Program SimAssem: Software for simulating species assemblages and estimating species richness

Methods in Ecology and Evolution

Volumn 4, Issue 9, 2013, Pages 891-896

  Reese, Gordon C ^a   Wilson, Kenneth R ^a   Flather, Curtis H ^b  

^a Veterinary Dentistry and Oral Surgery   (United States)

^b ROCKY MOUNTAIN RESEARCH STATION   (United States)

Author keywords

Biodiversity; Community ecology; Landscape ecology; Relative abundance distribution; Simulation; Spatial aggregation

Indexed keywords

EID: 84883362783     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210X.12070     Document Type: Article

References (55)

1. Arrhenius, O.(1921) Species and area. Journal of Ecology, 9, 95-99.
2. Ashbridge, J. & Goudie, I.B.J. (2000) Coverage-adjusted estimators for mark-recapture in heterogeneous populations. Communications in Statistics: Simulation and Computation, 29, 1215-1237.
3. Baltanás, A. (1992) On the use of some methods for the estimation of species richness. Oikos, 65, 484-492.
4. Beck, J. & Kitching, I.J. (2007) Estimating regional species richness of tropical insects from museum data: a comparison of a geography-based and sample-based methods. Journal of Applied Ecology, 44, 672-681.
5. Boulinier, T., Nichols, J.D., Sauer, J.R., Hines, J.E. & Pollock, K.H. (1998) Estimating species richness: the importance of heterogeneity in species detectability. Ecology, 79, 1018-1028.
6. Brose, U., Martinez, N.D. & Williams, R.J. (2003) Estimating species richness: sensitivity to sample coverage and insensitivity to spatial patterns. Ecology, 84, 2364-2377.
7. Burnham, K.P. & Overton, W.S. (1978) Estimation of the size of a closed population when capture probabilities vary among animals. Biometrika, 65, 623-633.
8. Burnham, K.P. & Overton, W.S. (1979) Robust estimation of population size when capture probabilities vary among animals. Ecology, 60, 927-936.
9. Burnham, K.P., Anderson, D.R., White, G.C., Brownie, C. & Pollock, K.H. (1987) Design and analysis methods for fish survival experiments based on release-recapture. American Fisheries Society Monograph No. 5. Bethesda, Maryland.
10. Cao, Y., Larsen, D.P. & Hughes, R.M. (2001) Estimating total species richness in fish assemblage surveys: a similarity based approach. Canadian Journal of Fisheries and Aquatic Sciences, 58, 1782-1793.
11. Cao, Y., Larsen, D.P. & White, D. (2004) Estimating regional species richness using a limited number of survey units. Ecoscience, 11, 23-35.
12. Chao, A. (1984) Non-parametric estimation of the number of classes in a population. Scandinavian Journal of Statistics, 11, 265-270.
13. Chao, A. (1987) Estimating the population size for capture-recapture data with unequal catchability. Biometrics, 43, 783-791.
14. Chao, A. (2005) Species estimation and applications. Encyclopedia of Statistical Sciences, 2nd edn., Vol. 12 (eds S. Kotz, N. Balakrishnan, C.B. Read & B. Vidakovic ), pp. 7907-7916. Wiley Press, New York.
15. Chao, A., Colwell, R.K., Lin, C.W. & Gotelli, N.J. (2009) Sufficient sampling for asymptotic minimum species richness estimators. Ecology, 90, 1125-1133.
16. Chao, A. & Lee, S.M. (1992) Estimating the number of classes via sample coverage. Journal of the American Statistical Association, 87, 210-217.
17. Chao, A. & Shen, T.-J. (2010). Program SPADE (Species Prediction and Diversity Estimation). Available at: http://chao.stat.nthu.edu.tw/softwareCE.html [accessed 1 June 2013].
18. Clark, P.J. & Evans, F.C. (1954) Distance to nearest neighbor as a measure of spatial relationships in populations. Ecology, 35, 445-453.
19. Clifford, H.T. & Stephenson, W. (1975) An Introduction to Numerical Classification. Academic Press, London.
20. Colwell, R.K. (2006). EstimateS Statistical Estimation of Species Richness and Shared Species from Samples, Version 8. Available at: http://viceroy.eeb.uconn.edu/EstimateS/ [accessed 1 June 2013].
21. Colwell, R.K. & Coddington, J.A. (1994) Estimating terrestrial biodiversity through extrapolation. Philosophical Transactions of the Royal Society of London B, 345, 101-118.
22. Darroch, J.N. & Ratcliff, D. (1980) A note on capture-recapture estimation. Biometrics, 36, 149-153.
23. Fisher, R.A., Corbet, A.S. & Williams, C.B. (1943) The relation between the number of species and the number of individuals in a random sample of an animal population. Journal of Animal Ecology, 12, 42-58.
24. Gaston, K.J. (1996) Biodiversity: A Biology of Numbers and Difference. Blackwell Science, Oxford.
25. Holdridge, L.R., Grenke, W.C., Hatheway, W.H., Liang, T. & Tosi, J.A. (1971) Forest Environments in Tropical Life Zones. Pergamon Press, Oxford.
26. Hubbell, S.P. (2001) The Unified Neutral Theory of Biodiversity and Biogeography. Princeton University Press, Princeton.
27. Keating, K.A. & Quinn, J.F. (1998) Estimating species richness: the Michaelis-Menten model revisited. Oikos, 81, 411-416.
28. Lee, S.M. & Chao, A. (1994) Estimating population size via sample coverage for closed capture-recapture models. Biometrics, 50, 88-97.
29. MacArthur, R.H. (1957) On the relative abundance of bird species. Proceedings of the National Academy of Science USA, 43, 293-295.
30. Magurran, A.E. (2004) Measuring Biological Diversity. Blackwell Publishing, Malden.
31. Matsumoto, M. & Nishimura, T. (1998) Mersenne twister: a 623-dimensionally equidistributed uniform pseudorandom number generator. ACM Transactions on Modeling and Computer Simulation, 8, 3-30.
32. Michaelis, M. & Menten, M.L. (1913) Der kinetic der invertinwirkung. Biochemische Zeitschrift, 49, 333-369.
33. Moreno, C., Zuria, I., García-Zenteno, M., Sánchez-Rojas, G., Castellanos, I., Martínez-Morales, M. et al. (2006) Trends in the measurement of alpha diversity in the last two decades. Interciencia, 31, 67-71.
34. Motomura, I. (1932) On the statistical treatment of communities. Japanese Journal of Zoology, 44, 379-383 (in Japanese).
35. O'Dea, N., Whittaker, R.J. & Ugland, K.I. (2006) Using spatial heterogeneity to extrapolate species richness: a new method test on Ecuadorian cloud forest birds. Journal of Applied Ecology, 43, 189-198.
36. Pledger, S. (2000) Unified maximum likelihood estimates for closed capture-recapture models using mixtures. Biometrics, 56, 434-442.
37. Poulin, R. (1998) Comparison of three estimators of species richness in parasite component communities. Journal of Parasitology, 84, 485-490.
38. Preston, F.W. (1948) The commonness, and rarity, of species. Ecology, 29, 254-283.
39. R Development Core Team (2009). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna. Available at: http://www.R-project.org [accessed 1 June 2013].
40. Reese, G.C. (2012) Simulating species assemblages and evaluating species richness estimators. PhD thesis, Colorado State University, Fort Collins. Available at: http://hdl.handle.net/10217/68193 [accessed 1 June 2013].
41. Reese, G.C., Wilson, K.R., Hoeting, J.A. & Flather, C.H. (2005) Factors affecting species distribution predictions: a simulation modeling experiment. Ecological Applications, 15, 554-564.
42. Schmit, J.P., Murphy, J.F. & Mueller, G.M. (1999) Macrofungal diversity of a temperate oak forest: a test of species richness estimators. Canadian Journal of Botany, 77, 1014-1027.
43. Shannon, C.E. & Weaver, W. (1949) The Mathematical Theory of Communication. University of Illinois Press, Urbana.
44. Smith, E.P. & van Belle, G. (1984) Nonparametric estimation of species richness. Biometrics, 40, 119-129.
45. Sugihara, G. (1980) Minimal community structure: an explanation of species abundance patterns. The American Naturalist, 116, 770-787.
46. Tjørve, E. (2009) Shapes and functions of species-area curves (II): a review of new models and parameterizations. Journal of Biogeography, 36, 1435-1445.
47. Tokeshi, M. (1990) Niche apportionment or random assortment: species abundance patterns revisited. Journal of Animal Ecology, 59, 1129-1146.
48. Tokeshi, M. (1993) Species abundance patterns and community structure. Advances in Ecological Research, 24, 111-186.
49. Tokeshi, M. (1996) Power fraction: a new explanation of relative abundance patterns in species-rich assemblages. Oikos, 75, 543-550.
50. Turner, W., Leitner, W. & Rosenzweig, M. (2003) ws2m Software for the Measurement and Analysis of Species Diversity. Version 3.2. Available at: http://www.mybiosoftware.com/population-genetics/9836 [accessed 1 June 2013].
51. Wagner, H.H. & Wildi, O. (2002) Realistic simulation of the effects of abundance distribution and spatial heterogeneity on non-parametric estimators of species richness. Ecoscience, 9, 241-250.
52. Walther, B.A. & Moore, J.L. (2005) The concepts of bias, precision and accuracy, and their use in testing the performance of species richness estimators, with a literature review of estimator performance. Ecography, 28, 815-829.
53. Walther, B.A. & Morand, S. (1998) Comparative performance of species richness estimation methods. Parasitology, 116, 395-405.
54. White, G.C. & Burnham, K.P. (1999) Program MARK: survival estimation from populations of marked animals. Bird Study, 46 (Supplement), 120-138.
55. Whittaker, R.H. (1977) Evolution of species diversity in land communities. Evolutionary Biology, Vol. 10 (eds M.K. Hecht, W.C. Steere & B. Wallace ), pp. 1-67. Plenum Publishing Corporation, New York.