-Biological Approach. A. Seitz and V. Loeschcke, eds. Birkhauser Verlag, Basel.
Akçakaya, H.R. and M.G. Raphael. 1998. Assessing human impact despite uncertainty: viability of the northern spotted owl metapopulation in the northwestern USA. Biodiversity and Conservation 7:875-894.
Akçakaya H.R. and P. Sjögren-Gulve. 2000. Population viability analysis in conservation planning: an overview. Ecological Bulletins 48:9-21.
Akçakaya, H. R., M. A. McCarthy and J. Pearce. 1995. Linking landscape data with population viability analysis: management options for the helmeted honeyeater. Biological Conservation 73:169-176.
Akçakaya, H. R., M. Burgman and L. Ginzburg. 1999. Applied Population Ecology: principles and computer exercises using RAMAS EcoLab 2.0. Second edition. Sinauer, Sunderland, MA. 285 pp.
Akçakaya, H.R., J.M. Halley, and P. Inchausti. 2003a. Population-level mechanisms for reddened spectra in ecological time series. Journal of Animal Ecology 72: 698-702.
Akçakaya, H.R., J.L. Atwood, D. Breininger, C.T. Collins, and B. Duncan. 2003b. Metapopulation dynamics of the California least tern. Journal of Wildlife Management 67:829-842.
Akçakaya, H.R., M.A. Burgman, O. Kindvall, C. Wood, P. Sjögren-Gulve, J. Hatfield, and M.A. McCarthy (editors). 2004a. Species Conservation and Management: Case Studies. Oxford University Press, New York.
Akçakaya, H.R., V.C. Radeloff, D.J. Mladenoff, and H.S. He. 2004b. Integrating landscape and metapopulation modeling approaches: viability of the sharp-tailed grouse in a dynamic landscape. Conservation Biology 18: 526-537.
Anders, A. D., and M. R. Marshall. 2005. Increasing the accuracy of productivity and survival estimates in assessing landbird population status. Conservation Biology 19:66-74.
Barker, R. J., and G. C. White. 2002. Joint analysis of live and dead encounters of marked animals. Proceedings of the 2nd International Wildlife Management Congress, Godollo, Hungary.
Brook, B.W., J. J. O'Grady, A. P. Chapman, M. A. Burgman, H. R. Akçakaya, R. Frankham. 2000. Predictive accuracy of population viability analysis in conservation biology. Nature 404:385-387.
Brook, B. W., D. W. Tonkyn, J. J. O'Grady, and R. Frankham. 2002. Contribution of inbreeding to extinction risk in threatened species. Conservation Ecology 6(1): 16. [online] URL: http://www.consecol.org/vol6/iss1/art16/
Burgman, M., S. Ferson and H. R. Akçakaya. 1993. Risk Assessment in Conservation Biology. Chapman & Hall, London. Population and Community Biology Series, 314 pp.
Caswell, H. 2001. Matrix Population Models: construction, analysis and interpretation. Sinauer, Sunderland, Massachusetts.
Conroy, M. J., J. E. Anderson, S. L. Rathbun, and D. G. Krementz. 1996. Statistical inference on patch-specific survival and movement rates from marked animals. Environmental and Ecological Statistics 3:99-116.
Dunham, A.E., H.R. Akçakaya, T. S. Bridges. 2006. Using scalar models for precautionary assessments of threatened species. Conservation Biology 20: 1499-1506.
Dunning, D., Ross, Q., Munch, S., & Ginzburg, L.R. (2002) Measurement error affects risk estimates for recruitment to the Hudson River stock of striped bass. The Scientific World Journal 2(S1), 238-253.
Ginzburg, L.R., S.F. Ferson and H. R. Akçakaya. 1990. Reconstructibility of density dependence and the conservative assessment of extinction risk. Conservation Biology 4:63-70.
Ginzburg, L.R. and C.X.J. Jensen. 2004. Rules of thumb for judging ecological theories. Trends in Ecology and Evolution 19(3): 121-126.
Gould, W.R. and J.D. Nichols. 1998. Estimation of temporal variability of survival in animal populations. Ecology 79: 2531-2538.
Gross, K. 2002. Efficient data collection for estimating growth rates of structured populations. Ecology 83:1762-1767.
Harrison, S. and J.F. Quinn. 1989. Correlated environments and the persistence of metapopulations. Oikos 56:293-298.
Hassell, M.P. 1986. Detecting density dependence. Trends in Ecology and Evolution 1: 90-93.
Hassell, M.P., J. Latto and R.M. May. 1989. Seeing the wood for the trees: detecting density dependence from existing life table studies. Journal of Animal Ecology 58:883-892.
Holmes, E. E. 2001. Estimating risks in declining populations with poor data. Proceedings of the National Academy of Sciences of the United States of America 98:5072-5077.
Holmes, E. E. 2004. Beyond theory to application and evaluation: Diffusion approximations for population viability analysis. Ecological Applications 14:1272-1293.
LaHaye, W. S., R. J. Gutierrez and H. R. Akçakaya. 1994. Spotted owl metapopulation dynamics in southern California. Journal of Animal Ecology 63:775-785.
Lande et al. 2002. Estimating density dependence in time-series of age-structured populations. Phil. Trans. of the Royal Soc. B 357:1179-1184.
Langton et al. 2002. The estimation of density dependence using census data from several sites. Oecologia133:466-473.
Liebhold, A., W. D. Koenig, and O. N. Bjornstad. 2004. Spatial synchrony in population dynamics. Annual Review of Ecology Evolution and Systematics 35:467-490.
Moloney, K.A. 1986. A generalized algorithm for determining category size. Oecologia 69: 176-180.
Morris, W.F. and D.F. Doak 2002. Quantitative Conservation Biology. Sinauer, Sunderland, Massachusetts.
Munzbergova Z., and J. Ehrlen. 2005. How best to collect demographic data for population viability analysis models. Journal of Applied Ecology 42:1115-1120.
Nasution, M. D., C. Brownie, K. H. Pollock, and R. E. Bennetts. 2001. Estimating survival from joint analysis of resighting and radiotelemetry capture-recapture data for wild animals. Journal of Agricultural Biological and Environmental Statistics 6:461-478.
Pollock, K. H., C. M. Bunck, S. R. Winterstein, and C. L. Chen. 1995. A capture-recapture survival analysis model for radio-tagged animals. Journal of Applied Statistics 22:661-672.
Pollock, K. H., H. H. Jiang, and J. E. Hightower. 2004. Combining telemetry and fisheries tagging models to estimate fishing and natural mortality rates. Transactions of the American Fisheries Society 133:639-648.
Pollock, K. H., S. R. Winterstein, C. M. Bunck, and P. D. Curtis. 1989. Survival Analysis in Telemetry Studies - the Staggered Entry Design. Journal of Wildlife Management 53:7-15.
Powell, L. A., M. J. Conroy, J. E. Hines, J. D. Nichols, and D. G. Krementz. 2000. Simultaneous use of mark-recapture and radiotelemetry to estimate survival, movement, and capture rates. Journal of Wildlife Management 64:302-313.
Ryu, H.Y., K.T. Shoemaker, E. Kneip, A. Pidgeon, P. Heglund, B. Bateman, W. Thogmartin, and H.R. Akçakaya. 2016. Developing population models with data from marked individuals. Biological Conservation 197:190-199. [Methods and data available at github.com/Akcakaya/MAPS-to-Models.]
Regan, H. M. and T. D. Auld. 2004. Australian shrub Grevillea caleyi: recovery through management of fire and predation. Pages 23-35 in Akçakaya, H.R., M.A. Burgman, O. Kindvall, C. Wood, P. Sjögren-Gulve, J. Hatfield, and M.A. McCarthy, editors. Species Conservation and Management: Case Studies. Oxford University Press.
Regan, H. M., M. Colyvan, and M. A. Burgman. 2002. A taxonomy and treatment of uncertainty for ecology and conservation biology. Ecological Applications 12: 618628.
Saether et al. 2002. Stochastic population dynamics of an introduced Swiss population of the ibex. Ecology 83:3457-3465
Sezen, Z., H. R. Akçakaya, and C. C. Bilgin. 2004. Turkish Mouflon (Ovis gmelinii anatolica) in Central Anatolia: population viability under scenarios of harvesting for trophy. Pages 459-468 in Akçakaya, H.R., M.A. Burgman, O. Kindvall, C. Wood, P. Sjögren-Gulve, J. Hatfield, and M.A. McCarthy, editors. Species Conservation and Management: Case Studies. Oxford University Press.
Smedbol, R. K., and R. L. Stephenson. 2004. Atlantic Herring (Clupea harengus) in the Northwest Atlantic Ocean: dynamics of nested population components under several harvest regimes. Pages 245-255 in Akçakaya, H.R., M.A. Burgman, O. Kindvall, C. Wood, P. Sjögren-Gulve, J. Hatfield, and M.A. McCarthy, editors. Species Conservation and Management: Case Studies. Oxford University Press.
Shaffer, M.L. 1981. Minimum population sizes for species conservation. BioScience 31:131-134.
Solow, A.R. 1990. Testing for density dependence. A cautionary note. Oecologia 83:47-49.
Tucker, W. T. and S. Ferson. 2003. Probability bounds analysis in environmental risk assessments. Applied Biomathematics.
Vandermeer, J.H. 1978. Choosing category size in a stage projection matrix. Oecologia 32: 79-84.
Walters, C.J. 1985. Bias in the estimation of functional relationships from time series data. Canadian Journal of Fisheries and Aquatic Sciences 42:147-149.
Werner, P.A. and Caswell, H. 1977. Population growth rates and age versus stage-distribution models for teasel (Dipsacus sylvestris Huds.) Ecology 58:1103-1111
White, G.C., A.B. Franklin, and T.M. Shenk. 2002. Estimating parameters of PVA models from data on marked animals. Pages 169-190 in Beissinger, S.R. and D.R. Mccullough (eds). Population Viability Analysis. University of Chicago Press, Chicago.
Zens, M.S. and D.R. Peart. 2003. Dealing with death data: individual hazards, mortality and bias. Trends in Ecology and Evolution 18 (7): 366-373
List of common mistakes in population modeling
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