A null model algorithm for presence-absence matrices based on proportional resampling

Ecological Modelling

Volumn 244, Issue , 2012, Pages 20-27

  Ulrich, Werner ^a   Gotelli, Nicholas J ^b  

^a NICOLAUS COPERNICUS UNIVERSITY   (Poland)

^b UNIVERSITY OF VERMONT   (United States)

Author keywords

Benchmark testing; Ecological presence absence matrix; Meta community; Statistical inference; Sums of square reduction

Indexed keywords

BENCHMARK TESTING; META-COMMUNITY; PRESENCE-ABSENCE; STATISTICAL INFERENCE; SUMS OF SQUARES;

ALGORITHMS; ECOLOGY; STATISTICAL METHODS;

MATRIX ALGEBRA;

ALGORITHM; BENCHMARKING; COMMUNITY STRUCTURE; DATA SET; ECOLOGICAL MODELING; EMPIRICAL ANALYSIS; MATRIX; NUMERICAL MODEL; SPECIES OCCURRENCE; VARIANCE ANALYSIS; VULNERABILITY;

EID: 84864359006     PISSN: 03043800     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecolmodel.2012.06.030     Document Type: Article

References (32)

1. Almeida-Neto M., Guimarães P.R., Lewinsohn T.M. On nestedness analyses: rethinking matrix temperature and anti-nestedness. Oikos 2007, 116:716-722.
2. Almeida-Neto M., Guimarães P., Guimarães P.R., Loyola R.D., Ulrich W. A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement. Oikos 2008, 117:1227-1239.
3. Atmar W., Patterson B.D. The Nestedness Temperature Calculator: A Visual Basic Program, Including 294 Presence-Absence Matrices 1995, AICS Research, University Park, NM and Field Museum, Chicago. http://aics-research.com/nestedness/tempcalc.html.
4. Bascompte J., Jordano P., Melián C.J., Olesen J.M. The nested assembly of plant-animal mutualistic networks. Proceedings of the National Academy of Sciences of the United States of America 2003, 100:9383-9387.
5. Connor E.H., Simberloff D. The assembly of species communities: chance or competition?. Ecology 1979, 60:1132-1140.
6. Diamond J.M. Assembly of species communities. Ecology and Evolution of Communities 1975, 342-444. Harvard University Press, Cambridge. M.L. Cody, J.M. Diamond (Eds.).
7. Diamond J.M., Gilpin M.E. Examination of the 'null' model of Connor and Simberloff for species co-occurrences on islands. Oecologia 1982, 52:64-74.
8. Gotelli N.J., Graves G.R. Null Models in Ecology 1996, Smithsonian Institution Press, Washington, DC, USA.
9. Gotelli N.J., Graves G.R., Rahbek C. Macroecological signals of species interactions in the Danish avifauna. Proceedings of the National Academy of Sciences of the United States of America 2010, 107:530-535.
10. Gotelli N.J. Null model analysis of species co-occurrence patterns. Ecology 2000, 81:2606-2621.
11. Gotelli N.J., McCabe D.J. Species co-occurrence: a meta-analysis of J.M. Diamond's assembly rules model. Ecology 2002, 83:2091-2096.
12. Gotelli N.J., Ulrich W. The empirical Bayes distribution as a tool to identify non-random species associations. Oecologia 2010, 162:463-477.
13. Gotelli N.J., Ulrich W. Statistical challenges in null model analysis. Oikos 2012, 121:171-180.
14. Haila Y., Jarvinen O., Vaisanen R.A. Habitat distributions and species associations of land bird populations on the åland Islands, SW Finland. Annales Zoologici Fennici 1980, 17:87-106.
15. Jenkins D.G. In search of quorum effects in metacommunity structure: species co-occurrence analyses. Ecology 2006, 87:1523-1531.
16. Jonsson B.G. A null model for randomisation tests of nestedness in species assemblages. Oecologia 2001, 127:309-313.
17. Miklós I., Podani J. Randomization of presence-absence matrices: comments and new algorithms. Ecology 2004, 85:86-92.
18. Navarro-Alberto J.A., Manly B.F.J. Null model analyses of presence-absence matrices need a definition of independence. Population Ecology 2009, 51:505-512.
19. Presley S.J., Higgins C.L., Willig M.R. A comprehensive framework for the evaluation of metacommunity structure. Oikos 2010, 119:908-917.
20. Quinn G.P., Keogh M.J. Experimental Design and Data Analysis for Biologists 2002, Cambridge University Press, New York.
21. Schluter D. A variance test for detecting species associations, with some example applications. Ecology 1984, 65:998-1005.
22. Stone L., Roberts A. The checkerboard score and species distributions. Oecologia 1990, 85:74-79.
23. Taylor L.R. Aggregation, variance and the mean. Nature 1961, 332:721-722.
24. Ulrich W., Gotelli N.J. Null model analysis of species nestedness patterns. Ecology 2007, 88:1824-1831.
25. Ulrich W., Gotelli N.J. Disentangling community patterns of nestedness and species co-occurrence. Oikos 2007, 116:2053-2061.
26. Ulrich W., Almeida-Neto M., Gotelli N.J. A consumer's guide to nestedness analysis. Oikos 2009, 118:3-17.
27. Ulrich, W., Gotelli, N.J. Pattern detection in null model analysis. Oikos, in press.
28. Willis E.O. The composition of avian communities in reminiscent woodlots in Southern Brazil. Avulsos de Zoologia 1979, 33:1-25.
29. Webb C.O., Ackerly D.D., McPeek M.A., Donoghue M.J. Phylogenies and community ecology. Annual Review of Ecology and Systematics 2002, 33:475-505.
30. Ecological Assembly Rules: Perspectives, Advances, Retreats 1999, Cambridge University Press, New York. E. Weiher, P.A. Keddy (Eds.).
31. Wright D.H., Patterson B.D., Mikkelson G.M., Cutler A., Atmar W. A comparative analysis of nested subset patterns of species composition. Oecologia 1998, 131:1-20.
32. Zaman A., Simberloff D. Random binary matrices in biogeographical ecology - instituting a good neighbor policy. Environmental and Ecological Statistics 2002, 9:405-421.