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Swap and fill algorithms in null model analysis: rethinking the knight's tour

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/0471667196.ess2169openalex-snapshot
Randomization Tests
inferredcites →https://doi.org/10.1007/bf00317210openalex-snapshot
Island-sharing by archipelago species
inferredcites →https://doi.org/10.1007/bf00317345openalex-snapshot
The checkerboard score and species distributions
inferredcites →https://doi.org/10.1007/bf00349013openalex-snapshot
Examination of the ?null? model of connor and simberloff for species co-occurrences on Islands
inferredcites →https://doi.org/10.1007/s004420050589openalex-snapshot
Null matrices and the analysis of species co-occurrences
inferredcites →https://doi.org/10.1007/s004420050784openalex-snapshot
Nested species subsets, gaps, and discrepancy
inferredcites →https://doi.org/10.1016/0022-5193(68)90070-2openalex-snapshot
Association among species of infrequent occurrence: The insect and spider fauna of Polyporus betulinus (Bulliard) Fries
inferredcites →https://doi.org/10.1017/cbo9780511542237openalex-snapshot
Ecological Assembly Rules
inferredcites →https://doi.org/10.1046/j.1461-0248.2000.00138.xopenalex-snapshot
Biogeographic effects of red fire ant invasion
inferredcites →https://doi.org/10.1071/mu9760187openalex-snapshot
Origin of the New Hebridean Avifauna
inferredcites →https://doi.org/10.1126/science.286.5445.1684aopenalex-snapshot
How Do Communities Come Together?
inferredcites →https://doi.org/10.1126/science.287.5455.960openalex-snapshot
Revealing Uncertainties in Computer Models
inferredcites →https://doi.org/10.1890/0012-9658(1998)079[0442:fsctsd]2.0.co;2openalex-snapshot
FROM STAR CHARTS TO STONEFLIES: DETECTING RELATIONSHIPS IN CONTINUOUS BIVARIATE DATA
inferredcites →https://doi.org/10.2307/177478openalex-snapshot
Null Model Analysis of Species Co-Occurrence Patterns
inferredcites →https://doi.org/10.2307/1936961openalex-snapshot
The Assembly of Species Communities: Chance or Competition?
inferredcites →https://doi.org/10.2307/1938071openalex-snapshot
A Variance Test for Detecting Species Associations, with Some Example Applications
inferredcites →https://doi.org/10.2307/1940919openalex-snapshot
A Note on the Analysis of Species Co‐Occurrences
inferredcites →https://doi.org/10.2307/2290299openalex-snapshot
Randomization and Monte Carlo Methods in Biology.
inferredcites →https://doi.org/10.2307/2657247openalex-snapshot
Sampling-Variance Effects on Detecting Density Dependence from Temporal Trends in Natural Populations
inferredcites →https://doi.org/10.2307/2844574openalex-snapshot
Statistical Distributions of West Indian Land Bird Families
inferredcites →https://doi.org/10.2307/3544105openalex-snapshot
Interspecific Competition and Species Co-Occurrence Patterns on Islands: Null Models and the Evaluation of Evidence
inferredcites →https://doi.org/10.2307/3546599openalex-snapshot
Co-Occurrence of Australian Land Birds: Diamond's Assembly Rules Revisited
inferredcites →https://doi.org/10.5860/choice.35-1501openalex-snapshot
The ecological detective: confronting models with data

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Null model analyses of presence–absence matrices need a definition of independence
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Ant community structure on a small Pacific island: only one native species living with the invaders
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Antigonon leptopus invasion is associated with plant community disassembly in a Caribbean island ecosystem
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Back to the future: conserving functional and phylogenetic diversity in amphibian-climate refuges
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Climate warming affects spatio-temporal biodiversity patterns of a highly vulnerable Neotropical avifauna
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Microhabitat changes induced by edge effects impact velvet ant (Hymenoptera: Mutillidae) communities in southeastern Amazonia, Brazil
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Earth mounds with the presence of palms have high evolutionary history in the Cerrado–Caatinga ecotone
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Recurring heavy rainfall resulting in degraded-upgraded phases in soil microbial networks that are reflected in soil functioning
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Problems with bins: A critical reassessment of Gotelli and Ulrich's Bayes approach using bird data
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Do the distribution patterns of plant functional traits change during early secondary succession in tropical montane cloud forests?
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Deterministic versus stochastic control in β-diversity, abundance and co-occurrence patterns of a soil nematode assemblage living in a Mediterranean soil
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Assemblages of bats are phylogenetically clustered on a regional scale
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Can protected areas really maintain mammalian diversity? Insights from a nestedness analysis of the Colorado Plateau
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Rehabilitation index for evaluating restoration of terrestrial ecosystems using the reptile assemblage as the bio-indicator
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Functional diversity of copepod assemblages along a basin-scale latitudinal gradient in the North Pacific Ocean
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Co-occurrence of earthworms in Lamto savanna: A null model analysis of community structure
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Climate change will drive mammal species loss and biotic homogenization in the Cerrado Biodiversity Hotspot
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Nestedness in complex networks: Observation, emergence, and implications
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Endemic fish promote ecological structure in a tropical biodiversity hotspot
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A new dispersal-informed null model for community ecology shows strong performance
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Convergent evolution of niche structure in Northeast Pacific kelp forests
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Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum
inferred← citeshttps://doi.org/10.1111/1751-7915.13391openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/aec.12389openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/aje.12177openalex-snapshot
Size‐related habitat selection of a population of Nile monitors (Varanus niloticus) from western N igeria
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Flower functional trait responses to restoration time
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Are Assemblages of Aquatic‐Breeding Anurans (Amphibia) Niches Structured or Neutral?
inferred← citeshttps://doi.org/10.1111/btp.70187openalex-snapshot
Urbanization Effects on Taxonomic and Functional Beta Diversity of Dung Beetles in an Amazonian Landscape
inferred← citeshttps://doi.org/10.1111/ddi.12919openalex-snapshot
Assembly processes of waterbird communities across subsidence wetlands in China: A functional and phylogenetic approach
inferred← citeshttps://doi.org/10.1111/ecog.02070openalex-snapshot
Phylogenetic community structure metrics and null models: a review with new methods and software
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A hierarchical model of whole assemblage island biogeography
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The community ecology of invasive species: where are we and what's next?
inferred← citeshttps://doi.org/10.1111/eff.12152openalex-snapshot
Environmental and spatial processes: what controls the functional structure of fish assemblages in tropical rivers and headwater streams?
inferred← citeshttps://doi.org/10.1111/fwb.12804openalex-snapshot
Newly created ponds complement natural waterbodies for restoration of macroinvertebrate assemblages
inferred← citeshttps://doi.org/10.1111/gcb.15755openalex-snapshot
Taxonomic and functional homogenization of farmland birds along an urbanization gradient in a tropical megacity
inferred← citeshttps://doi.org/10.1111/geb.12667openalex-snapshot
Biotic interchange has structured Western Hemisphere mammal communities
inferred← citeshttps://doi.org/10.1111/geb.12859openalex-snapshot
PER‐SIMPER—A new tool for inferring community assembly processes from taxon occurrences
inferred← citeshttps://doi.org/10.1111/j.0030-1299.2004.12786.xopenalex-snapshot
Relating niche and spatial overlap at the community level
inferred← citeshttps://doi.org/10.1111/j.0030-1299.2004.12981.xopenalex-snapshot
Species co‐occurrences and neutral models: reassessing J. M. Diamond's assembly rules
inferred← citeshttps://doi.org/10.1111/j.0030-1299.2005.13590.xopenalex-snapshot
Richness, structure and functioning in metazoan parasite communities
inferred← citeshttps://doi.org/10.1111/j.0030-1299.2008.16644.xopenalex-snapshot
A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement
inferred← citeshttps://doi.org/10.1111/j.0307-6946.2006.00754.xopenalex-snapshot
Spatial and temporal organisation of the pre‐dispersal seed predator guild in a perennial legume, Vicia tenuifolia
inferred← citeshttps://doi.org/10.1111/j.0906-7590.2006.04626.xopenalex-snapshot
Null models for species co‐occurrence patterns: assessing bias and minimum iteration number for the sequential swap
inferred← citeshttps://doi.org/10.1111/j.0906-7590.2008.5289.xopenalex-snapshot
Does species richness drive speciation? A reassessment with the Hawaiian biota
inferred← citeshttps://doi.org/10.1111/j.0906-7590.2008.5317.xopenalex-snapshot
The relationship between proportion of endemics and species diversity on islands: expectations from a null model
inferred← citeshttps://doi.org/10.1111/j.1365-2028.2009.01088.xopenalex-snapshot
Co‐occurrence patterns of five species of anurans at a pond network in Victoria Lake, Kenya
inferred← citeshttps://doi.org/10.1111/j.1365-2311.2011.01326.xopenalex-snapshot
Limited effects of dominant ants on assemblage species richness in three Amazon forests
inferred← citeshttps://doi.org/10.1111/j.1365-2656.2006.01156.xopenalex-snapshot
Are ectoparasite communities structured? Species co‐occurrence, temporal variation and null models
inferred← citeshttps://doi.org/10.1111/j.1365-2656.2008.01450.xopenalex-snapshot
Dominant ants can control assemblage species richness in a South African savanna
inferred← citeshttps://doi.org/10.1111/j.1365-2656.2010.01688.xopenalex-snapshot
Nestedness versus modularity in ecological networks: two sides of the same coin?
inferred← citeshttps://doi.org/10.1111/j.1365-2699.2006.01444.xopenalex-snapshot
A new algorithm to calculate the nestedness temperature of presence–absence matrices
inferred← citeshttps://doi.org/10.1111/j.1365-2699.2006.01449.xopenalex-snapshot
The generation of diversity in systems of patches and ranked dominance
inferred← citeshttps://doi.org/10.1111/j.1365-2699.2007.01840.xopenalex-snapshot
An improved method for the identification of areas of endemism using species co‐occurrences
inferred← citeshttps://doi.org/10.1111/j.1365-2699.2010.02433.xopenalex-snapshot
Phylogenetic diversity, trait diversity and niches: species assembly of ferns along a tropical elevational gradient
inferred← citeshttps://doi.org/10.1111/j.1365-2745.2008.01421.xopenalex-snapshot
Testing the spatial phylogenetic structure of local communities: statistical performances of different null models and test statistics on a locally neutral community
inferred← citeshttps://doi.org/10.1111/j.1365-294x.2012.05692.xopenalex-snapshot
The role of epiphytism in architecture and evolutionary constraint within mycorrhizal networks of tropical orchids
inferred← citeshttps://doi.org/10.1111/j.1365-3180.2012.00920.xopenalex-snapshot
Non‐random distribution of weed species abundance in arable fields
inferred← citeshttps://doi.org/10.1111/j.1442-9993.2010.02155.xopenalex-snapshot
Local‐scale spatial dynamics of ants in a temperate agroecosystem
inferred← citeshttps://doi.org/10.1111/j.1461-0248.2009.01322.xopenalex-snapshot
Predation leads to assembly rules in fragmented fish communities
inferred← citeshttps://doi.org/10.1111/j.1466-822x.2005.00192.xopenalex-snapshot
Species co‐occurrence: the case of congeneric species and a causal approach to patterns of species association
inferred← citeshttps://doi.org/10.1111/j.1469-1795.2012.00528.xopenalex-snapshot
Bird functional diversity and wildfires in the A mazon: the role of forest structure
inferred← citeshttps://doi.org/10.1111/j.1472-4642.2007.00462.xopenalex-snapshot
Bat assemblages on Neotropical land‐bridge islands: nested subsets and null model analyses of species co‐occurrence patterns
inferred← citeshttps://doi.org/10.1111/j.1600-0587.2013.00060.xopenalex-snapshot
Contribution of rare and common species to richness patterns at local scales
inferred← citeshttps://doi.org/10.1111/j.1600-0706.2009.18228.xopenalex-snapshot
Coexistence patterns of benthic gastropods on the Uruguayan shelf
inferred← citeshttps://doi.org/10.1111/j.1600-0706.2011.19451.xopenalex-snapshot
A new conceptual and methodological framework for exploring and explaining pattern in presence – absence data
inferred← citeshttps://doi.org/10.1111/j.1600-0706.2012.20261.xopenalex-snapshot
Mechanisms of ecological succession: insights from plant functional strategies
inferred← citeshttps://doi.org/10.1111/j.2007.0030-1299.16173.xopenalex-snapshot
Disentangling community patterns of nestedness and species co‐occurrence
inferred← citeshttps://doi.org/10.1111/j.2007.0906-7590.05289.xopenalex-snapshot
Does species richness drive speciation? A reassessment with the Hawaiian biota
inferred← citeshttps://doi.org/10.1111/j.2008.0906-7590.05317.xopenalex-snapshot
The relationship between proportion of endemics and species diversity on islands: expectations from a null model
inferred← citeshttps://doi.org/10.1111/jbi.70287openalex-snapshot
Contrasting Forest Trajectories Drive Changes in Bird Functional Traits
inferred← citeshttps://doi.org/10.1111/jen.13409openalex-snapshot
Diversity and Relevance of Non‐Sphingid Moths as Pollinators in the Neotropics
inferred← citeshttps://doi.org/10.1111/jfb.13029openalex-snapshot
Estuarization increases functional diversity of demersal fish assemblages in tropical coastal ecosystems
inferred← citeshttps://doi.org/10.1111/jvs.12408openalex-snapshot
The impact of non‐reproductive plant species on assessments of community structure and species co‐occurrence patterns
inferred← citeshttps://doi.org/10.1111/jvs.12754openalex-snapshot
Mass effects explain sapling community assembly in Araucaria mixed forest metacommunities
inferred← citeshttps://doi.org/10.1111/jvs.13099openalex-snapshot
Resource competition, not facilitation, structures gravel beach plant communities
inferred← citeshttps://doi.org/10.1111/jvs.13310openalex-snapshot
Quantitative evaluation of internal cluster validation indices using binary data sets
inferred← citeshttps://doi.org/10.1111/zsc.12638openalex-snapshot
Unveiling the spatiotemporal evolutionary patterns of eriophyoid mites in China
inferred← citeshttps://doi.org/10.1126/sciadv.1602929openalex-snapshot
Cost-effective conservation of amphibian ecology and evolution
inferred← citeshttps://doi.org/10.1128/mmbr.00002-17openalex-snapshot
Stochastic Community Assembly: Does It Matter in Microbial Ecology?
inferred← citeshttps://doi.org/10.1145/3412815.3416887openalex-snapshot
Non-Uniform Sampling of Fixed Margin Binary Matrices
inferred← citeshttps://doi.org/10.1155/tbed/9976509openalex-snapshot
Toxoplasma gondii and Trypanosoma lewisi Infection in Urban Small Mammals From Cotonou, Benin, With Special Emphasis on Coinfection Patterns
inferred← citeshttps://doi.org/10.1163/156853806778190051openalex-snapshot
Null models, co-occurrence patterns, and ecological modelling of a Mediterranean community of snakes
inferred← citeshttps://doi.org/10.1177/1094428113478838openalex-snapshot
Methodological Advances in the Analysis of Bipartite Networks
inferred← citeshttps://doi.org/10.1186/s12859-016-1402-1openalex-snapshot
Efficient randomization of biological networks while preserving functional characterization of individual nodes
inferred← citeshttps://doi.org/10.1186/s12898-019-0249-5openalex-snapshot
Comparison of feeding habits and habitat use between invasive raccoons and native raccoon dogs in Hokkaido, Japan
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005557openalex-snapshot
Predicting cryptic links in host-parasite networks
inferred← citeshttps://doi.org/10.1371/journal.pcsy.0000010openalex-snapshot
Pattern detection in bipartite networks: A review of terminology, applications, and methods
inferred← citeshttps://doi.org/10.1371/journal.pone.0001697openalex-snapshot
Influenza A H5N1 Immigration Is Filtered Out at Some International Borders
inferred← citeshttps://doi.org/10.1371/journal.pone.0004390openalex-snapshot
Phylogenetic Resolution and Quantifying the Phylogenetic Diversity and Dispersion of Communities
inferred← citeshttps://doi.org/10.1371/journal.pone.0021273openalex-snapshot
Exploring Tree-Habitat Associations in a Chinese Subtropical Forest Plot Using a Molecular Phylogeny Generated from DNA Barcode Loci
inferred← citeshttps://doi.org/10.1371/journal.pone.0035942openalex-snapshot
Compositional Divergence and Convergence in Local Communities and Spatially Structured Landscapes
inferred← citeshttps://doi.org/10.1371/journal.pone.0067720openalex-snapshot
Factors Determining Forest Diversity and Biomass on a Tropical Volcano, Mt. Rinjani, Lombok, Indonesia
inferred← citeshttps://doi.org/10.1371/journal.pone.0090177openalex-snapshot
The Effect of Phylogeny, Environment and Morphology on Communities of a Lianescent Clade (Bignonieae-Bignoniaceae) in Neotropical Biomes
inferred← citeshttps://doi.org/10.1371/journal.pone.0095703openalex-snapshot
Different Relationships between Temporal Phylogenetic Turnover and Phylogenetic Similarity and in Two Forests Were Detected by a New Null Model
inferred← citeshttps://doi.org/10.1371/journal.pone.0119741openalex-snapshot
Multivariate and Phylogenetic Analyses Assessing the Response of Bacterial Mat Communities from an Ancient Oligotrophic Aquatic Ecosystem to Different Scenarios of Long-Term Environmental Disturbance
inferred← citeshttps://doi.org/10.1371/journal.pone.0154581openalex-snapshot
Diatom Cooccurrence Shows Less Segregation than Predicted from Niche Modeling
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