RANDOMIZATION OF PRESENCE–ABSENCE MATRICES: COMMENTS AND NEW ALGORITHMS

By István Miklós, János Podani. 2004

272 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Geometry and Topology, Nature and Landscape Conservation

View Paper: https://www.semanticscholar.org/paper/ce5c6e9b9d5000f9d3ed7a7d7aa5a66f5af40222

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Citations in the corpus

SOCPROG programs: analysing animal social structures (2009, unknown): “They are based upon the procedure outlined by Bejder et al. (1998), although they contain extensions and modifications to deal with issues that have come to light in recent years (Miklós and Podani 2004; Whitehead 1999; Whitehead et al. 2005).”
Beta diversity of diatom species and ecological guilds: Response to environmental and spatial mechanisms along the stream watercourse (2018, methodology): “We tested the validity of NODF against null models conserving row and column totals following the algorithms developed by Mikl os and Podani (2004), and used z-scores to test if values in observed data were different than those expected by chance.”
Broad-scale patterns of invertebrate richness and community composition in temporary rivers: effects of flow intermittence (2014, methodology): “The significance of nestedness was 249 11 then tested against constrained null models (showing the same marginal totals as the original 250 data) using the “quasiswap” method (Miklós and Podani 2004).”
The Mid‐Domain Effect: There’s a Baby in the Bathwater (2005, background): “…widely accepted precedents for this approach in the extensive literature on null models for patterns of species co-occurrence (e.g., Gotelli 2000; Miklos and Podani 2004), niche overlap (Sale 1974; Winemiller and Pianka 1990), and phenological patterns (Poole and Rathcke 1979; Armbruster 1986;…”
Stochastic Community Assembly: Does It Matter in Microbial Ecology? (2017, background): “, all observed taxa have equal probabilities of being present in a community) (211, 212, 218) or proportional (205, 209, 210, 212, 216) or fixed (31, 204, 217, 219, 220) to the observed frequency.”
Assembly rules operating along a primary riverbed–grassland successional sequence (2006, methodology): “The general randomization procedure used to create the null model was the trial-swap method described in Miklos & Podani (2004).”
Identifying compartments in presence–absence matrices and bipartite networks: insights into modularity measures (2013, methodology): “Future research will need to evaluate additional methods and null model algorithms for detecting modularity (Miklós & Podani, 2004; Blondel et al., 2008), to further test for the presence of modular patterns in presence–absence matrices, as well as to investigate what mechanisms lie behind these…”
How to be a specialist? Quantifying specialisation in pollination networks (2011, unknown): “For binary networks, the approaches proposed by Miklós & Podani (2004) could be used (see also below for evaluation of binary indices, suggesting that binary matrices do not contain sufficient information to derive specialisation).”
Firm-network characteristics and economic robustness to natural disasters (2012, unknown): “A description of this procedure in the unweighted directed case can be found Rao et al. (1996) or Miklós and Podani (2004) ; the statistical uniformity of this process is discussed in Roberts (2000).”
Disentangling community patterns of nestedness and species co‐occurrence (2007, methodology): “The sequential swap algorithm has been extensively studied in the context of species cooccurrence and nestedness analyses (Gotelli 2000, Simberloff and Zaman 2000, Miklós and Podani 2004, Ulrich 2004, Ulrich and Gotelli 2007).”
Null models for species co-occurrence patterns: assessing bias and minimum iteration number for the sequential swap (2006, methodology): “Although Miklos and Podani (2004) proposed a new unbiased randomisation method, we suggest using the original ‘‘sequential swap’’ and performing a frequency correction afterwards as described by Zaman and Simberloff (2002).”